Starting phenix.real_space_refine (version: dev) on Wed Dec 21 22:40:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/12_2022/7vot_32059_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/12_2022/7vot_32059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/12_2022/7vot_32059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/12_2022/7vot_32059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/12_2022/7vot_32059_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/12_2022/7vot_32059_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 44984 Number of models: 1 Model: "" Number of chains: 128 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1955 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 234} Chain: "A" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "K" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "R" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "2" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 328 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "7" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "X" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Y" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 375 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "l" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "h" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1955 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 234} Chain: "a" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "d" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "e" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "g" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "i" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "j" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "k" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "n" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "o" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "p" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "r" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "s" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "t" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "u" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "v" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "w" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "c" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "5" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "b1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "4" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 328 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "6" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "b8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "b0" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "x" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "y" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 375 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "L" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 412 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 69 Chain: "A" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 220 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 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: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 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: "3" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 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: "l" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 412 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 32 Chain: "h" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 69 Chain: "a" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 220 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "b" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "e" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "j" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 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: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "o" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "s" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "v" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "w" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 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: "5" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "b1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 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: "b8" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "b9" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 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 Time building chain proxies: 23.88, per 1000 atoms: 0.53 Number of scatterers: 44984 At special positions: 0 Unit cell: (215.28, 140.4, 104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 176 16.00 P 26 15.00 Mg 64 11.99 O 6792 8.00 N 6276 7.00 C 31648 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=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.27 Conformation dependent library (CDL) restraints added in 5.0 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 194 helices and 8 sheets defined 66.5% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.638A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 131 " --> pdb=" O ALA L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.025A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.627A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 267 removed outlier: 3.728A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 259 through 267' Processing helix chain 'M' and