Starting phenix.real_space_refine on Wed Mar 20 04:09:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdv_37466/03_2024/8wdv_37466_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdv_37466/03_2024/8wdv_37466.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/8wdv_37466/03_2024/8wdv_37466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdv_37466/03_2024/8wdv_37466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdv_37466/03_2024/8wdv_37466_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdv_37466/03_2024/8wdv_37466_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= 0.006 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 8 9.91 5 Fe 5 7.16 5 P 20 5.49 5 Mg 37 5.21 5 S 101 5.16 5 C 18058 2.51 5 N 3539 2.21 5 O 4493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26261 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: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 407 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} 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: "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: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 349 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} 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: 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: "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: 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: "S" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 412 Classifications: {'peptide': 51} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 47} 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: "T" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 349 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 412 Classifications: {'peptide': 51} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 47} 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: "V" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 349 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 50} 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: "X" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 349 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Y" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 511 Classifications: {'peptide': 64} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 58} 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: "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: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 489 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 56} 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: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 341 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 38} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "8" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 287 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} 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: 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: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 252 Unusual residues: {' CA': 1, ' MG': 1, 'HEM': 4, 'PGV': 1, 'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 433 Unusual residues: {'BCL': 2, 'BPH': 1, 'PGV': 3, 'UQ8': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 72 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: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 629 Unusual residues: {' CA': 1, ' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 3, 'CRT': 1, 'LDA': 1, 'LMT': 1, 'MQ8': 1, 'PGV': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 11 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} 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: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 164 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" 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: "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: 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: "K" 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: "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: 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: "Q" 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: "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: 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: "T" 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: "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: 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: "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: 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: "Y" 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: "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: 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: "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: 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 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: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "0" 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: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 134 Classifications: {'water': 134} Link IDs: {None: 133} 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: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} 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: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" 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: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 15.69, per 1000 atoms: 0.60 Number of scatterers: 26261 At special positions: 0 Unit cell: (132.02, 122.18, 135.3, 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 8 19.99 S 101 16.00 P 20 15.00 Mg 37 11.99 O 4493 8.00 N 3539 7.00 C 18058 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: 