Starting phenix.real_space_refine (version: dev) on Fri Feb 24 08:47:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lnk_4481/02_2023/5lnk_4481_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lnk_4481/02_2023/5lnk_4481.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lnk_4481/02_2023/5lnk_4481_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lnk_4481/02_2023/5lnk_4481_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lnk_4481/02_2023/5lnk_4481_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lnk_4481/02_2023/5lnk_4481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lnk_4481/02_2023/5lnk_4481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lnk_4481/02_2023/5lnk_4481_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lnk_4481/02_2023/5lnk_4481_updated.pdb" } resolution = 3.9 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= 0.018 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 Process input model Symmetric amino acids flipped Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "b TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 235": "NH1" <-> "NH2" Residue "d PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 81": "NH1" <-> "NH2" Residue "q TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 33": "NH1" <-> "NH2" Residue "v TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 142": "NH1" <-> "NH2" Residue "w PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 44": "NH1" <-> "NH2" Residue "Z TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 63760 Number of models: 1 Model: "" Number of chains: 61 Chain: "1" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3328 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 21, 'TRANS': 410} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1655 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 21, 'TRANS': 192} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3098 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 365} Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 144} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 922 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "M" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3645 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 21, 'TRANS': 437} Chain: "K" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 649 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "L" Number of atoms: 4456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4456 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 26, 'TRANS': 572} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "J" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1188 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 87 Chain: "a" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1000 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "d" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2473 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 17, 'TRANS': 296} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "e" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "f" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "i" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1200 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "k" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2268 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 14, 'TRANS': 305} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 210 Chain: "l" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 792 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 578 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 841 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 105} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "q" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1151 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "r" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 752 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "s" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 988 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "t" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1434 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 14, 'TRANS': 151} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 563 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 7, 'TRANS': 58} Chain: "v" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 861 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 125} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 496 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 13, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 237 Chain: "w" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 715 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "x" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "y" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 457 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "z" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 568 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "X" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "V" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 595 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "M" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 128 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 84 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "J" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "o" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'3PE': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "X" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2731 SG CYS 1 365 106.873 55.272 243.734 1.00 68.83 S ATOM 3055 SG CYS 1 405 109.324 49.014 244.026 1.00 75.11 S ATOM 2711 SG CYS 1 362 109.950 53.210 239.055 1.00 67.51 S ATOM 2692 SG CYS 1 359 113.117 54.078 244.884 1.00 73.89 S ATOM 4140 SG CYS 2 103 102.938 49.364 263.236 1.00103.39 S ATOM 4174 SG CYS 2 108 101.409 46.698 265.824 1.00103.35 S ATOM 4454 SG CYS 2 144 105.213 45.989 260.322 1.00104.61 S ATOM 4477 SG CYS 2 148 103.902 42.781 262.352 1.00105.54 S ATOM 5809 SG CYS 3 114 108.520 72.120 230.042 1.00 63.81 S ATOM 5748 SG CYS 3 105 102.938 75.804 230.956 1.00 56.62 S ATOM 5769 SG CYS 3 108 108.814 77.469 233.102 1.00 59.43 S ATOM 6141 SG CYS 3 156 115.085 65.328 234.476 1.00 62.60 S ATOM 6118 SG CYS 3 153 113.140 68.410 240.089 1.00 60.06 S ATOM 6165 SG CYS 3 159 119.392 67.974 238.480 1.00 70.84 S ATOM 6495 SG CYS 3 203 115.367 71.599 234.823 1.00 61.89 S ATOM 5254 SG CYS 3 41 115.178 58.785 232.564 1.00 64.70 S ATOM 5340 SG CYS 3 52 111.646 58.782 230.822 1.00 59.72 S ATOM 5365 SG CYS 3 55 111.810 54.360 228.889 1.00 64.53 S ATOM 5466 SG CYS 3 69 115.479 53.367 230.392 1.00 73.90 S ATOM 15829 SG CYS 6 119 92.014 97.275 205.577 1.00 62.07 S ATOM 16059 SG CYS 6 149 88.837 95.174 210.528 1.00 63.60 S ATOM 15331 SG CYS 6 55 86.427 100.360 207.217 1.00 68.99 S ATOM 15325 SG CYS 6 54 86.082 94.671 204.533 1.00 70.52 S ATOM 17277 SG CYS 9 119 92.388 89.875 215.767 1.00 58.31 S ATOM 17251 SG CYS 9 116 93.489 95.994 217.412 1.00 58.54 S ATOM 17298 SG CYS 9 122 93.904 91.521 221.884 1.00 52.42 S ATOM 17025 SG CYS 9 87 98.354 91.549 216.875 1.00 53.05 S ATOM 17327 SG CYS 9 126 96.025 88.520 229.910 1.00 54.94 S ATOM 16998 SG CYS 9 83 99.851 90.293 224.913 1.00 50.39 S ATOM 16956 SG CYS 9 77 101.631 92.032 230.596 1.00 49.03 S ATOM 16975 SG CYS 9 80 101.298 85.430 229.086 1.00 53.69 S ATOM 34657 SG CYS b 59 97.220 84.719 245.066 1.00 72.35 S ATOM 34835 SG CYS b 84 100.752 84.672 243.242 1.00 63.48 S ATOM 34857 SG CYS b 87 97.831 87.622 243.120 1.00 65.40 S Time building chain proxies: 26.65, per 1000 atoms: 0.42 Number of scatterers: 63760 At special positions: 0 Unit cell: (182, 201.6, 299.6, 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) Zn 1 29.99 Fe 28 26.01 S 443 16.00 P 22 15.00 O 11445 8.00 N 10782 7.00 C 41039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 57 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS s 58 " - pdb=" SG CYS s 89 " distance=2.03 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 Simple disulfide: pdb=" SG CYS w 112 " - pdb=" SG CYS Z 154 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 76 " - pdb=" SG CYS Z 83 