resid 37 through 42 removed outlier: 4.321A pdb=" N PHE M 42 " --> pdb=" O LEU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 77 Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 113 through 140 Processing helix chain 'M' and resid 145 through 161 removed outlier: 3.663A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) 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: 3.622A 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 229 removed outlier: 4.619A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 removed outlier: 3.620A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 289 removed outlier: 3.885A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER M 287 " --> pdb=" O GLY M 283 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'H' and resid 12 through 37 removed outlier: 4.067A pdb=" N ARG H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.917A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.978A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 247 No H-bonds generated for 'chain 'H' and resid 245 through 247' Processing helix chain 'H' and resid 251 through 255 Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 13 through 37 Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.580A pdb=" N ALA A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'D' and resid 2 through 10 removed outlier: 4.202A pdb=" N TYR D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'F' and resid 2 through 10 removed outlier: 3.874A pdb=" N TYR F 5 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 37 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'G' and resid 14 through 45 Processing helix chain 'I' and resid 4 through 10 Processing helix chain 'I' and resid 13 through 37 Processing helix chain 'I' and resid 43 through 51 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'K' and resid 4 through 10 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'O' and resid 4 through 10 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 43 through 50 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.590A pdb=" N TYR Q 5 " --> pdb=" O SER Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 37 Processing helix chain 'Q' and resid 43 through 50 removed outlier: 4.100A pdb=" N SER Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 45 Processing helix chain 'S' and resid 4 through 9 Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'U' and resid 4 through 10 Processing helix chain 'U' and resid 13 through 37 Processing helix chain 'U' and resid 43 through 50 Processing helix chain 'V' and resid 14 through 45 Processing helix chain 'W' and resid 4 through 9 Processing helix chain 'W' and resid 13 through 37 Processing helix chain 'W' and resid 43 through 51 Processing helix chain 'C' and resid 14 through 45 Processing helix chain '3' and resid 2 through 10 removed outlier: 4.306A pdb=" N TYR 3 5 " --> pdb=" O SER 3 2 " (cutoff:3.500A) Processing helix chain '3' and resid 13 through 37 Processing helix chain '3' and resid 43 through 51 Processing helix chain 'Z' and resid 14 through 45 Processing helix chain '1' and resid 6 through 10 Processing helix chain '1' and resid 13 through 37 Processing helix chain '1' and resid 43 through 50 Processing helix chain '2' and resid 14 through 45 Processing helix chain '7' and resid 4 through 10 Processing helix chain '7' and resid 13 through 37 Processing helix chain '7' and resid 43 through 46 No H-bonds generated for 'chain '7' and resid 43 through 46' Processing helix chain '8' and resid 14 through 45 Processing helix chain '9' and resid 4 through 10 Processing helix chain '9' and resid 13 through 37 Processing helix chain '9' and resid 43 through 50 Processing helix chain '0' and resid 14 through 45 Processing helix chain 'X' and resid 19 through 54 Processing helix chain 'Y' and resid 6 through 28 Processing helix chain 'Y' and resid 32 through 47 Processing helix chain 'l' and resid 7 through 9 No H-bonds generated for 'chain 'l' and resid 7 through 9' Processing helix chain 'l' and resid 32 through 56 Processing helix chain 'l' and resid 71 through 73 No H-bonds generated for 'chain 'l' and resid 71 through 73' Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 84 through 111 Processing helix chain 'l' and resid 116 through 132 removed outlier: 3.638A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU l 131 " --> pdb=" O ALA l 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 134 through 139 Processing helix chain 'l' and resid 142 through 144 No H-bonds generated for 'chain 'l' and resid 142 through 144' Processing helix chain 'l' and resid 152 through 164 removed outlier: 4.026A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 167 through 169 No H-bonds generated for 'chain 'l' and resid 167 through 169' Processing helix chain 'l' and resid 171 through 198 Processing helix chain 'l' and resid 209 through 220 Processing helix chain 'l' and resid 226 through 249 removed outlier: 3.627A pdb=" N HIS l 230 " --> pdb=" O THR l 226 " (cutoff:3.500A) Processing helix chain 'l' and resid 259 through 267 removed outlier: 3.728A pdb=" N TRP l 263 " --> pdb=" O TRP l 259 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN l 264 " --> pdb=" O VAL l 260 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 259 through 267' Processing helix chain 'm' and resid 37 through 42 removed outlier: 4.322A pdb=" N PHE m 42 " --> pdb=" O LEU m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 54 through 77 Processing helix chain 'm' and resid 82 through 87 Processing helix chain 'm' and resid 99 through 101 No H-bonds generated