13.46 Conformation dependent library (CDL) restraints added in 3.9 seconds 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 5 sheets defined 59.7% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 106 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 204 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 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 307 through 311 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: 3.631A pdb=" N PHE L 129 " --> pdb=" O PHE L 125 " (cutoff:3.500A) removed outlier: 3.710A 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: 3.992A 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: 3.618A pdb=" N PHE L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 256 Processing helix chain 'L' and resid 265 through 273 removed outlier: 4.065A pdb=" N TRP L 269 " --> pdb=" O TRP L 265 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN L 270 " --> pdb=" O PRO L 266 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TRP L 271 " --> pdb=" O GLU L 267 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP L 272 " --> pdb=" O TRP L 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 43 removed outlier: 3.588A 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 139 Processing helix chain 'M' and resid 145 through 161 Processing helix chain 'M' and resid 163 through 168 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 removed outlier: 3.588A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) 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 225 Processing helix chain 'M' and resid 227 through 229 No H-bonds generated for 'chain 'M' and resid 227 through 229' 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: 3.839A 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 'H' and resid 11 through 36 removed outlier: 3.929A 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 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 216 through 221 removed outlier: 3.769A pdb=" N ALA H 220 " --> pdb=" O ALA H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 249 removed outlier: 3.575A pdb=" N GLY H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS H 247 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 4.064A 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 37 Processing helix chain 'E' and resid 12 through 43 Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 16 through 38 Processing helix chain 'G' and resid 12 through 43 removed outlier: 3.531A pdb=" N ILE G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 11 removed outlier: 3.573A pdb=" N ILE I 11 " --> pdb=" O ILE I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 38 Processing helix chain 'J' and resid 17 through 43 Processing helix chain 'K' and resid 7 through 11 Processing helix chain 'K' and resid 14 through 38 removed outlier: 3.584A pdb=" N VAL K 19 " --> pdb=" O ARG K 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 43 removed outlier: 3.886A pdb=" N GLN N 16 " --> pdb=" O GLU N 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 10 Processing helix chain 'O' and resid 14 through 38 Processing helix chain 'O' and resid 40 through 42 No H-bonds generated for 'chain 'O' and resid 40 through 42' Processing helix chain 'P' and resid 12 through 43 Processing helix chain 'Q' and resid 7 through 10 Processing helix chain 'Q' and resid 14 through 38 removed outlier: 3.545A pdb=" N VAL Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 43 Processing helix chain 'S' and resid 5 through 11 Processing helix chain 'S' and resid 14 through 37 Processing helix chain 'T' and resid 12 through 43 Processing helix chain 'U' and resid 3 through 10 removed outlier: 4.466A pdb=" N TRP U 6 " --> pdb=" O PRO U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 38 Processing helix chain 'V' and resid 12 through 43 Processing helix chain 'W' and resid 6 through 10 Processing helix chain 'W' and resid 14 through 38 Processing helix chain 'X' and resid 12 through 43 Processing helix chain 'Y' and resid 5 through 10 removed outlier: 3.542A pdb=" N TRP Y 9 " --> pdb=" O TRP Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 38 Processing helix chain 'Z' and resid 12 through 43 Processing helix chain '1' and resid 7 through 10 Processing helix chain '1' and resid 14 through 38 Processing helix chain '2' and resid 12 through 43 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 12 through 43 removed outlier: 3.591A pdb=" N GLN 4 16 " --> pdb=" O GLU 4 12 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 4 21 " --> pdb=" O GLU 4 17 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN 4 24 " --> pdb=" O GLY 4 20 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 9 No H-bonds generated for 'chain '5' and resid 7 through 9' Processing helix chain '5' and resid 14 through 38 Processing helix chain '6' and resid 12 through 43 removed outlier: 3.732A pdb=" N GLU 6 17 " --> pdb=" O GLN 6 13 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE 6 18 " --> pdb=" O GLU 6 14 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 10 Processing helix chain '7' and resid 14 through 38 removed outlier: 3.596A pdb=" N LEU 7 18 " --> pdb=" O PRO 7 14 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL 7 19 " --> pdb=" O ARG 7 15 " (cutoff:3.500A) Processing helix chain '8' and resid 17 through 43 removed outlier: 3.686A pdb=" N ILE 8 21 " --> pdb=" O GLU 8 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN 8 24 " --> pdb=" O GLY 8 20 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA 8 28 " --> pdb=" O GLN 8 24 " (cutoff:3.500A) Processing helix chain '9' and resid 14 through 38 removed outlier: 3.725A pdb=" N VAL 9 19 " --> pdb=" O ARG 9 15 " (cutoff:3.500A) 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: 6.830A pdb=" N GLU H 