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 35 " - pdb=" SG CYS Y 65 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 45 " - pdb=" SG CYS Y 55 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 77 " - pdb=" SG CYS Y 109 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 87 " - pdb=" SG CYS Y 99 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.54 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb=" FES 3 803 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 500 " pdb="FE1 SF4 1 500 " - pdb=" SG CYS 1 365 " pdb="FE2 SF4 1 500 " - pdb=" SG CYS 1 405 " pdb="FE4 SF4 1 500 " - pdb=" SG CYS 1 359 " pdb="FE3 SF4 1 500 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb=" SF4 6 300 " pdb="FE4 SF4 6 300 " - pdb=" SG CYS 6 54 " pdb="FE1 SF4 6 300 " - pdb=" SG CYS 6 119 " pdb="FE3 SF4 6 300 " - pdb=" SG CYS 6 55 " pdb="FE2 SF4 6 300 " - pdb=" SG CYS 6 149 " pdb=" SF4 9 502 " pdb="FE4 SF4 9 502 " - pdb=" SG CYS 9 87 " pdb="FE3 SF4 9 502 " - pdb=" SG CYS 9 122 " pdb="FE1 SF4 9 502 " - pdb=" SG CYS 9 119 " pdb="FE2 SF4 9 502 " - pdb=" SG CYS 9 116 " pdb=" SF4 9 503 " pdb="FE2 SF4 9 503 " - pdb=" SG CYS 9 83 " pdb="FE3 SF4 9 503 " - pdb=" SG CYS 9 77 " pdb="FE4 SF4 9 503 " - pdb=" SG CYS 9 80 " pdb="FE1 SF4 9 503 " - pdb=" SG CYS 9 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 307 helices and 26 sheets defined 50.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain '1' and resid 33 through 38 Processing helix chain '1' and resid 45 through 51 Processing helix chain '1' and resid 53 through 63 Processing helix chain '1' and resid 75 through 83 removed outlier: 4.356A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN 1 83 " --> pdb=" O TRP 1 79 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 removed outlier: 4.111A pdb=" N ILE 1 110 " --> pdb=" O LYS 1 106 " (cutoff:3.500A) Processing helix chain '1' and resid 115 through 129 Processing helix chain '1' and resid 140 through 158 removed outlier: 3.697A pdb=" N TYR 1 143 " --> pdb=" O GLY 1 140 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN 1 144 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA 1 146 " --> pdb=" O TYR 1 143 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 184 through 187 Processing helix chain '1' and resid 191 through 197 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 237 Proline residue: 1 232 - end of helix Processing helix chain '1' and resid 240 through 244 Processing helix chain '1' and resid 276 through 281 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 309 through 312 No H-bonds generated for 'chain '1' and resid 309 through 312' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.818A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 3.583A pdb=" N ILE 1 389 " --> pdb=" O PRO 1 386 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) Processing helix chain '1' and resid 406 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix removed outlier: 3.670A pdb=" N GLU 1 427 " --> pdb=" O ARG 1 423 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU 1 428 " --> pdb=" O PRO 1 424 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG 1 429 " --> pdb=" O GLU 1 425 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 37 removed outlier: 3.928A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 57 removed outlier: 3.901A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 63 through 73 Processing helix chain '2' and resid 77 through 86 Processing helix chain '2' and resid 109 through 111 No H-bonds generated for 'chain '2' and resid 109 through 111' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 166 through 178 Processing helix chain '3' and resid 26 through 32 Processing helix chain '3' and resid 84 through 99 Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 196 through 202 Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 274 removed outlier: 4.220A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 309 Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 326 through 338 Processing helix chain '3' and resid 359 through 362 No H-bonds generated for 'chain '3' and resid 359 through 362' Processing helix chain '3' and resid 368 through 370 No H-bonds generated for 'chain '3' and resid 368 through 370' Processing helix chain '3' and resid 389 through 400 Processing helix chain '3' and resid 426 through 433 Processing helix chain '3' and resid 441 through 445 Processing helix chain '3' and resid 455 through 459 Processing helix chain '3' and resid 463 through 479 Processing helix chain '3' and resid 499 through 505 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 629 through 631 No H-bonds generated for 'chain '3' and resid 629 through 631' Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 87 through 93 removed outlier: 3.742A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 105 Proline residue: 4 101 - end of helix Processing helix chain '4' and resid 112 through 126 Processing helix chain '4' and resid 132 through 161 Processing helix chain '4' and resid 164 through 185 removed outlier: 4.360A pdb=" N PHE 4 168 " --> pdb=" O MET 4 164 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG 4 183 " --> pdb=" O GLU 4 179 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 228 removed outlier: 3.939A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 238 Processing helix chain '4' and resid 247 through 253 Processing helix chain '4' and resid 258 through 262 Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 277 through 279 No H-bonds generated for 'chain '4' and resid 277 through 279' Processing helix chain '4' and resid 294 through 317 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 408 removed outlier: 3.796A pdb=" N ALA 4 400 " --> pdb=" O PHE 4 396 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY 4 401 " --> pdb=" O ALA 4 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU 4 402 " --> pdb=" O HIS 4 398 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS 4 407 " --> pdb=" O ASP 4 403 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY 4 408 " --> pdb=" O LYS 4 404 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.506A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 428 No H-bonds generated for 'chain '4' and resid 425 through 428' Processing helix chain '5' and resid 17 through 32 Processing helix chain '5' and resid 57 through 65 Processing helix chain '5' and resid 120 through 122 No H-bonds generated for 'chain '5' and resid 120 through 122' Processing helix chain '5' and resid 125 through 137 removed outlier: 4.044A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR 5 130 " --> pdb=" O ALA 5 127 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU 5 133 " --> pdb=" O TYR 5 130 " (cutoff:3.500A) Processing helix chain '6' and resid 27 through 44 Processing helix chain '6' and resid 55 through 63 Processing helix chain '6' and resid 70 through 72 No H-bonds generated for 'chain '6' and resid 70 through 72' Processing helix chain '6' and resid 94 through 105 Proline residue: 6 98 - end of helix Processing helix chain '6' and resid 117 through 120 No H-bonds generated for 'chain '6' and resid 117 through 120' Processing helix chain '6' and resid 153 through 170 removed outlier: 4.191A pdb=" N ARG 6 169 " --> pdb=" O LYS 6 165 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU 6 170 " --> pdb=" O LYS 6 166 " (cutoff:3.500A) Processing helix chain '6' and resid 172 through 176 removed outlier: 3.691A pdb=" N TRP 6 176 " --> pdb=" O ARG 6 172 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 172 through 176' Processing helix chain '9' and resid 17 through 26 Processing helix chain '9' and resid 28 through 42 removed outlier: 5.193A pdb=" N LEU 9 41 " --> pdb=" O THR 9 37 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE 9 42 " --> pdb=" O LEU 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 85 No H-bonds generated for 'chain '9' and resid 82 through 85' Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 151 through 160 Processing helix chain '9' and resid 163 through 175 removed outlier: 5.650A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 31 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.703A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) Proline residue: H 