for 'chain 'm' and resid 99 through 101' Processing helix chain 'm' and resid 113 through 140 Processing helix chain 'm' and resid 145 through 161 removed outlier: 3.662A pdb=" N ALA m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU m 156 " --> pdb=" O SER m 152 " (cutoff:3.500A) 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: 3.622A 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 229 removed outlier: 4.619A pdb=" N ARG m 228 " --> pdb=" O LEU m 224 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N PHE m 229 " --> pdb=" O ALA m 225 " (cutoff:3.500A) Processing helix chain 'm' and resid 234 through 239 Processing helix chain 'm' and resid 243 through 256 removed outlier: 3.620A pdb=" N TRP m 252 " --> pdb=" O ALA m 248 " (cutoff:3.500A) Processing helix chain 'm' and resid 264 through 289 removed outlier: 3.885A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE m 282 " --> pdb=" O LEU m 278 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER m 287 " --> pdb=" O GLY m 283 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY m 288 " --> pdb=" O ILE m 284 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR m 289 " --> pdb=" O LEU m 285 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 301 Processing helix chain 'h' and resid 12 through 37 removed outlier: 4.066A pdb=" N ARG h 37 " --> pdb=" O THR h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 69 No H-bonds generated for 'chain 'h' and resid 67 through 69' Processing helix chain 'h' and resid 104 through 107 No H-bonds generated for 'chain 'h' and resid 104 through 107' Processing helix chain 'h' and resid 110 through 112 No H-bonds generated for 'chain 'h' and resid 110 through 112' Processing helix chain 'h' and resid 193 through 195 No H-bonds generated for 'chain 'h' and resid 193 through 195' Processing helix chain 'h' and resid 210 through 215 removed outlier: 3.917A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 227 through 243 removed outlier: 3.977A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 245 through 247 No H-bonds generated for 'chain 'h' and resid 245 through 247' Processing helix chain 'h' and resid 251 through 255 Processing helix chain 'a' and resid 4 through 10 Processing helix chain 'a' and resid 13 through 37 Processing helix chain 'a' and resid 43 through 50 removed outlier: 3.580A pdb=" N ALA a 48 " --> pdb=" O LEU a 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 45 Processing helix chain 'd' and resid 2 through 10 removed outlier: 4.202A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 37 Processing helix chain 'd' and resid 43 through 50 Processing helix chain 'e' and resid 14 through 45 Processing helix chain 'f' and resid 2 through 10 removed outlier: 3.874A pdb=" N TYR f 5 " --> pdb=" O SER f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 37 Processing helix chain 'f' and resid 43 through 50 Processing helix chain 'g' and resid 14 through 45 Processing helix chain 'i' and resid 4 through 10 Processing helix chain 'i' and resid 13 through 37 Processing helix chain 'i' and resid 43 through 51 Processing helix chain 'j' and resid 14 through 45 Processing helix chain 'k' and resid 4 through 10 Processing helix chain 'k' and resid 13 through 37 Processing helix chain 'k' and resid 43 through 50 Processing helix chain 'n' and resid 14 through 45 Processing helix chain 'o' and resid 4 through 10 Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 50 Processing helix chain 'p' and resid 14 through 45 Processing helix chain 'q' and resid 2 through 10 removed outlier: 3.591A pdb=" N TYR q 5 " --> pdb=" O SER q 2 " (cutoff:3.500A) Processing helix chain 'q' and resid 13 through 37 Processing helix chain 'q' and resid 43 through 50 removed outlier: 4.099A pdb=" N SER q 47 " --> pdb=" O TRP q 43 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA q 48 " --> pdb=" O LEU q 44 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 45 Processing helix chain 's' and resid 4 through 9 Processing helix chain 's' and resid 13 through 37 Processing helix chain 's' and resid 43 through 50 Processing helix chain 't' and resid 14 through 45 Processing helix chain 'u' and resid 4 through 10 Processing helix chain 'u' and resid 13 through 37 Processing helix chain 'u' and resid 43 through 50 Processing helix chain 'v' and resid 14 through 45 Processing helix chain 'w' and resid 4 through 9 Processing helix chain 'w' and resid 13 through 37 Processing helix chain 'w' and resid 43 through 51 Processing helix chain 'c' and resid 14 through 45 Processing helix chain '5' and resid 2 through 10 removed outlier: 4.306A pdb=" N TYR 5 5 " --> pdb=" O SER 5 2 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 37 Processing helix chain '5' and resid 43 through 51 Processing helix chain 'z' and resid 14 through 45 Processing helix chain 'b1' and resid 6 through 10 Processing helix chain 'b1' and resid 13 through 37 Processing helix chain 'b1' and resid 43 through 50 Processing helix chain '4' and resid 14 through 45 Processing helix chain '6' and resid 4 through 10 Processing helix chain '6' and resid 13 through 37 Processing helix chain '6' and resid 43 through 46 No H-bonds generated for 'chain '6' and resid 43 through 46' Processing helix chain 'b8' and resid 14 through 45 Processing helix chain 'b9' and resid 4 through 10 Processing helix chain 'b9' and resid 13 through 37 Processing helix chain 'b9' and resid 43 through 50 Processing helix chain 'b0' and resid 14 through 45 Processing helix chain 'x' and resid 19 through 54 Processing helix chain 'y' and resid 6 through 28 Processing helix chain 'y' and resid 32 through 47 Processing sheet with id= A, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.680A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 202 through 204 removed outlier: 3.789A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'h' and resid 62 through 65 Processing sheet with id= F, first strand: chain 'h' and resid 87 through 89 Processing sheet with id= G, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.680A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE h 178 " --> pdb=" O ILE h 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'h' and resid 202 through 204 removed outlier: 3.788A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2296 hydrogen bonds defined for protein. 