183 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.776A 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: 6.279A pdb=" N THR H 155 " --> pdb=" O VAL H 209 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3345 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: 6.75 Time building geometry restraints manager: 14.20 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: 9334 1.38 - 1.56: 17198 1.56 - 1.75: 40 1.75 - 1.93: 190 1.93 - 2.11: 156 Bond restraints: 26918 Sorted by residual: bond pdb=" CA7 CDL M 409 " pdb=" OA8 CDL M 409 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" CA7 CDL M 411 " pdb=" OA8 CDL M 411 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" CA7 CDL M 412 " pdb=" OA8 CDL M 412 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" CB7 CDL M 412 " pdb=" OB8 CDL M 412 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.14e+02 bond pdb=" CB7 CDL D 502 " pdb=" OB8 CDL D 502 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.13e+02 ... (remaining 26913 not shown) Histogram of bond angle deviations from ideal: 82.21 - 101.52: 403 101.52 - 120.82: 28436 120.82 - 140.13: 8057 140.13 - 159.43: 38 159.43 - 178.74: 80 Bond angle restraints: 37014 Sorted by residual: angle pdb=" C40 CRT M 407 " pdb=" C38 CRT M 407 " pdb=" O2 CRT M 407 " ideal model delta sigma weight residual 111.40 86.40 25.00 3.00e+00 1.11e-01 6.95e+01 angle pdb=" C2 CRT K 101 " pdb=" C1 CRT K 101 " pdb=" C4 CRT K 101 " ideal model delta sigma weight residual 110.24 85.73 24.51 3.00e+00 1.11e-01 6.68e+01 angle pdb=" C39 CRT V 103 " pdb=" C38 CRT V 103 " pdb=" O2 CRT V 103 " ideal model delta sigma weight residual 111.76 87.28 24.48 3.00e+00 1.11e-01 6.66e+01 angle pdb=" C40 CRT 2 103 " pdb=" C38 CRT 2 103 " pdb=" O2 CRT 2 103 " ideal model delta sigma weight residual 111.40 87.77 23.63 3.00e+00 1.11e-01 6.21e+01 angle pdb=" C2 CRT Q 101 " pdb=" C1 CRT Q 101 " pdb=" C4 CRT Q 101 " ideal model delta sigma weight residual 110.24 86.63 23.61 3.00e+00 1.11e-01 6.19e+01 ... (remaining 37009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 14437 35.99 - 71.98: 656 71.98 - 107.97: 165 107.97 - 143.96: 62 143.96 - 179.94: 9 Dihedral angle restraints: 15329 sinusoidal: 7933 harmonic: 7396 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 -78.00 -102.00 1 6.00e+00 2.78e-02 3.22e+02 dihedral pdb=" C1 BCL 0 102 " pdb=" CGA BCL 0 102 " pdb=" O2A BCL 0 102 " pdb=" CBA BCL 0 102 " ideal model delta sinusoidal sigma weight residual -180.00 -79.62 -100.38 1 6.00e+00 2.78e-02 3.15e+02 dihedral pdb=" C1 BCL M 404 " pdb=" C2 BCL M 404 " pdb=" C3 BCL M 404 " pdb=" C5 BCL M 404 " ideal model delta sinusoidal sigma weight residual -180.00 -0.06 -179.94 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 15326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3298 0.077 - 0.153: 373 0.153 - 0.230: 55 0.230 - 0.307: 23 0.307 - 0.383: 3 Chirality restraints: 3752 Sorted by residual: chirality pdb=" CBD BCL M 404 " pdb=" CAD BCL M 404 " pdb=" CGD BCL M 404 " pdb=" CHA BCL M 404 " both_signs ideal model delta sigma weight residual False 2.62 3.01 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CBD BCL T 101 " pdb=" CAD BCL T 101 " pdb=" CGD BCL T 101 " pdb=" CHA BCL T 101 " both_signs ideal model delta sigma weight residual False 2.62 2.30 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CBD BCL X 102 " pdb=" CAD BCL X 102 " pdb=" CGD BCL X 102 " pdb=" CHA BCL X 102 " both_signs ideal model delta sigma weight residual False 2.62 2.31 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 3749 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL K 102 " -0.387 3.00e-02 1.11e+03 3.17e-01 5.58e+02 pdb=" CBA BCL K 102 " -0.155 3.00e-02 1.11e+03 pdb=" CGA BCL K 102 " 0.088 3.00e-02 1.11e+03 pdb=" O1A BCL K 102 " -0.102 3.00e-02 1.11e+03 pdb=" O2A BCL K 102 " 0.556 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 0 102 " 0.359 3.00e-02 1.11e+03 3.01e-01 5.04e+02 pdb=" CBA BCL 0 102 " 0.061 3.00e-02 1.11e+03 pdb=" CGA BCL 0 102 " -0.071 3.00e-02 1.11e+03 pdb=" O1A BCL 0 102 " 0.183 3.00e-02 1.11e+03 pdb=" O2A BCL 0 102 " -0.532 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL T 101 " 0.357 3.00e-02 1.11e+03 3.00e-01 4.98e+02 pdb=" CBA BCL T 101 " 0.055 3.00e-02 1.11e+03 pdb=" CGA BCL T 101 " -0.070 3.00e-02 1.11e+03 pdb=" O1A BCL T 101 " 0.186 3.00e-02 1.11e+03 pdb=" O2A BCL T 101 " -0.528 3.00e-02 1.11e+03 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 4 2.08 - 2.78: 5598 2.78 - 3.49: 36220 3.49 - 4.19: 74997 4.19 - 4.90: 125779 Nonbonded interactions: 242598 Sorted by model distance: nonbonded pdb=" OE2 GLU M 96 " pdb=" O HOH M 501 " model vdw 1.372 2.440 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 402 " model vdw 1.996 2.260 nonbonded pdb="MG MG C 405 " pdb=" O HOH M 501 " model vdw 2.039 2.170 nonbonded pdb=" NE2 HIS L 196 " pdb="FE FE M 402 " model vdw 2.069 2.340 nonbonded pdb=" OE1 GLN C 183 " pdb="MG MG C 405 " model vdw 2.084 2.170 ... (remaining 242593 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 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '2' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '4' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '6' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'B' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'E' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'G' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'J' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'N' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'P' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'R' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'T' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'V' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'X' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'Z' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) } ncs_group { reference = (chain '1' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain '5' and resid 6 through 46) selection = (chain '7' and resid 6 through 46) selection = (chain '9' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'A' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'I' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'K' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'O' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'Q' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) } ncs_group { reference = (chain 'D' and resid 2 through 50) selection = (chain 'F' and resid 2 through 50) selection = (chain 'S' and resid 2 through 50) selection = (chain 'U' and resid 2 through 50) selection = (chain 'W' and resid 2 through 50) } 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: 3.870 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: 11.510 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 69.510 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.100 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:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 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 0.214 26918 Z= 0.938 Angle : 1.861 25.003 37014 Z= 0.797 Chirality : 0.056 0.383 3752 Planarity : 0.018 0.317 4384 Dihedral : 22.604 179.944 10537 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.77 % Allowed : 3.82 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.38 (0.16), residues: 2500 helix: 2.32 (0.12), residues: 1477 sheet: -0.51 (1.22), residues: 20 loop : 0.60 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 9 HIS 0.008 0.001 HIS L 159 PHE 0.020 0.001 PHE L 170 TYR 0.018 0.002 TYR C 200 ARG 0.003 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 391 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.9418 (mtp) cc_final: 0.9082 (mtp) REVERT: C 308 MET cc_start: 0.9514 (tpp) cc_final: 0.9252 (tpp) REVERT: L 218 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8480 (mt-10) REVERT: M 33 LYS cc_start: 0.7803 (tppp) cc_final: 0.7267 (tppt) REVERT: M 124 MET cc_start: 0.9200 (mmp) cc_final: 0.8996 (mmm) REVERT: H 205 LYS cc_start: 0.7702 (mtmt) cc_final: 0.7371 (mttt) REVERT: B 12 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 16 GLN cc_start: 0.7880 (tp40) cc_final: 0.7645 (tp40) REVERT: I 7 LYS cc_start: 0.8502 (mttt) cc_final: 0.8140 (mmtp) REVERT: O 15 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.7939 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8167 (t0) cc_final: 0.7900 (t0) REVERT: S 16 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7598 (mtt180) REVERT: U 5 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8565 (mm) REVERT: W 16 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7462 (tpp80) REVERT: Y 5 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8514 (tt) REVERT: Y 6 TRP cc_start: 0.8898 (p-90) cc_final: 0.8402 (p-90) REVERT: Z 13 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: 3 12 PHE cc_start: 0.8006 (m-80) cc_final: 0.7779 (m-80) REVERT: 7 11 ILE cc_start: 0.5962 (OUTLIER) cc_final: 0.5721 (tt) outliers start: 38 outliers final: 15 residues processed: 415 average time/residue: 1.3259 time to fit residues: 639.5683 Evaluate side-chains 371 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 352 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR 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 225 LEU Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain 5 residue 6 HIS Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 7 residue 11 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 150 HIS L 207 GLN E 24 GLN J 24 GLN N 24 GLN P 13 GLN P 24 GLN T 24 GLN V 24 GLN ** 2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 43 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26918 Z= 0.181 Angle : 0.741 17.404 37014 Z= 0.276 Chirality : 0.040 0.204 3752 Planarity : 0.004 0.048 4384 Dihedral : 19.480 179.993 6010 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.09 % Allowed : 8.75 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.72 (0.16), residues: 2500 helix: 2.60 (0.12), residues: 1512 sheet: -0.34 (1.20), residues: 20 loop : 0.64 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 271 HIS 0.006 0.001 HIS L 159 PHE 0.016 0.001 PHE H 19 TYR 0.016 0.001 TYR H 234 ARG 0.004 0.000 ARG K 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 359 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 236 MET cc_start: 0.9588 (mmt) cc_final: 0.9217 (mmt) REVERT: L 8 ARG cc_start: 0.8667 (ttm-80) cc_final: 0.8359 (ttm170) REVERT: L 208 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7009 (tmtp) REVERT: L 218 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8496 (mt-10) REVERT: M 33 LYS cc_start: 0.7826 (tppp) cc_final: 0.7389 (tppt) REVERT: M 75 MET cc_start: 0.9372 (mtt) cc_final: 0.9057 (mtp) REVERT: M 124 MET cc_start: 0.9155 (mmp) cc_final: 0.8950 (mmm) REVERT: H 205 LYS cc_start: 0.7692 (mtmt) cc_final: 0.7336 (mptt) REVERT: B 12 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7678 (mm-30) REVERT: I 7 LYS cc_start: 0.8518 (mttt) cc_final: 0.8180 (mmtp) REVERT: K 16 ARG cc_start: 0.7156 (mtp-110) cc_final: 0.6709 (mmt90) REVERT: O 15 ARG cc_start: 0.8088 (ttt-90) cc_final: 0.7690 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8188 (t0) cc_final: 0.7915 (t0) REVERT: S 16 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7631 (mtt180) REVERT: U 5 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8642 (mm) REVERT: U 16 ARG cc_start: 0.7803 (mtt90) cc_final: 0.7343 (mtm110) REVERT: W 16 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7330 (tpp80) REVERT: Y 5 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8603 (tt) REVERT: Y 6 TRP cc_start: 0.8855 (p-90) cc_final: 0.8269 (p-90) REVERT: Z 17 GLU cc_start: 0.7823 (tt0) cc_final: 0.7597 (tm-30) REVERT: 3 12 PHE cc_start: 0.8010 (m-80) cc_final: 0.7771 (m-80) REVERT: 9 6 HIS cc_start: 0.8180 (p-80) cc_final: 0.7956 (p90) outliers start: 45 outliers final: 19 residues processed: 375 average time/residue: 1.3189 time to fit residues: 575.7090 Evaluate side-chains 362 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 340 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 5 residue 6 HIS Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 6 residue 27 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN H 192 ASN B 24 GLN N 24 GLN P 13 GLN P 24 GLN T 24 GLN V 24 GLN 6 16 GLN 0 16 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26918 Z= 0.281 Angle : 0.734 17.654 37014 Z= 0.285 Chirality : 0.041 0.211 3752 Planarity : 0.004 0.046 4384 Dihedral : 17.920 179.819 6002 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.79 % Allowed : 9.68 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.61 (0.16), residues: 2500 helix: 2.51 (0.12), residues: 1519 sheet: 0.15 (0.91), residues: 30 loop : 0.58 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 252 HIS 0.011 0.002 HIS L 159 PHE 0.020 0.002 PHE H 19 TYR 0.022 0.002 TYR C 200 ARG 0.006 0.000 ARG L 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 353 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 MET cc_start: 0.9635 (mmt) cc_final: 0.9300 (mmt) REVERT: C 308 MET cc_start: 0.9537 (tpp) cc_final: 0.9246 (tpp) REVERT: L 8 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8382 (ttm170) REVERT: L 208 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7016 (tmtp) REVERT: M 33 LYS cc_start: 0.7891 (tppp) cc_final: 0.7107 (mptt) REVERT: M 124 MET cc_start: 0.9260 (mmp) cc_final: 0.9029 (mmm) REVERT: M 138 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: H 205 LYS cc_start: 0.7699 (mtmt) cc_final: 0.7335 (mptt) REVERT: I 7 LYS cc_start: 0.8495 (mttt) cc_final: 0.8051 (mmtp) REVERT: K 16 ARG cc_start: 0.7100 (mtp-110) cc_final: 0.6696 (mmt90) REVERT: O 15 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7736 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8181 (t0) cc_final: 0.7906 (t0) REVERT: S 16 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7591 (mtt180) REVERT: U 5 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8594 (mm) REVERT: W 16 ARG cc_start: 0.7810 (mtt-85) cc_final: 0.7379 (tpp80) REVERT: X 16 LYS cc_start: 0.8537 (mtpm) cc_final: 0.8229 (mtpp) REVERT: Y 5 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8596 (tt) REVERT: Y 6 TRP cc_start: 0.8870 (p-90) cc_final: 0.8332 (p-90) REVERT: Z 17 GLU cc_start: 0.7875 (tt0) cc_final: 0.7629 (tm-30) REVERT: 3 6 TYR cc_start: 0.6238 (p90) cc_final: 0.5893 (p90) REVERT: 3 12 PHE cc_start: 0.8020 (m-80) cc_final: 0.7800 (m-80) outliers start: 60 outliers final: 25 residues processed: 373 average time/residue: 1.3453 time to fit residues: 582.3993 Evaluate side-chains 371 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 342 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 138 GLU 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 225 LEU Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 5 residue 6 HIS Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 9 residue 7 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN M 74 ASN H 192 ASN N 24 GLN P 13 GLN P 24 GLN T 24 GLN 2 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 26918 Z= 0.333 Angle : 0.756 15.789 37014 Z= 0.296 Chirality : 0.042 0.173 3752 Planarity : 0.004 0.050 4384 Dihedral : 17.783 179.890 5999 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.79 % Allowed : 10.10 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.47 (0.16), residues: 2500 helix: 2.38 (0.12), residues: 1523 sheet: 0.08 (0.90), residues: 30 loop : 0.54 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 252 HIS 0.012 0.002 HIS L 159 PHE 0.021 0.002 PHE H 19 TYR 0.023 0.002 TYR C 200 ARG 0.004 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 349 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 MET cc_start: 0.9629 (mmt) cc_final: 0.9324 (mmt) REVERT: C 308 MET cc_start: 0.9538 (tpp) cc_final: 0.9234 (tpp) REVERT: L 8 ARG cc_start: 0.8706 (ttm-80) cc_final: 0.8383 (ttm170) REVERT: L 208 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7069 (tmtp) REVERT: M 33 LYS cc_start: 0.7876 (tppp) cc_final: 0.7459 (tppt) REVERT: M 124 MET cc_start: 0.9255 (mmp) cc_final: 0.9023 (mmm) REVERT: H 205 LYS cc_start: 0.7667 (mtmt) cc_final: 0.7263 (mttt) REVERT: I 7 LYS cc_start: 0.8441 (mttt) cc_final: 0.8041 (mmtp) REVERT: I 10 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: K 16 ARG cc_start: 0.7056 (mtp-110) cc_final: 0.6847 (mtp-110) REVERT: O 15 ARG cc_start: 0.8160 (ttt-90) cc_final: 0.7908 (ttt-90) REVERT: Q 8 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8951 (tp) REVERT: Q 13 ASP cc_start: 0.8161 (t0) cc_final: 0.7893 (t0) REVERT: S 16 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7585 (mtt180) REVERT: U 5 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8629 (mm) REVERT: X 34 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9111 (mt) REVERT: Y 4 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6826 (p0) REVERT: Y 5 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8588 (tt) REVERT: Y 6 TRP cc_start: 0.8884 (p-90) cc_final: 0.8314 (p-90) REVERT: Z 11 THR cc_start: 0.8297 (p) cc_final: 0.7713 (p) REVERT: Z 17 GLU cc_start: 0.7916 (tt0) cc_final: 0.7457 (tm-30) REVERT: 3 6 TYR cc_start: 0.6386 (p90) cc_final: 0.6091 (p90) REVERT: 3 12 PHE cc_start: 0.8045 (m-80) cc_final: 0.7804 (m-80) REVERT: 8 26 MET cc_start: 0.8104 (mtp) cc_final: 0.7860 (mtp) outliers start: 