75 - end of helix removed outlier: 4.437A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 119 removed outlier: 4.813A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 3.677A pdb=" N ILE H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU H 146 " --> pdb=" O TYR H 142 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 170 removed outlier: 3.893A pdb=" N GLU H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 180 through 193 removed outlier: 3.853A pdb=" N GLU H 192 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 214 Processing helix chain 'H' and resid 217 through 241 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 291 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'N' and resid 5 through 22 removed outlier: 4.196A pdb=" N THR N 12 " --> pdb=" O ILE N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 43 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 79 removed outlier: 3.777A pdb=" N THR N 62 " --> pdb=" O LYS N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 105 Processing helix chain 'N' and resid 112 through 121 Proline residue: N 116 - end of helix Processing helix chain 'N' and resid 124 through 131 Processing helix chain 'N' and resid 133 through 148 removed outlier: 3.881A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 4.276A pdb=" N TYR N 143 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU N 146 " --> pdb=" O TYR N 143 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 167 Processing helix chain 'N' and resid 175 through 195 removed outlier: 3.514A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU N 195 " --> pdb=" O THR N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 221 Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'N' and resid 238 through 250 Processing helix chain 'N' and resid 258 through 271 Proline residue: N 262 - end of helix removed outlier: 3.529A pdb=" N MET N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU N 269 " --> pdb=" O ILE N 266 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 298 removed outlier: 4.206A pdb=" N THR N 285 " --> pdb=" O LEU N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 334 Processing helix chain 'N' and resid 342 through 346 Processing helix chain 'A' and resid 2 through 26 removed outlier: 3.558A pdb=" N ALA A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 53 through 78 Proline residue: A 74 - end of helix removed outlier: 5.694A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'M' and resid 2 through 16 Proline residue: M 7 - end of helix Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 41 removed outlier: 3.886A pdb=" N THR M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 135 Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 147 through 157 removed outlier: 4.639A pdb=" N GLY M 156 " --> pdb=" O TYR M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 171 Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 204 Processing helix chain 'M' and resid 213 through 221 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 246 removed outlier: 5.268A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 256 No H-bonds generated for 'chain 'M' and resid 253 through 256' Processing helix chain 'M' and resid 258 through 278 removed outlier: 3.890A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 302 removed outlier: 4.159A pdb=" N ILE M 286 " --> pdb=" O LYS M 283 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU M 302 " --> pdb=" O VAL M 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 334 Processing helix chain 'M' and resid 353 through 366 removed outlier: 4.489A pdb=" N ALA M 357 " --> pdb=" O PRO M 353 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP M 358 " --> pdb=" O LEU M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 393 through 410 Processing helix chain 'M' and resid 431 through 447 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 453 No H-bonds generated for 'chain 'M' and resid 451 through 453' Processing helix chain 'K' and resid 4 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 57 through 65 Proline residue: K 60 - end of helix removed outlier: 3.626A pdb=" N LEU K 63 " --> pdb=" O PRO K 60 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL K 65 " --> pdb=" O ILE K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.735A pdb=" N LEU K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 23 removed outlier: 4.231A pdb=" N THR L 11 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR L 16 " --> pdb=" O ILE L 13 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.880A pdb=" N ASN L 23 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 30 Processing helix chain 'L' and resid 32 through 46 Processing helix chain 'L' and resid 48 through 57 removed outlier: 3.513A pdb=" N MET L 52 " --> pdb=" O MET L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 107 Proline residue: L 91 - end of helix Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 Processing helix chain 'L' and resid 198 through 203 removed outlier: 3.840A pdb=" N PHE L 202 " --> pdb=" O LEU L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 223 removed outlier: 3.802A pdb=" N LYS L 223 " --> pdb=" O ALA L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 238 removed outlier: 4.939A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 248 Processing helix chain 'L' and resid 252 through 262 removed outlier: 3.869A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE L 258 " --> pdb=" O ALA L 255 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE L 261 " --> pdb=" O PHE L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 292 removed outlier: 4.060A pdb=" N ALA L 282 " --> pdb=" O LEU L 278 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET L 283 " --> pdb=" O CYS L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 317 Processing helix chain 'L' and resid 322 through 350 removed outlier: 4.048A pdb=" N SER L 345 " --> pdb=" O MET L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 380 Processing helix chain 'L' and resid 388 through 399 removed outlier: 5.704A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA L 399 " --> pdb=" O ILE L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 407 through 430 removed outlier: 3.653A pdb=" N MET L 411 " --> pdb=" O TRP L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 470 removed outlier: 3.531A pdb=" N PHE L 463 " --> pdb=" O ILE L 459 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN L 470 " --> pdb=" O PHE L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 505 Processing helix chain 'L' and resid 517 through 524 removed outlier: 3.627A pdb=" N ASN L 524 " --> pdb=" O PHE L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 565 Proline residue: L 538 - end of helix Proline residue: L 563 - end of helix Processing helix chain 'L' and resid 568 through 572 Processing helix chain 'L' and resid 581 through 590 Processing helix chain 'L' and resid 592 through 595 No H-bonds generated for 'chain 'L' and resid 592 through 595' Processing helix chain 'J' and resid 5 through 20 removed outlier: 3.697A pdb=" N PHE J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 46 removed outlier: 4.311A pdb=" N LEU J 31 " --> pdb=" O ILE J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 56 Processing helix chain 'J' and resid 59 through 75 Processing helix chain 'J' and resid 87 through 104 Processing helix chain 'J' and resid 140 through 149 Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'a' and resid 41 through 45 Processing helix chain 'a' and resid 50 through 57 Processing helix chain 'b' and resid 23 through 28 Processing helix chain 'b' and resid 41 through 44 No H-bonds generated for 'chain 'b' and resid 41 through 44' Processing helix chain 'c' and resid 28 through 32 Processing helix chain 'c' and resid 89 through 99 Processing helix chain 'c' and resid 118 through 121 Processing helix chain 'd' and resid 29 through 40 removed outlier: 4.162A pdb=" N GLY d 39 " --> pdb=" O ASN d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 55 through 62 removed outlier: 4.019A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 84 Processing helix chain 'd' and resid 106 through 109 No H-bonds generated for 'chain 'd' and resid 