6540 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: 14.16 Time building geometry restraints manager: 20.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 12008 1.35 - 1.56: 34042 1.56 - 1.76: 52 1.76 - 1.97: 342 1.97 - 2.17: 256 Bond restraints: 46700 Sorted by residual: bond pdb=" C3C BPB L 303 " pdb=" CAC BPB L 303 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C3C BPB l 303 " pdb=" CAC BPB l 303 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C3C BPB M 403 " pdb=" CAC BPB M 403 " ideal model delta sigma weight residual 1.334 1.546 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3C BPB m 403 " pdb=" CAC BPB m 403 " ideal model delta sigma weight residual 1.334 1.546 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" OB3 CDL m 406 " pdb=" PB2 CDL m 406 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.00e-02 1.00e+04 5.21e+01 ... (remaining 46695 not shown) Histogram of bond angle deviations from ideal: 84.90 - 100.45: 292 100.45 - 115.99: 29876 115.99 - 131.54: 33330 131.54 - 147.08: 512 147.08 - 162.63: 128 Bond angle restraints: 64138 Sorted by residual: angle pdb=" C51 CDL m 406 " pdb=" CB5 CDL m 406 " pdb=" OB6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.72 -9.39 1.32e+00 5.72e-01 5.05e+01 angle pdb=" C51 CDL M 406 " pdb=" CB5 CDL M 406 " pdb=" OB6 CDL M 406 " ideal model delta sigma weight residual 111.33 120.72 -9.39 1.32e+00 5.72e-01 5.04e+01 angle pdb=" C11 CDL h 303 " pdb=" CA5 CDL h 303 " pdb=" OA6 CDL h 303 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL H 303 " pdb=" CA5 CDL H 303 " pdb=" OA6 CDL H 303 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL m 406 " pdb=" CA5 CDL m 406 " pdb=" OA6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.07 -8.74 1.32e+00 5.72e-01 4.37e+01 ... (remaining 64133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 24104 35.97 - 71.94: 462 71.94 - 107.92: 56 107.92 - 143.89: 6 143.89 - 179.86: 4 Dihedral angle restraints: 24632 sinusoidal: 11346 harmonic: 13286 Sorted by residual: dihedral pdb=" C1 BCL G 101 " pdb=" C2 BCL G 101 " pdb=" C3 BCL G 101 " pdb=" C5 BCL G 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.14 179.86 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL g 101 " pdb=" C2 BCL g 101 " pdb=" C3 BCL g 101 " pdb=" C5 BCL g 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.19 179.81 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 2 101 " pdb=" C2 BCL 2 101 " pdb=" C3 BCL 2 101 " pdb=" C5 BCL 2 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.54 -179.46 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 24629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4686 0.042 - 0.084: 1306 0.084 - 0.126: 203 0.126 - 0.168: 12 0.168 - 0.210: 9 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2C BPB m 403 " pdb=" C1C BPB m 403 " pdb=" C3C BPB m 403 " pdb=" CMC BPB m 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.57 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C2C BPB M 403 " pdb=" C1C BPB M 403 " pdb=" C3C BPB M 403 " pdb=" CMC BPB M 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.57 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG M 247 " pdb=" N ARG M 247 " pdb=" C ARG M 247 " pdb=" CB ARG M 247 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 6213 not shown) Planarity restraints: 7888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2C BPB L 303 " -0.381 2.00e-02 2.50e+03 5.00e-01 3.13e+03 pdb=" C3C BPB L 303 " 0.502 2.00e-02 2.50e+03 pdb=" C4C BPB L 303 " -0.207 2.00e-02 2.50e+03 pdb=" CAC BPB L 303 " 0.678 2.00e-02 2.50e+03 pdb=" CBC BPB L 303 " -0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB l 303 " 0.382 2.00e-02 2.50e+03 5.00e-01 3.12e+03 pdb=" C3C BPB l 303 " -0.502 2.00e-02 2.50e+03 pdb=" C4C BPB l 303 " 0.207 2.00e-02 2.50e+03 pdb=" CAC BPB l 303 " -0.678 2.00e-02 2.50e+03 pdb=" CBC BPB l 303 " 0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB M 403 " -0.007 2.00e-02 2.50e+03 2.37e-01 7.03e+02 pdb=" C3C BPB M 403 " -0.333 2.00e-02 2.50e+03 pdb=" C4C BPB M 403 " 0.140 2.00e-02 2.50e+03 pdb=" CAC BPB M 403 " 0.356 2.00e-02 2.50e+03 pdb=" CBC BPB M 403 " -0.156 2.00e-02 2.50e+03 ... (remaining 7885 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1003 2.70 - 3.25: 42324 3.25 - 3.80: 77608 3.80 - 4.35: 105894 4.35 - 4.90: 171554 Nonbonded interactions: 398383 Sorted by model distance: nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE2 m 401 " model vdw 2.147 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE2 M 401 " model vdw 2.147 3.080 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE2 M 401 " model vdw 2.150 3.000 nonbonded pdb=" OE1 GLU m 234 " pdb="FE FE2 m 401 " model vdw 2.151 3.000 nonbonded pdb=" NE2 HIS M 219 " pdb="FE FE2 M 401 " model vdw 2.158 3.080 ... (remaining 398378 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 49) selection = (chain '2' and