60 outliers final: 29 residues processed: 372 average time/residue: 1.3938 time to fit residues: 599.6927 Evaluate side-chains 379 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 343 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR 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 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain Y residue 4 ASP Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 9 residue 7 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 214 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN N 24 GLN P 13 GLN P 24 GLN T 24 GLN 6 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26918 Z= 0.329 Angle : 0.744 14.764 37014 Z= 0.294 Chirality : 0.042 0.171 3752 Planarity : 0.004 0.049 4384 Dihedral : 17.512 179.967 5997 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.98 % Allowed : 10.20 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.42 (0.16), residues: 2500 helix: 2.35 (0.12), residues: 1523 sheet: -0.10 (0.91), residues: 30 loop : 0.51 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 252 HIS 0.013 0.002 HIS L 159 PHE 0.021 0.002 PHE L 170 TYR 0.023 0.002 TYR C 200 ARG 0.003 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 344 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 236 MET cc_start: 0.9609 (mmt) cc_final: 0.9340 (mmt) REVERT: C 308 MET cc_start: 0.9530 (tpp) cc_final: 0.9217 (tpp) REVERT: L 8 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8370 (ttm170) REVERT: L 208 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7084 (tmtp) REVERT: M 33 LYS cc_start: 0.7938 (tppp) cc_final: 0.7533 (tppt) REVERT: M 124 MET cc_start: 0.9256 (mmp) cc_final: 0.9020 (mmm) REVERT: H 205 LYS cc_start: 0.7605 (mtmt) cc_final: 0.7221 (mptt) REVERT: F 41 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: I 7 LYS cc_start: 0.8441 (mttt) cc_final: 0.8073 (mmtp) REVERT: I 10 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: K 16 ARG cc_start: 0.7122 (mtp-110) cc_final: 0.6889 (mtp-110) REVERT: O 15 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7890 (ttt-90) REVERT: P 10 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8047 (mp) REVERT: Q 8 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8990 (tp) REVERT: Q 13 ASP cc_start: 0.8164 (t0) cc_final: 0.7908 (t0) REVERT: S 16 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7596 (mtt180) REVERT: Y 4 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6896 (p0) REVERT: Y 5 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8589 (tt) REVERT: Y 6 TRP cc_start: 0.8891 (p-90) cc_final: 0.8331 (p-90) REVERT: Z 17 GLU cc_start: 0.7930 (tt0) cc_final: 0.7710 (tm-30) REVERT: 3 6 TYR cc_start: 0.6342 (p90) cc_final: 0.6122 (p90) REVERT: 3 12 PHE cc_start: 0.8041 (m-80) cc_final: 0.7791 (m-80) REVERT: 5 8 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7199 (mp) outliers start: 64 outliers final: 35 residues processed: 369 average time/residue: 1.3605 time to fit residues: 583.2555 Evaluate side-chains 379 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 336 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain Y residue 4 ASP Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 9 residue 7 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 110 optimal weight: 0.0870 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN P 13 GLN P 24 GLN T 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26918 Z= 0.213 Angle : 0.659 14.478 37014 Z= 0.261 Chirality : 0.038 0.152 3752 Planarity : 0.004 0.045 4384 Dihedral : 16.937 179.991 5995 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.56 % Allowed : 11.36 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.67 (0.16), residues: 2500 helix: 2.60 (0.12), residues: 1510 sheet: -0.51 (0.83), residues: 35 loop : 0.57 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 252 HIS 0.011 0.001 HIS L 159 PHE 0.019 0.001 PHE L 170 TYR 0.019 0.001 TYR C 200 ARG 0.002 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 340 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 236 MET cc_start: 0.9527 (mmt) cc_final: 0.9283 (mmt) REVERT: L 8 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8357 (ttm170) REVERT: L 208 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.6951 (tmtp) REVERT: M 33 LYS cc_start: 0.7947 (tppp) cc_final: 0.7257 (mptt) REVERT: M 124 MET cc_start: 0.9228 (mmp) cc_final: 0.9000 (mmm) REVERT: H 205 LYS cc_start: 0.7617 (mtmt) cc_final: 0.7202 (mttt) REVERT: F 41 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: I 7 LYS cc_start: 0.8447 (mttt) cc_final: 0.8092 (mmtp) REVERT: K 16 ARG cc_start: 0.7082 (mtp-110) cc_final: 0.6847 (mtp-110) REVERT: O 15 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7893 (ttt-90) REVERT: Q 8 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8941 (tp) REVERT: Q 13 ASP cc_start: 0.8195 (t0) cc_final: 0.7936 (t0) REVERT: S 16 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7615 (mtt180) REVERT: V 24 GLN cc_start: 0.8308 (tt0) cc_final: 0.7818 (mt0) REVERT: W 19 ILE cc_start: 0.8974 (mm) cc_final: 0.8705 (mt) REVERT: Y 4 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6789 (p0) REVERT: Y 5 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8576 (tt) REVERT: Y 6 TRP cc_start: 0.8855 (p-90) cc_final: 0.8317 (p-90) REVERT: Z 17 GLU cc_start: 0.7886 (tt0) cc_final: 0.7404 (tt0) REVERT: 4 7 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.5526 (ttp) REVERT: 5 8 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7285 (mp) outliers start: 55 outliers final: 27 residues processed: 360 average time/residue: 1.3244 time to fit residues: 554.8063 Evaluate side-chains 368 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 334 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain Y residue 4 