106 through 109' Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 158 Processing helix chain 'd' and resid 179 through 184 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 239 through 247 removed outlier: 3.843A pdb=" N VAL d 245 " --> pdb=" O VAL d 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE d 246 " --> pdb=" O GLN d 243 " (cutoff:3.500A) Processing helix chain 'd' and resid 281 through 288 Processing helix chain 'd' and resid 311 through 318 Processing helix chain 'e' and resid 27 through 46 removed outlier: 5.009A pdb=" N VAL e 41 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU e 42 " --> pdb=" O LYS e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 83 through 95 Processing helix chain 'f' and resid 19 through 36 Processing helix chain 'f' and resid 42 through 60 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 94 Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 69 removed outlier: 4.129A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 92 Processing helix chain 'g' and resid 99 through 105 Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 7 through 13 Processing helix chain 'h' and resid 53 through 56 No H-bonds generated for 'chain 'h' and resid 53 through 56' Processing helix chain 'i' and resid 3 through 16 Processing helix chain 'i' and resid 19 through 29 removed outlier: 3.821A pdb=" N TYR i 23 " --> pdb=" O GLY i 19 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU i 24 " --> pdb=" O LEU i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 70 No H-bonds generated for 'chain 'i' and resid 68 through 70' Processing helix chain 'i' and resid 84 through 90 Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 36 through 39 No H-bonds generated for 'chain 'j' and resid 36 through 39' Processing helix chain 'j' and resid 44 through 56 Processing helix chain 'j' and resid 64 through 69 removed outlier: 4.588A pdb=" N LYS j 69 " --> pdb=" O ILE j 65 " (cutoff:3.500A) Processing helix chain 'j' and resid 73 through 84 Processing helix chain 'k' and resid 4 through 10 removed outlier: 4.261A pdb=" N TYR k 8 " --> pdb=" O GLY k 4 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE k 9 " --> pdb=" O PRO k 5 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 16 No H-bonds generated for 'chain 'k' and resid 13 through 16' Processing helix chain 'k' and resid 35 through 45 removed outlier: 4.188A pdb=" N ALA k 39 " --> pdb=" O LYS k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 62 Processing helix chain 'k' and resid 79 through 83 Processing helix chain 'k' and resid 94 through 118 Processing helix chain 'k' and resid 130 through 141 removed outlier: 4.087A pdb=" N GLN k 141 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 148 through 162 removed outlier: 5.182A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 178 through 182 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 214 Proline residue: k 212 - end of helix Processing helix chain 'k' and resid 228 through 242 removed outlier: 4.989A pdb=" N ASP k 237 " --> pdb=" O LYS k 233 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU k 241 " --> pdb=" O ASP k 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 247 through 251 Processing helix chain 'k' and resid 253 through 260 removed outlier: 3.912A pdb=" N HIS k 257 " --> pdb=" O ARG k 254 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN k 258 " --> pdb=" O LYS k 255 " (cutoff:3.500A) Processing helix chain 'k' and resid 265 through 273 Processing helix chain 'k' and resid 276 through 284 Proline residue: k 280 - end of helix removed outlier: 4.439A pdb=" N THR k 283 " --> pdb=" O LEU k 279 " (cutoff:3.500A) Processing helix chain 'k' and resid 298 through 305 Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 50 through 54 Processing helix chain 'l' and resid 56 through 66 Processing helix chain 'l' and resid 69 through 87 removed outlier: 3.569A pdb=" N GLN l 81 " --> pdb=" O ALA l 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS l 84 " --> pdb=" O ARG l 80 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS l 87 " --> pdb=" O ASP l 83 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 34 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 47 removed outlier: 3.695A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 81 No H-bonds generated for 'chain 'm' and resid 78 through 81' Processing helix chain 'n' and resid 28 through 38 Processing helix chain 'n' and resid 46 through 52 Processing helix chain 'n' and resid 70 through 83 removed outlier: 4.116A pdb=" N VAL n 81 " --> pdb=" O PHE n 77 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY n 82 " --> pdb=" O VAL n 78 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA n 83 " --> pdb=" O VAL n 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 6 No H-bonds generated for 'chain 'o' and resid 3 through 6' Processing helix chain 'o' and resid 18 through 20 No H-bonds generated for 'chain 'o' and resid 18 through 20' Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 60 through 95 Processing helix chain 'p' and resid 28 through 48 Processing helix chain 'p' and resid 65 through 72 Processing helix chain 'p' and resid 85 through 92 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 32 through 96 removed outlier: 4.041A pdb=" N ILE q 39 " --> pdb=" O ALA q 36 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR q 46 " --> pdb=" O LEU q 43 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET q 49 " --> pdb=" O TYR q 46 " (cutoff:3.500A) Proline residue: q 72 - end of helix removed outlier: 3.746A pdb=" N GLU q 77 " --> pdb=" O LEU q 74 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU q 93 " --> pdb=" O LEU q 90 " (cutoff:3.500A) Processing helix chain 'q' and resid 130 through 136 removed outlier: 3.819A pdb=" N SER q 134 " --> pdb=" O GLU q 130 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 25 Processing helix chain 'r' and resid 64 through 91 Proline residue: r 77 - end of helix removed outlier: 4.592A pdb=" N THR r 90 " --> pdb=" O LYS r 86 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 13 No H-bonds generated for 'chain 's' and resid 11 through 13' Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 removed outlier: 3.974A pdb=" N ARG s 64 " --> pdb=" O HIS s 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG s 70 " --> pdb=" O LEU s 66 " (cutoff:3.500A) Processing helix chain 's' and resid 81 through 120 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 34 through 46 Processing helix chain 't' and resid 57 through 73 removed outlier: 3.825A pdb=" N GLY t 73 " --> pdb=" O GLU t 69 " (cutoff:3.500A) Processing helix chain 't' and resid 94 through 96 No H-bonds generated for 'chain 't' and resid 94 through 96' Processing helix chain 't' and resid 108 through 113 Processing helix chain 't' and resid 118 through 129 Processing helix chain 't' and resid 133 through 142 Processing helix chain 't' and resid 145 through 147 No H-bonds generated for 'chain 't' and resid 145 through 147' Processing helix chain 'u' and resid 19 through 41 Processing helix chain 'u' and resid 54 through 57 Processing helix chain 'u' and resid 60 through 62 No H-bonds generated for 'chain 'u' and resid 60 through 62' Processing helix chain 'v' and resid 16 through 21 Processing helix chain 'v' and resid 28 through 41 Proline residue: v 36 - end of helix Processing helix chain 'v' and resid 99 through 116 removed outlier: 3.596A pdb=" N GLY v 107 " --> pdb=" O LYS v 103 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE v 116 " --> pdb=" O MET v 112 " (cutoff:3.500A) Processing helix chain 'w' and resid 54 through 66 Processing helix chain 'w' and resid 68 through 76 Processing helix chain 'w' and resid 86 through 102 Processing helix chain 'x' and resid 14 through 45 Processing helix chain 'y' and resid 5 through 8 Processing helix chain 'y' and resid 14 through 33 removed outlier: 3.980A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 3 through 30 Proline residue: z 7 - end of helix removed outlier: 3.696A pdb=" N LEU z 16 " --> pdb=" O GLY z 13 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix removed outlier: 3.547A pdb=" N ALA z 24 " --> pdb=" O MET z 21 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER z 30 " --> pdb=" O HIS z 27 " (cutoff:3.500A) Processing helix chain 'z' and resid 42 through 55 Processing helix chain 'z' and resid 66 through 68 No H-bonds generated for 'chain 'z' and resid 66 through 68' Processing helix chain 'Z' and resid 6 through 8 No H-bonds generated for 'chain 'Z' and resid 6 through 8' Processing helix chain 'Z' and resid 30 through 39 Processing helix chain 'Z' and resid 42 through 57 removed outlier: 4.259A pdb=" N VAL Z 47 " --> pdb=" O PRO Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 81 through 116 removed outlier: 4.904A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA Z 87 " --> pdb=" O CYS Z 83 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS Z 110 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 141 Processing helix chain 'Z' and resid 152 through 170 Processing helix chain 'Y' and resid 9 through 11 No H-bonds generated for 'chain 'Y' and resid 9 through 11' Processing helix chain 'Y' and resid 21 through 34 removed outlier: 3.699A pdb=" N ALA Y 26 " --> pdb=" O SER Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 48 removed outlier: 4.085A pdb=" N GLU Y 41 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 75 Processing helix chain 'Y' and resid 79 through 90 removed outlier: 3.803A pdb=" N TYR Y 90 " --> pdb=" O THR Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 114 Processing helix chain 'Y' and resid 120 through 122 No H-bonds generated for 'chain 'Y' and resid 120 through 122' Processing helix chain 'X' and resid 8 through 21 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 68 Processing helix chain 'X' and resid 73 through 83 Processing helix chain 'W' and resid 16 through 45 Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 70 through 79 Processing helix chain 'W' and resid 83 through 117 removed outlier: 3.943A pdb=" N ARG W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA W 116 " --> pdb=" O ARG W 112 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 36 Processing helix chain 'V' and resid 49 through 71 Processing helix chain 'V' and resid 79 through 93 Processing helix chain 'V' and resid 102 through 118 Processing sheet with id= A, first strand: chain '1' and resid 220 through 224 removed outlier: 7.004A pdb=" N TYR 1 92 " --> pdb=" O THR 1 221 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA 1 223 " --> pdb=" O TYR 1 92 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL 1 94 " --> pdb=" O ALA 1 223 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '1' and resid 253 through 258 Processing sheet with id= C, first strand: chain '1' and resid 296 through 298 Processing sheet with id= D, first strand: chain '2' and resid 98 through 103 removed outlier: 3.718A pdb=" N VAL 2 102 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 9 through 13 Processing sheet with id= F, first strand: chain '3' and resid 146 through 148 Processing sheet with id= G, first strand: chain '3' and resid 174 through 177 Processing sheet with id= H, first strand: chain '3' and resid 223 through 228 removed outlier: 3.566A pdb=" N ARG 3 249 " --> pdb=" O SER 3 241 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG 3 243 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL 3 247 " --> pdb=" O ARG 3 243 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 283 through 285 Processing sheet with id= J, first strand: chain '3' and resid 315 through 319 removed outlier: 5.657A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 405 through 408 removed outlier: 4.072A pdb=" N VAL 3 452 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN 3 491 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '3' and resid 572 through 574 Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 removed outlier: 3.844A pdb=" N GLY 4 375 " --> pdb=" O LYS 4 392 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 63 through 69 removed outlier: 3.574A pdb=" N ARG 4 63 " --> pdb=" O HIS 4 79 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 4 65 " --> pdb=" O ASP 4 77 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 74 through 82 removed outlier: 7.181A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE 5 105 " --> pdb=" O LEU 5 96 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER 5 103 " --> pdb=" O SER 5 98 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN 5 39 " --> pdb=" O CYS 5 51 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 172 through 177 removed outlier: 3.541A pdb=" N GLU 5 186 " --> pdb=" O GLU 5 173 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG 5 175 " --> pdb=" O VAL 5 184 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP 5 177 " --> pdb=" O ARG 5 182 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG 5 182 " --> pdb=" O ASP 5 177 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '6' and resid 86 through 88 removed outlier: 6.148A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '9' and resid 93 through 95 Processing sheet with id= S, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= T, first strand: chain 'b' and resid 56 through 59 removed outlier: 3.642A pdb=" N ILE b 57 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL b 71 " --> pdb=" O CYS b 59 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'c' and resid 56 through 59 Processing sheet with id= V, first strand: chain 'd' and resid 46 through 49 removed outlier: 6.144A pdb=" N ILE d 69 " --> pdb=" O VAL d 47 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR d 49 " --> pdb=" O ILE d 69 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET d 71 " --> pdb=" O TYR d 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'd' and resid 130 through 134 removed outlier: 5.872A pdb=" N THR d 164 " --> pdb=" O HIS d 131 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER d 133 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE d 166 " --> pdb=" O SER d 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'e' and resid 51 through 55 removed outlier: 3.951A pdb=" N ILE e 18 " --> pdb=" O PRO e 51 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL e 76 " --> pdb=" O LEU e 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA e 66 " --> pdb=" O LYS e 74 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'i' and resid 47 through 50 Processing sheet with id= Z, first strand: chain 'k' and resid 25 through 29 removed outlier: 7.191A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z 2621 hydrogen bonds defined for protein. 7209 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: 18.34 Time building geometry restraints manager: 24.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.38: 25051 1.38 - 1.61: 39430 1.61 - 1.84: 715 1.84 - 2.08: 1 2.08 - 2.31: 80 Bond restraints: 65277 Sorted by residual: bond pdb=" C LEU e 50 " pdb=" N PRO e 51 " ideal model delta sigma weight residual 1.334 1.150 0.184 2.34e-02 1.83e+03 6.18e+01 bond pdb=" C PRO t 163 " pdb=" N PRO t 164 " ideal model delta sigma weight residual 1.334 1.511 -0.177 2.34e-02 1.83e+03 5.70e+01 bond pdb=" C VAL k 174 " pdb=" N PRO k 175 " ideal model delta sigma weight residual 1.334 1.175 0.158 2.34e-02 1.83e+03 4.58e+01 bond pdb=" C16 ZMP j 101 " pdb=" N2 ZMP j 101 " ideal model delta sigma weight residual 1.452 1.333 0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C34 PNS X 401 " pdb=" N36 PNS X 401 " ideal model delta sigma weight residual 1.452 1.335 0.117 2.00e-02 2.50e+03 3.43e+01 ... (remaining 65272 not shown) Histogram of bond angle deviations from ideal: 70.13 - 83.75: 72 83.75 - 97.37: 10 97.37 - 110.99: 25219 110.99 - 124.60: 61609 124.60 - 138.22: 1582 Bond angle restraints: 88492 Sorted by residual: angle pdb=" C LEU k 164 " pdb=" N PRO k 165 " pdb=" CA PRO k 165 " ideal model delta sigma weight residual 120.38 138.22 -17.84 1.03e+00 9.43e-01 3.00e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.25 -23.51 1.95e+00 2.62e-01 1.45e+02 angle pdb=" S1 FES 2 300 " pdb="FE2 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 90.99 13.34 1.14e+00 7.69e-01 1.37e+02 angle pdb="FE1 FES 2 300 " pdb=" S2 FES 2 300 " pdb="FE2 FES 2 300 " ideal model delta sigma weight residual 75.66 88.60 -12.94 1.14e+00 7.69e-01 1.29e+02 angle pdb=" S1 FES 2 300 " pdb="FE1 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 