resid 10 through 49) selection = (chain '4' and resid 10 through 49) selection = (chain '8' and resid 10 through 49) selection = (chain 'B' and resid 10 through 49) selection = (chain 'C' and resid 10 through 49) selection = (chain 'E' and resid 10 through 49) selection = (chain 'G' and resid 10 through 49) selection = (chain 'J' and resid 10 through 49) selection = (chain 'N' and resid 10 through 49) selection = (chain 'P' and resid 10 through 49) selection = (chain 'R' and resid 10 through 49) selection = (chain 'T' and resid 10 through 49) selection = (chain 'V' and resid 10 through 49) selection = (chain 'Z' and resid 10 through 49) selection = (chain 'b' and resid 10 through 49) selection = (chain 'b0' and resid 10 through 49) selection = (chain 'b8' and resid 10 through 49) selection = (chain 'c' and resid 10 through 49) selection = (chain 'e' and resid 10 through 49) selection = (chain 'g' and resid 10 through 49) selection = (chain 'j' and resid 10 through 49) selection = (chain 'n' and resid 10 through 49) selection = (chain 'p' and resid 10 through 49) selection = (chain 'r' and resid 10 through 49) selection = (chain 't' and resid 10 through 49) selection = (chain 'v' and resid 10 through 49) selection = (chain 'z' and resid 10 through 49) } ncs_group { reference = (chain '1' and resid 2 through 48) selection = (chain '3' and resid 2 through 48) selection = (chain '5' and resid 2 through 48) selection = (chain '6' and resid 2 through 48) selection = (chain '7' and resid 2 through 48) selection = (chain '9' and resid 2 through 48) selection = (chain 'A' and resid 2 through 48) selection = (chain 'D' and resid 2 through 48) selection = (chain 'F' and resid 2 through 48) selection = (chain 'I' and resid 2 through 48) selection = (chain 'K' and resid 2 through 48) selection = (chain 'O' and resid 2 through 48) selection = (chain 'Q' and resid 2 through 48) selection = (chain 'S' and resid 2 through 48) selection = (chain 'U' and resid 2 through 48) selection = (chain 'W' and resid 2 through 48) selection = (chain 'a' and resid 2 through 48) selection = (chain 'b1' and resid 2 through 48) selection = (chain 'b9' and resid 2 through 48) selection = (chain 'd' and resid 2 through 48) selection = (chain 'f' and resid 2 through 48) selection = (chain 'i' and resid 2 through 48) selection = (chain 'k' and resid 2 through 48) selection = (chain 'o' and resid 2 through 48) selection = (chain 'q' and resid 2 through 48) selection = (chain 's' and resid 2 through 48) selection = (chain 'u' and resid 2 through 48) selection = (chain 'w' and resid 2 through 48) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Y' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 26 5.49 5 Mg 64 5.21 5 S 176 5.16 5 C 31648 2.51 5 N 6276 2.21 5 O 6792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.260 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: 0.000 Extract box with map and model: 19.010 Check model and map are aligned: 0.660 Convert atoms to be neutral: 0.440 Process input model: 107.600 Find NCS groups from input model: 3.670 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.006 0.217 46700 Z= 0.341 Angle : 0.796 16.237 64138 Z= 0.329 Chirality : 0.038 0.210 6216 Planarity : 0.009 0.500 7888 Dihedral : 14.466 179.859 16092 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.64 (0.12), residues: 4462 helix: 2.48 (0.09), residues: 2912 sheet: -0.44 (0.84), residues: 48 loop : 0.42 (0.17), residues: 1502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1153 time to evaluate : 4.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 1160 average time/residue: 1.2119 time to fit residues: 1822.2671 Evaluate side-chains 852 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 842 time to evaluate : 5.085 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 4 average time/residue: 0.4556 time to fit residues: 9.6596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 341 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 395 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 199 ASN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN H 194 GLN D 20 GLN I 20 GLN N 18 GLN R 16 GLN V 18 GLN 3 20 GLN Z 18 GLN 7 20 GLN ** l 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 307 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 194 GLN h 199 GLN i 20 GLN k 42 ASN k 52 ASN n 18 GLN o 20 GLN ** q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 52 ASN r 16 GLN s 20 GLN v 18 GLN z 16 GLN 6 20 GLN x 26 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 46700 Z= 0.330 Angle : 0.684 11.299 64138 Z= 0.295 Chirality : 0.040 0.152 6216 Planarity : 0.004 0.044 7888 Dihedral : 15.534 180.000 8066 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.31 (0.12), residues: 4462 helix: 2.22 (0.08), residues: 2908 sheet: -0.67 (0.81), residues: 48 loop : 0.31 (0.17), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 940 time to evaluate : 5.