ASP Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 4 residue 7 MET Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 27 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 174 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN P 13 GLN P 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 26918 Z= 0.401 Angle : 0.787 14.744 37014 Z= 0.312 Chirality : 0.044 0.185 3752 Planarity : 0.004 0.052 4384 Dihedral : 17.568 179.995 5995 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.93 % Allowed : 11.27 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.36 (0.16), residues: 2500 helix: 2.30 (0.12), residues: 1522 sheet: -0.15 (0.91), residues: 30 loop : 0.50 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 9 HIS 0.014 0.002 HIS L 159 PHE 0.022 0.002 PHE M 65 TYR 0.025 0.002 TYR C 200 ARG 0.004 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 340 time to evaluate : 2.533 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9621 (mmt) cc_final: 0.9314 (mmt) REVERT: L 208 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7082 (tmtp) REVERT: M 33 LYS cc_start: 0.7932 (tppp) cc_final: 0.7212 (mptt) REVERT: M 124 MET cc_start: 0.9292 (mmp) cc_final: 0.9048 (mmm) REVERT: H 205 LYS cc_start: 0.7594 (mtmt) cc_final: 0.7198 (mptt) REVERT: F 41 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: I 7 LYS cc_start: 0.8356 (mttt) cc_final: 0.8039 (mmtp) REVERT: I 10 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: K 16 ARG cc_start: 0.7112 (mtp-110) cc_final: 0.6717 (mmt90) REVERT: O 15 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7886 (ttt-90) REVERT: P 10 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8070 (mp) REVERT: Q 8 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8973 (tp) REVERT: Q 13 ASP cc_start: 0.8135 (t0) cc_final: 0.7872 (t0) REVERT: S 16 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7573 (mtt180) REVERT: Y 4 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6793 (p0) REVERT: Y 5 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8626 (tt) REVERT: Y 6 TRP cc_start: 0.8891 (p-90) cc_final: 0.8366 (p-90) REVERT: Z 17 GLU cc_start: 0.7943 (tt0) cc_final: 0.7689 (tm-30) REVERT: 4 7 MET cc_start: 0.5709 (ttm) cc_final: 0.5488 (ttp) outliers start: 63 outliers final: 36 residues processed: 370 average time/residue: 1.4069 time to fit residues: 602.7623 Evaluate side-chains 378 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 335 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain Y residue 4 ASP Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 7 residue 27 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN P 13 GLN P 24 GLN 0 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26918 Z= 0.352 Angle : 0.754 14.196 37014 Z= 0.301 Chirality : 0.042 0.176 3752 Planarity : 0.004 0.050 4384 Dihedral : 17.464 179.987 5995 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.79 % Allowed : 11.36 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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 (0.16), residues: 2500 helix: 2.35 (0.12), residues: 1514 sheet: -0.21 (0.91), residues: 30 loop : 0.48 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 252 HIS 0.014 0.002 HIS L 159 PHE 0.021 0.002 PHE L 170 TYR 0.023 0.002 TYR C 200 ARG 0.004 0.000 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 340 time to evaluate : 2.595 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9597 (mmt) cc_final: 0.9304 (mmt) REVERT: C 308 MET cc_start: 0.9614 (tpp) cc_final: 0.9164 (tpp) REVERT: L 208 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7103 (tmtp) REVERT: M 33 LYS cc_start: 0.7957 (tppp) cc_final: 0.7231 (mptt) REVERT: M 124 MET cc_start: 0.9258 (mmp) cc_final: 0.9017 (mmm) REVERT: H 205 LYS cc_start: 0.7650 (mtmt) cc_final: 0.7248 (mptt) REVERT: F 41 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: I 7 LYS cc_start: 0.8388 (mttt) cc_final: 0.8024 (mmtp) REVERT: I 10 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: K 16 ARG cc_start: 0.7146 (mtp-110) cc_final: 0.6720 (mmt90) REVERT: O 15 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7863 (ttt-90) REVERT: P 10 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8081 (mp) REVERT: Q 8 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8966 (tp) REVERT: Q 13 ASP cc_start: 0.8151 (t0) cc_final: 0.7891 (t0) REVERT: S 16 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7603 (mtt180) REVERT: V 24 GLN cc_start: 0.8354 (tt0) cc_final: 0.7845 (mt0) REVERT: V 26 MET cc_start: 0.8889 (ttp) cc_final: 0.8623 (ttp) REVERT: Y 4 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6842 (p0) REVERT: Y 5 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8614 (tt) REVERT: Y 6 TRP cc_start: 0.8893 (p-90) cc_final: 0.8345 (p-90) REVERT: 4 7 MET cc_start: 0.5674 (ttm) cc_final: 0.5443 (ttp) outliers start: 60 outliers final: 38 residues processed: 367 average time/residue: 1.3759 time to fit residues: 585.3088 Evaluate side-chains 381 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 336 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain Y residue 4 ASP Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 7 residue 27 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN P 13 GLN P 24 GLN 0 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26918 Z= 0.200 Angle : 0.658 14.106 37014 Z= 0.262 Chirality : 0.038 0.147 3752 Planarity : 0.004 0.045 4384 Dihedral : 16.798 179.975 5995 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.00 % Allowed : 12.66 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.69 (0.16), residues: 2500 helix: 2.64 (0.12), residues: 1502 sheet: -0.55 (0.84), residues: 35 loop : 0.55 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 9 HIS 0.010 0.001 HIS L 159 PHE 0.018 0.001 PHE L 170 TYR 0.017 0.001 TYR C 