90.83 13.50 1.20e+00 6.94e-01 1.27e+02 ... (remaining 88487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.80: 37850 19.80 - 39.60: 1107 39.60 - 59.40: 245 59.40 - 79.20: 32 79.20 - 99.00: 26 Dihedral angle restraints: 39260 sinusoidal: 15857 harmonic: 23403 Sorted by residual: dihedral pdb=" CA THR N 340 " pdb=" C THR N 340 " pdb=" N PRO N 341 " pdb=" CA PRO N 341 " ideal model delta harmonic sigma weight residual 180.00 123.76 56.24 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA PRO k 165 " pdb=" C PRO k 165 " pdb=" N PRO k 166 " pdb=" CA PRO k 166 " ideal model delta harmonic sigma weight residual -180.00 -126.71 -53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ALA k 225 " pdb=" C ALA k 225 " pdb=" N TRP k 226 " pdb=" CA TRP k 226 " ideal model delta harmonic sigma weight residual 180.00 128.45 51.55 0 5.00e+00 4.00e-02 1.06e+02 ... (remaining 39257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.223: 9781 4.223 - 8.446: 0 8.446 - 12.670: 0 12.670 - 16.893: 0 16.893 - 21.116: 24 Chirality restraints: 9805 Sorted by residual: chirality pdb="FE3 SF4 3 801 " pdb=" S1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.56 -21.12 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 9 503 " pdb=" S1 SF4 9 503 " pdb=" S2 SF4 9 503 " pdb=" S3 SF4 9 503 " both_signs ideal model delta sigma weight residual False 10.55 -10.56 21.11 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE2 SF4 3 801 " pdb=" S1 SF4 3 801 " pdb=" S3 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.55 21.10 2.00e-01 2.50e+01 1.11e+04 ... (remaining 9802 not shown) Planarity restraints: 11174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN 1 501 " 0.022 2.00e-02 2.50e+03 2.29e-02 2.50e+01 pdb=" C10 FMN 1 501 " -0.002 2.00e-02 2.50e+03 pdb=" C2 FMN 1 501 " 0.016 2.00e-02 2.50e+03 pdb=" C4 FMN 1 501 " -0.009 2.00e-02 2.50e+03 pdb=" C4A FMN 1 501 " -0.002 2.00e-02 2.50e+03 pdb=" C5A FMN 1 501 " -0.003 2.00e-02 2.50e+03 pdb=" C6 FMN 1 501 " 0.018 2.00e-02 2.50e+03 pdb=" C7 FMN 1 501 " 0.013 2.00e-02 2.50e+03 pdb=" C7M FMN 1 501 " 0.055 2.00e-02 2.50e+03 pdb=" C8 FMN 1 501 " -0.018 2.00e-02 2.50e+03 pdb=" C8M FMN 1 501 " -0.014 2.00e-02 2.50e+03 pdb=" C9 FMN 1 501 " -0.042 2.00e-02 2.50e+03 pdb=" C9A FMN 1 501 " -0.024 2.00e-02 2.50e+03 pdb=" N1 FMN 1 501 " 0.014 2.00e-02 2.50e+03 pdb=" N10 FMN 1 501 " -0.016 2.00e-02 2.50e+03 pdb=" N3 FMN 1 501 " 0.003 2.00e-02 2.50e+03 pdb=" N5 FMN 1 501 " 0.003 2.00e-02 2.50e+03 pdb=" O2 FMN 1 501 " 0.026 2.00e-02 2.50e+03 pdb=" O4 FMN 1 501 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NDP d 401 " 0.062 2.00e-02 2.50e+03 2.66e-02 1.94e+01 pdb=" C2A NDP d 401 " -0.013 2.00e-02 2.50e+03 pdb=" C4A NDP d 401 " -0.014 2.00e-02 2.50e+03 pdb=" C5A NDP d 401 " -0.010 2.00e-02 2.50e+03 pdb=" C6A NDP d 401 " 0.004 2.00e-02 2.50e+03 pdb=" C8A NDP d 401 " -0.026 2.00e-02 2.50e+03 pdb=" N1A NDP d 401 " -0.002 2.00e-02 2.50e+03 pdb=" N3A NDP d 401 " -0.013 2.00e-02 2.50e+03 pdb=" N6A NDP d 401 " 0.046 2.00e-02 2.50e+03 pdb=" N7A NDP d 401 " -0.019 2.00e-02 2.50e+03 pdb=" N9A NDP d 401 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 53 " 0.031 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE K 53 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE K 53 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE K 53 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE K 53 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE K 53 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE K 53 " 0.004 2.00e-02 2.50e+03 ... (remaining 11171 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1158 2.61 - 3.18: 65622 3.18 - 3.76: 98379 3.76 - 4.33: 137257 4.33 - 4.90: 214109 Nonbonded interactions: 516525 Sorted by model distance: nonbonded pdb=" OE1 GLU 9 152 " pdb=" OH TYR i 127 " model vdw 2.038 2.440 nonbonded pdb=" OH TYR q 142 " pdb=" O ARG z 37 " model vdw 2.039 2.440 nonbonded pdb=" O ALA M 300 " pdb=" OG SER M 308 " model vdw 2.049 2.440 nonbonded pdb=" OD1 ASN 5 69 " pdb=" OG SER h 95 " model vdw 2.051 2.440 nonbonded pdb=" OD1 ASP Z 72 " pdb=" NE2 GLN Z 90 " model vdw 2.057 2.520 ... (remaining 516520 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 'X' and resid 3 through 87) selection = (chain 'j' and resid 3 through 87) } 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 28 7.16 5 Zn 1 6.06 5 P 22 5.49 5 S 443 5.16 5 C 41039 2.51 5 N 10782 2.21 5 O 11445 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=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 14.360 Check model and map are aligned: 0.720 Process input model: 143.300 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.470 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0032 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 : 0.007 0.209 65277 Z= 0.452 Angle : 1.051 23.511 88492 Z= 0.562 Chirality : 1.044 21.116 9805 Planarity : 0.006 0.090 11174 Dihedral : 10.848 99.000 24102 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 12.58 % Favored : 86.91 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 2.16 % Twisted General : 0.38 % 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: -4.85 (0.07), residues: 7824 helix: -3.24 (0.06), residues: 3880 sheet: -2.22 (0.25), residues: 325 loop : -3.24 (0.08), residues: 3619 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 551 time to evaluate : 6.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 570 average time/residue: 0.5998 time to fit residues: 586.2367 Evaluate side-chains 486 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 479 time to evaluate : 6.055 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4698 time to fit residues: 14.0714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 660 optimal weight: 40.0000 chunk 592 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 chunk 202 optimal weight: 40.0000 chunk 399 optimal weight: 0.2980 chunk 316 optimal weight: 50.0000 chunk 612 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 372 optimal weight: 40.0000 chunk 456 optimal weight: 20.0000 chunk 710 optimal weight: 8.9990 overall best weight: 9.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 293 ASN 1 361 GLN 1 431 GLN 2 16 ASN ** 2 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 121 GLN ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 119 GLN ** 3 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 491 ASN 3 581 GLN ** 4 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 201 GLN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 347 HIS ** 4 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 106 GLN ** 6 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 162 GLN 9 65 HIS 9 157 ASN H 47 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN H 235 ASN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN N 204 ASN ** N 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS L 115 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 GLN L 248 HIS L 270 ASN L 405 ASN L 479 GLN ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN c 50 ASN d 3 HIS ** d 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN ** d 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 ASN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 200 GLN k 222 GLN l 24 GLN m 45 ASN m 68 HIS m 70 GLN n 20 GLN ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 12 GLN r 25 GLN s 42 GLN s 60 HIS t 25 HIS ** t 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 HIS u 16 GLN u 21 GLN v 104 HIS v 126 GLN y 30 ASN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 GLN ** Z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 GLN W 135 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0333 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.313 65277 Z= 0.622 Angle : 1.720 50.813 88492 Z= 1.084 Chirality : 0.316 6.553 9805 Planarity : 0.007 0.097 11174 Dihedral : 9.591 90.932 9247 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.88 % Favored : 90.75 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.16 % 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: -2.94 (0.09), residues: 7824 helix: -1.22 (0.08), residues: 3912 sheet: -1.74 (0.26), residues: 345 loop : -2.83 (0.09), residues: 3567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 486 time to evaluate : 5.