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 65 residues processed: 1003 average time/residue: 1.2052 time to fit residues: 1576.2588 Evaluate side-chains 911 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 846 time to evaluate : 4.800 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 39 residues processed: 30 average time/residue: 0.6129 time to fit residues: 35.7866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 329 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 396 optimal weight: 9.9990 chunk 428 optimal weight: 5.9990 chunk 353 optimal weight: 2.9990 chunk 393 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 318 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN H 194 GLN I 20 GLN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN N 18 GLN ** W 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 18 GLN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN X 26 GLN Y 51 ASN l 199 ASN m 307 ASN h 35 ASN h 194 GLN i 20 GLN k 52 ASN n 16 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 16 GLN ** z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 18 GLN x 58 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 46700 Z= 0.324 Angle : 0.678 11.496 64138 Z= 0.290 Chirality : 0.040 0.146 6216 Planarity : 0.004 0.044 7888 Dihedral : 15.492 179.943 8066 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 4.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.15 (0.12), residues: 4462 helix: 2.08 (0.08), residues: 2938 sheet: -0.76 (0.80), residues: 48 loop : 0.26 (0.17), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 926 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 84 residues processed: 1017 average time/residue: 1.1805 time to fit residues: 1575.4654 Evaluate side-chains 943 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 859 time to evaluate : 4.564 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 56 residues processed: 31 average time/residue: 0.5161 time to fit residues: 32.5338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 391 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 266 optimal weight: 0.5980 chunk 398 optimal weight: 5.9990 chunk 421 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 377 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN I 20 GLN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN S 20 GLN W 20 GLN 3 20 GLN Z 18 GLN Y 51 ASN ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN n 16 GLN o 20 GLN 4 18 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 46700 Z= 0.214 Angle : 0.622 11.333 64138 Z= 0.267 Chirality : 0.037 0.153 6216 Planarity : 0.003 0.064 7888 Dihedral : 15.095 179.935 8066 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.12), residues: 4462 helix: 2.26 (0.08), residues: 2934 sheet: -0.62 (0.81), residues: 48 loop : 0.28 (0.17), residues: 1480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 927 time to evaluate : 4.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 77 residues processed: 1008 average time/residue: 1.1788 time to fit residues: 1558.4824 Evaluate side-chains 945 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 868 time to evaluate : 4.694 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 59 residues processed: 22 average time/residue: 0.4805 time to fit residues: 24.3105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 378 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN I 20 GLN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 18 GLN Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 ASN i 20 GLN k 20 GLN k 42 ASN k 52 ASN o 20 GLN x 58 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 46700 Z= 0.404 Angle : 0.753 11.206 64138 Z= 0.318 Chirality : 0.042 0.227 6216 Planarity : 0.004 0.051 7888 Dihedral : 15.571 179.850 8066 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.12), residues: 4462 helix: 1.92 (0.08), residues: 2930 sheet: -0.84 (0.79), residues: 48 loop : 0.14 (0.17), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 900 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 109 residues processed: 1001 average time/residue: 1.1721 time to fit residues: 1542.7320 Evaluate side-chains 977 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 868 time to evaluate : 4.655 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 70 residues processed: 41 average time/residue: 0.6370 time to fit residues: 47.0682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 2.9990 chunk 379 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 421 optimal weight: 2.9990 chunk 350 optimal weight: 4.9990 chunk 195 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 221 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 20 GLN K 52 ASN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 GLN x 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 46700 Z= 0.190 Angle : 0.627 11.176 64138 Z= 0.270 Chirality : 0.037 0.298 6216 Planarity : 0.003 0.049 7888 Dihedral : 14.982 179.979 8066 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.37 (0.12), residues: 4462 helix: 2.29 (0.09), residues: 2908 sheet: -0.61 (0.83), residues: 48 loop : 0.28 (0.17), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 935 time to evaluate : 4.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 72 residues processed: 1019 average time/residue: 1.1651 time to fit residues: 1569.7841 Evaluate side-chains 942 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 870 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 58 residues processed: 16 average time/residue: 0.5054 time to fit residues: 19.4156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 406 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 308 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 355 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 420 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 20 GLN K 52 ASN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN k 20 GLN k 52 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 GLN r 16 GLN c 18 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 46700 Z= 0.266 Angle : 0.685 11.039 64138 Z= 0.292 Chirality : 0.039 0.271 6216 Planarity : 0.004 0.050 7888 Dihedral : 15.000 179.926 8066 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.20 (0.12), residues: 4462 helix: 2.17 (0.09), residues: 2924 sheet: -0.64 (0.83), residues: 48 loop : 0.17 (0.17), residues: 1490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 895 time to evaluate : 7.