200 ARG 0.007 0.000 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 336 time to evaluate : 2.755 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9499 (mmt) cc_final: 0.9243 (mmt) REVERT: C 308 MET cc_start: 0.9578 (tpp) cc_final: 0.9099 (tpp) REVERT: L 8 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8360 (ttm170) REVERT: M 33 LYS cc_start: 0.7951 (tppp) cc_final: 0.7260 (mptt) REVERT: M 75 MET cc_start: 0.9456 (mtt) cc_final: 0.9094 (mtp) REVERT: M 124 MET cc_start: 0.9221 (mmp) cc_final: 0.8992 (mmm) REVERT: H 204 LYS cc_start: 0.7565 (mttp) cc_final: 0.7198 (mptt) REVERT: H 205 LYS cc_start: 0.7585 (mtmt) cc_final: 0.7174 (mptt) REVERT: I 7 LYS cc_start: 0.8395 (mttt) cc_final: 0.8013 (mmtp) REVERT: I 10 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: J 12 GLU cc_start: 0.7331 (tt0) cc_final: 0.7126 (tt0) REVERT: K 16 ARG cc_start: 0.7146 (mtp-110) cc_final: 0.6707 (mmt90) REVERT: O 15 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7868 (ttt-90) REVERT: Q 8 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8974 (tp) REVERT: Q 13 ASP cc_start: 0.8206 (t0) cc_final: 0.7935 (t0) REVERT: S 16 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7619 (mtt180) REVERT: T 16 LYS cc_start: 0.8628 (mtpm) cc_final: 0.8375 (mtpt) REVERT: V 24 GLN cc_start: 0.8339 (tt0) cc_final: 0.7846 (mt0) REVERT: W 19 ILE cc_start: 0.8970 (mm) cc_final: 0.8702 (mt) REVERT: X 16 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8204 (mtpp) REVERT: Y 4 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6791 (p0) REVERT: Y 5 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8575 (tt) REVERT: Y 6 TRP cc_start: 0.8850 (p-90) cc_final: 0.8282 (p-90) REVERT: Z 17 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7673 (tm-30) REVERT: 4 7 MET cc_start: 0.5644 (ttm) cc_final: 0.5420 (ttp) REVERT: 5 8 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7312 (mp) outliers start: 43 outliers final: 24 residues processed: 353 average time/residue: 1.3638 time to fit residues: 561.0203 Evaluate side-chains 360 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 331 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain Y residue 4 ASP Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 7 residue 27 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN P 13 GLN P 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26918 Z= 0.247 Angle : 0.688 14.246 37014 Z= 0.276 Chirality : 0.039 0.157 3752 Planarity : 0.004 0.045 4384 Dihedral : 16.818 179.995 5995 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.72 % Allowed : 13.04 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.59 (0.16), residues: 2500 helix: 2.53 (0.12), residues: 1514 sheet: -0.54 (0.83), residues: 35 loop : 0.54 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 9 HIS 0.012 0.002 HIS L 159 PHE 0.020 0.002 PHE L 170 TYR 0.021 0.002 TYR C 200 ARG 0.008 0.000 ARG L 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 329 time to evaluate : 2.462 Fit side-chains REVERT: C 236 MET cc_start: 0.9562 (mmt) cc_final: 0.9324 (mmt) REVERT: C 308 MET cc_start: 0.9582 (tpp) cc_final: 0.9244 (tpp) REVERT: L 8 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8366 (ttm170) REVERT: L 208 LYS cc_start: 0.7936 (tttm) cc_final: 0.7550 (mmtm) REVERT: M 33 LYS cc_start: 0.7939 (tppp) cc_final: 0.7239 (mptt) REVERT: M 124 MET cc_start: 0.9245 (mmp) cc_final: 0.9038 (mmm) REVERT: H 204 LYS cc_start: 0.7576 (mttp) cc_final: 0.7146 (mptt) REVERT: H 205 LYS cc_start: 0.7585 (mtmt) cc_final: 0.7174 (mptt) REVERT: I 7 LYS cc_start: 0.8345 (mttt) cc_final: 0.8061 (mmtp) REVERT: K 16 ARG cc_start: 0.7139 (mtp-110) cc_final: 0.6706 (mmt90) REVERT: O 15 ARG cc_start: 0.8173 (ttt-90) cc_final: 0.7872 (ttt-90) REVERT: Q 8 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.9011 (tp) REVERT: Q 13 ASP cc_start: 0.8197 (t0) cc_final: 0.7917 (t0) REVERT: S 16 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7608 (mtt180) REVERT: V 24 GLN cc_start: 0.8353 (tt0) cc_final: 0.7859 (mt0) REVERT: V 26 MET cc_start: 0.8839 (ttp) cc_final: 0.8601 (ttp) REVERT: W 19 ILE cc_start: 0.8968 (mm) cc_final: 0.8697 (mt) REVERT: X 16 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8235 (mtpp) REVERT: Y 4 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6764 (p0) REVERT: Y 5 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8593 (tt) REVERT: Y 6 TRP cc_start: 0.8837 (p-90) cc_final: 0.8307 (p-90) REVERT: 3 6 TYR cc_start: 0.6209 (p90) cc_final: 0.5866 (p90) REVERT: 4 7 MET cc_start: 0.5655 (ttm) cc_final: 0.5432 (ttp) outliers start: 37 outliers final: 25 residues processed: 350 average time/residue: 1.3693 time to fit residues: 555.8391 Evaluate side-chains 353 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 325 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain Y residue 4 ASP Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN P 13 GLN P 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.082312 restraints weight = 32696.677| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.35 r_work: 0.2733 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26918 Z= 0.213 Angle : 0.663 14.100 37014 Z= 0.266 Chirality : 0.038 0.153 3752 Planarity : 0.004 0.045 4384 Dihedral : 16.583 179.982 5995 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.96 % Allowed : 12.99 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.63 (0.16), residues: 2500 helix: 2.57 (0.12), residues: 1513 sheet: -0.50 (0.84), residues: 35 loop : 0.54 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 9 HIS 0.011 0.001 HIS L 159 PHE 0.019 0.001 PHE L 170 TYR 0.019 0.002 TYR C 200 ARG 0.008 0.000 ARG L 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10149.87 seconds wall clock time: 179 minutes 48.87 seconds (10788.87 seconds total)