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 44 residues processed: 561 average time/residue: 0.5941 time to fit residues: 579.2350 Evaluate side-chains 487 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 443 time to evaluate : 5.129 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.4732 time to fit residues: 46.6221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 394 optimal weight: 40.0000 chunk 220 optimal weight: 20.0000 chunk 591 optimal weight: 7.9990 chunk 483 optimal weight: 40.0000 chunk 195 optimal weight: 20.0000 chunk 711 optimal weight: 6.9990 chunk 768 optimal weight: 30.0000 chunk 633 optimal weight: 50.0000 chunk 705 optimal weight: 5.9990 chunk 242 optimal weight: 30.0000 chunk 570 optimal weight: 10.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 157 HIS 4 217 ASN ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 150 ASN H 138 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN M 81 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 332 HIS L 484 HIS ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN d 134 HIS ** d 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 49 GLN ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN r 88 HIS y 30 ASN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0492 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.288 65277 Z= 0.559 Angle : 1.688 52.315 88492 Z= 1.073 Chirality : 0.316 6.513 9805 Planarity : 0.006 0.085 11174 Dihedral : 8.880 90.721 9247 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.73 % Favored : 89.98 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.09 % 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: -2.24 (0.09), residues: 7824 helix: -0.51 (0.08), residues: 3927 sheet: -1.65 (0.27), residues: 339 loop : -2.63 (0.10), residues: 3558 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 469 time to evaluate : 5.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 54 residues processed: 539 average time/residue: 0.5984 time to fit residues: 560.4539 Evaluate side-chains 502 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 448 time to evaluate : 5.111 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.4968 time to fit residues: 57.3555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 702 optimal weight: 0.9980 chunk 534 optimal weight: 5.9990 chunk 369 optimal weight: 40.0000 chunk 78 optimal weight: 50.0000 chunk 339 optimal weight: 9.9990 chunk 477 optimal weight: 30.0000 chunk 713 optimal weight: 50.0000 chunk 755 optimal weight: 9.9990 chunk 373 optimal weight: 50.0000 chunk 676 optimal weight: 50.0000 chunk 203 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 99 HIS ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 51 ASN 3 119 GLN ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 72 ASN o 88 HIS ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 GLN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 113 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0548 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.258 65277 Z= 0.546 Angle : 1.663 50.777 88492 Z= 1.062 Chirality : 0.314 6.412 9805 Planarity : 0.005 0.088 11174 Dihedral : 8.419 93.251 9247 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.62 % Favored : 90.09 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.08 % 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: -1.84 (0.09), residues: 7824 helix: -0.12 (0.08), residues: 3916 sheet: -1.51 (0.28), residues: 334 loop : -2.51 (0.10), residues: 3574 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 460 time to evaluate : 6.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 61 residues processed: 550 average time/residue: 0.6160 time to fit residues: 590.9899 Evaluate side-chains 504 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 443 time to evaluate : 5.163 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5069 time to fit residues: 65.3082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 629 optimal weight: 10.0000 chunk 429 optimal weight: 50.0000 chunk 10 optimal weight: 20.0000 chunk 562 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 chunk 645 optimal weight: 0.0040 chunk 522 optimal weight: 50.0000 chunk 0 optimal weight: 100.0000 chunk 385 optimal weight: 40.0000 chunk 678 optimal weight: 30.0000 chunk 190 optimal weight: 20.0000 overall best weight: 12.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 144 ASN 1 361 GLN 2 91 ASN ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 179 ASN 3 259 ASN 3 286 ASN ** 3 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 581 GLN ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 201 GLN ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 ASN M 293 HIS L 136 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 GLN L 323 HIS ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS d 131 HIS ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 GLN ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 122 GLN ** j 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 141 GLN ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 35 HIS ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0762 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.355 65277 Z= 0.564 Angle : 1.682 51.779 88492 Z= 1.070 Chirality : 0.315 6.693 9805 Planarity : 0.006 0.089 11174 Dihedral : 8.282 95.633 9247 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.34 % Favored : 89.37 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.03 % 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: -1.78 (0.09), residues: 7824 helix: 0.03 (0.08), residues: 3855 sheet: -1.57 (0.29), residues: 319 loop : -2.56 (0.10), residues: 3650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 473 time to evaluate : 5.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 64 residues processed: 571 average time/residue: 0.6023 time to fit residues: 596.7309 Evaluate side-chains 519 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 455 time to evaluate : 6.144 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.4809 time to fit residues: 65.1859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 254 optimal weight: 50.0000 chunk 680 optimal weight: 0.2980 chunk 149 optimal weight: 9.9990 chunk 443 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 756 optimal weight: 6.9990 chunk 628 optimal weight: 30.0000 chunk 350 optimal weight: 40.0000 chunk 62 optimal weight: 50.0000 chunk 250 optimal weight: 20.0000 chunk 397 optimal weight: 30.0000 overall best weight: 7.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 201 GLN 5 88 ASN ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 27 HIS ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 150 ASN X 47 GLN X 74 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0740 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.272 65277 Z= 0.539 Angle : 1.653 51.101 88492 Z= 1.058 Chirality : 0.314 6.562 9805 Planarity : 0.005 0.087 11174 Dihedral : 7.908 97.118 9247 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.46 % Favored : 90.27 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.01 % 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: -1.53 (0.09), residues: 7824 helix: 0.27 (0.08), residues: 3865 sheet: -1.33 (0.28), residues: 334 loop : -2.49 (0.10), residues: 3625 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 462 time to evaluate : 5.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 33 residues processed: 514 average time/residue: 0.6150 time to fit residues: 549.0619 Evaluate side-chains 486 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 453 time to evaluate : 5.291 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4761 time to fit residues: 38.1254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 729 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 431 optimal weight: 50.0000 chunk 552 optimal weight: 0.0770 chunk 428 optimal weight: 40.0000 chunk 636 optimal weight: 20.0000 chunk 422 optimal weight: 7.9990 chunk 753 optimal weight: 0.0470 chunk 471 optimal weight: 0.0040 chunk 459 optimal weight: 20.0000 chunk 347 optimal weight: 10.0000 overall best weight: 3.6254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 190 HIS 4 201 GLN ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 HIS ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 ASN ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0710 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.265 65277 Z= 0.534 Angle : 1.641 50.819 88492 Z= 1.053 Chirality : 0.314 6.472 9805 Planarity : 0.005 0.087 11174 Dihedral : 7.591 98.251 9247 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.80 % Favored : 89.92 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.03 % 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: -1.33 (0.10), residues: 7824 helix: 0.45 (0.08), residues: 3874 sheet: -1.22 (0.28), residues: 344 loop : -2.43 (0.10), residues: 3606 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 458 time to evaluate : 5.