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 87 residues processed: 982 average time/residue: 1.2249 time to fit residues: 1607.9221 Evaluate side-chains 965 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 878 time to evaluate : 4.660 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 63 residues processed: 26 average time/residue: 0.6783 time to fit residues: 34.1508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 259 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 267 optimal weight: 0.7980 chunk 286 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 330 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 20 GLN K 52 ASN Q 20 GLN W 20 GLN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 58 GLN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN k 52 ASN n 16 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 16 GLN x 58 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 46700 Z= 0.213 Angle : 0.658 11.528 64138 Z= 0.285 Chirality : 0.038 0.277 6216 Planarity : 0.003 0.058 7888 Dihedral : 14.842 179.968 8066 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.12), residues: 4462 helix: 2.28 (0.09), residues: 2912 sheet: -0.52 (0.85), residues: 48 loop : 0.27 (0.18), residues: 1502 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 905 time to evaluate : 4.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 81 residues processed: 984 average time/residue: 1.1693 time to fit residues: 1512.4510 Evaluate side-chains 952 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 871 time to evaluate : 4.444 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 63 residues processed: 20 average time/residue: 0.5403 time to fit residues: 23.6735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 6.9990 chunk 402 optimal weight: 5.9990 chunk 367 optimal weight: 2.9990 chunk 391 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 370 optimal weight: 3.9990 chunk 390 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN I 20 GLN K 52 ASN Q 20 GLN W 20 GLN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN k 52 ASN p 18 GLN r 16 GLN x 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 46700 Z= 0.367 Angle : 0.769 12.440 64138 Z= 0.329 Chirality : 0.042 0.290 6216 Planarity : 0.004 0.068 7888 Dihedral : 15.242 179.924 8066 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.12), residues: 4462 helix: 1.95 (0.09), residues: 2936 sheet: -0.71 (0.82), residues: 48 loop : 0.10 (0.17), residues: 1478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 885 time to evaluate : 4.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 85 residues processed: 964 average time/residue: 1.1806 time to fit residues: 1498.0245 Evaluate side-chains 952 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 867 time to evaluate : 4.826 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 66 residues processed: 21 average time/residue: 0.6900 time to fit residues: 28.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 257 optimal weight: 0.9980 chunk 414 optimal weight: 0.9980 chunk 252 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 434 optimal weight: 0.9980 chunk 399 optimal weight: 0.9980 chunk 345 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 267 optimal weight: 0.8980 chunk 212 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 52 ASN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 58 GLN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN k 52 ASN p 18 GLN x 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 46700 Z= 0.196 Angle : 0.685 13.075 64138 Z= 0.298 Chirality : 0.039 0.302 6216 Planarity : 0.003 0.070 7888 Dihedral : 14.869 179.998 8066 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.31 (0.12), residues: 4462 helix: 2.23 (0.09), residues: 2910 sheet: -0.54 (0.85), residues: 48 loop : 0.29 (0.18), residues: 1504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 893 time to evaluate : 5.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 77 residues processed: 963 average time/residue: 1.1602 time to fit residues: 1480.3431 Evaluate side-chains 938 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 861 time to evaluate : 4.558 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 70 residues processed: 14 average time/residue: 0.4501 time to fit residues: 16.9389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 274 optimal weight: 1.9990 chunk 368 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 346 optimal weight: 0.4980 chunk 144 optimal weight: 0.9980 chunk 355 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 52 ASN N 16 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN k 52 ASN p 18 GLN x 58 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114246 restraints weight = 64359.396| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.94 r_work: 0.3178 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 46700 Z= 0.195 Angle : 0.673 12.748 64138 Z= 0.293 Chirality : 0.039 0.329 6216 Planarity : 0.003 0.065 7888 Dihedral : 14.627 179.985 8066 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.31 (0.12), residues: 4462 helix: 2.19 (0.09), residues: 2954 sheet: -0.49 (0.86), residues: 48 loop : 0.32 (0.18), residues: 1460 =============================================================================== Job complete usr+sys time: 20612.30 seconds wall clock time: 362 minutes 23.78 seconds (21743.78 seconds total)