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 487 average time/residue: 0.6176 time to fit residues: 523.5002 Evaluate side-chains 471 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 449 time to evaluate : 5.184 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4925 time to fit residues: 28.1222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 466 optimal weight: 5.9990 chunk 300 optimal weight: 0.9990 chunk 450 optimal weight: 0.0770 chunk 227 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 479 optimal weight: 30.0000 chunk 513 optimal weight: 5.9990 chunk 372 optimal weight: 50.0000 chunk 70 optimal weight: 10.0000 chunk 592 optimal weight: 50.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 HIS N 204 ASN ** N 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN L 65 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 HIS v 126 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0720 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.263 65277 Z= 0.534 Angle : 1.643 50.721 88492 Z= 1.052 Chirality : 0.314 6.465 9805 Planarity : 0.005 0.092 11174 Dihedral : 7.423 98.695 9247 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.76 % Favored : 89.95 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.01 % 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: -1.24 (0.10), residues: 7824 helix: 0.52 (0.08), residues: 3880 sheet: -1.07 (0.29), residues: 334 loop : -2.40 (0.10), residues: 3610 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 457 time to evaluate : 5.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 23 residues processed: 476 average time/residue: 0.6091 time to fit residues: 504.1605 Evaluate side-chains 473 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 450 time to evaluate : 5.268 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4895 time to fit residues: 28.9497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 685 optimal weight: 30.0000 chunk 722 optimal weight: 40.0000 chunk 658 optimal weight: 30.0000 chunk 702 optimal weight: 50.0000 chunk 721 optimal weight: 9.9990 chunk 422 optimal weight: 0.0970 chunk 305 optimal weight: 30.0000 chunk 551 optimal weight: 0.5980 chunk 215 optimal weight: 10.0000 chunk 634 optimal weight: 8.9990 chunk 664 optimal weight: 20.0000 overall best weight: 5.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 113 HIS ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 309 ASN L 65 ASN L 136 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 354 GLN ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 HIS ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0762 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.257 65277 Z= 0.536 Angle : 1.647 50.870 88492 Z= 1.054 Chirality : 0.314 6.463 9805 Planarity : 0.005 0.089 11174 Dihedral : 7.346 99.656 9247 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.14 % Favored : 89.58 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.03 % 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: -1.19 (0.10), residues: 7824 helix: 0.58 (0.08), residues: 3879 sheet: -1.05 (0.30), residues: 325 loop : -2.39 (0.10), residues: 3620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 455 time to evaluate : 5.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 469 average time/residue: 0.6322 time to fit residues: 515.4468 Evaluate side-chains 461 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 450 time to evaluate : 5.156 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4954 time to fit residues: 18.0948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 699 optimal weight: 9.9990 chunk 461 optimal weight: 8.9990 chunk 742 optimal weight: 50.0000 chunk 453 optimal weight: 6.9990 chunk 352 optimal weight: 20.0000 chunk 516 optimal weight: 40.0000 chunk 779 optimal weight: 40.0000 chunk 717 optimal weight: 7.9990 chunk 620 optimal weight: 50.0000 chunk 64 optimal weight: 9.9990 chunk 479 optimal weight: 7.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 84 HIS ** 4 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 106 GLN ** 6 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 135 GLN k 97 GLN ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 45 HIS ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0827 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.269 65277 Z= 0.541 Angle : 1.653 50.852 88492 Z= 1.056 Chirality : 0.314 6.450 9805 Planarity : 0.005 0.093 11174 Dihedral : 7.379 101.174 9247 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.25 % Favored : 89.49 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.03 % 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: -1.22 (0.10), residues: 7824 helix: 0.59 (0.09), residues: 3853 sheet: -1.17 (0.29), residues: 334 loop : -2.42 (0.10), residues: 3637 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 449 time to evaluate : 5.276 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: 15 outliers final: 10 residues processed: 453 average time/residue: 0.6258 time to fit residues: 493.0276 Evaluate side-chains 456 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 446 time to evaluate : 5.186 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.5196 time to fit residues: 17.3318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 380 optimal weight: 5.9990 chunk 492 optimal weight: 30.0000 chunk 660 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 572 optimal weight: 30.0000 chunk 91 optimal weight: 40.0000 chunk 172 optimal weight: 50.0000 chunk 621 optimal weight: 20.0000 chunk 260 optimal weight: 6.9990 chunk 638 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 144 HIS ** 9 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 GLN ** a 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 ASN ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 HIS l 76 ASN ** p 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS w 45 HIS ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5618 r_free = 0.5618 target = 0.397773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5383 r_free = 0.5383 target = 0.354533 restraints weight = 702331.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5466 r_free = 0.5466 target = 0.367804 restraints weight = 368100.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5506 r_free = 0.5506 target = 0.374723 restraints weight = 240758.569| |-----------------------------------------------------------------------------| r_work (final): 0.5433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5617 r_free = 0.5617 target_work(ls_wunit_k1) = 0.398 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5617 r_free = 0.5617 target_work(ls_wunit_k1) = 0.397 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.5617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1410 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.267 65277 Z= 0.544 Angle : 1.660 50.912 88492 Z= 1.059 Chirality : 0.314 6.470 9805 Planarity : 0.005 0.090 11174 Dihedral : 7.432 103.087 9247 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.24 % Favored : 89.49 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -1.27 (0.10), residues: 7824 helix: 0.55 (0.09), residues: 3851 sheet: -1.26 (0.29), residues: 323 loop : -2.45 (0.10), residues: 3650 =============================================================================== Job complete usr+sys time: 10189.94 seconds wall clock time: 182 minutes 57.46 seconds (10977.46 seconds total)