Starting phenix.real_space_refine (version: dev) on Sun Dec 18 14:42:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/12_2022/8dzi_27799.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/12_2022/8dzi_27799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/12_2022/8dzi_27799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/12_2022/8dzi_27799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/12_2022/8dzi_27799.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/12_2022/8dzi_27799.pdb" } resolution = 3.5 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C GLU 616": "OE1" <-> "OE2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C GLU 915": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "E GLU 278": "OE1" <-> "OE2" Residue "E GLU 462": "OE1" <-> "OE2" Residue "E GLU 513": "OE1" <-> "OE2" Residue "E GLU 616": "OE1" <-> "OE2" Residue "E GLU 651": "OE1" <-> "OE2" Residue "E GLU 770": "OE1" <-> "OE2" Residue "E GLU 865": "OE1" <-> "OE2" Residue "E GLU 985": "OE1" <-> "OE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 31470 Number of models: 1 Model: "" Number of chains: 32 Chain: "C" Number of atoms: 8496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8496 Classifications: {'peptide': 1083} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 60, 'TRANS': 1022} Chain breaks: 9 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 8467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8467 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 59, 'TRANS': 1020} Chain breaks: 8 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 8420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8420 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 59, 'TRANS': 1014} Chain breaks: 8 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "G" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.73, per 1000 atoms: 0.53 Number of scatterers: 31470 At special positions: 0 Unit cell: (177.62, 146.59, 218.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 6134 8.00 N 5161 7.00 C 20037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.04 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 298 " distance=2.02 Simple disulfide: pdb=" SG CYS E 333 " - pdb=" SG CYS E 358 " distance=2.03 Simple disulfide: pdb=" SG CYS E 376 " - pdb=" SG CYS E 429 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 522 " distance=2.03 Simple disulfide: pdb=" SG CYS E 477 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS E 535 " - pdb=" SG CYS E 587 " distance=2.03 Simple disulfide: pdb=" SG CYS E 614 " - pdb=" SG CYS E 646 " distance=2.03 Simple disulfide: pdb=" SG CYS E 659 " - pdb=" SG CYS E 668 " distance=2.04 Simple disulfide: pdb=" SG CYS E 735 " - pdb=" SG CYS E 757 " distance=2.03 Simple disulfide: pdb=" SG CYS E 740 " - pdb=" SG CYS E 746 " distance=2.03 Simple disulfide: pdb=" SG CYS E 837 " - pdb=" SG CYS E 848 " distance=2.03 Simple disulfide: pdb=" SG CYS E1029 " - pdb=" SG CYS E1040 " distance=2.03 Simple disulfide: pdb=" SG CYS E1079 " - pdb=" SG CYS E1123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A1301 " - " ASN A 600 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 654 " " NAG A1305 " - " ASN A1131 " " NAG A1307 " - " ASN A 231 " " NAG A1308 " - " ASN A 340 " " NAG A1309 " - " ASN A 367 " " NAG C1301 " - " ASN C 600 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 613 " " NAG C1304 " - " ASN C 654 " " NAG E1301 " - " ASN E 231 " " NAG E1302 " - " ASN E 61 " " NAG E1303 " - " ASN E 328 " " NAG E1304 " - " ASN E 613 " " NAG E1305 " - " ASN E 654 " " NAG E1306 " - " ASN E1071 " " NAG E1307 " - " ASN E 340 " " NAG E1308 " - " ASN E 160 " " NAG E1309 " - " ASN E 135 " " NAG I 1 " - " ASN C1095 " " NAG J 1 " - " ASN C1131 " " NAG K 1 " - " ASN C 706 " " NAG M 1 " - " ASN C 714 " " NAG N 1 " - " ASN C 798 " " NAG O 1 " - " ASN C1071 " " NAG P 1 " - " ASN C 279 " " NAG Q 1 " - " ASN A1095 " " NAG R 1 " - " ASN A 706 " " NAG S 1 " - " ASN A 714 " " NAG T 1 " - " ASN A 798 " " NAG U 1 " - " ASN A1071 " " NAG V 1 " - " ASN A 279 " " NAG W 1 " - " ASN E 120 " " NAG X 1 " - " ASN E 279 " " NAG Y 1 " - " ASN E 706 " " NAG Z 1 " - " ASN E1131 " " NAG a 1 " - " ASN E1095 " " NAG b 1 " - " ASN E 714 " " NAG c 1 " - " ASN E 798 " Time building additional restraints: 14.56 Conformation dependent library (CDL) restraints added in 5.0 seconds 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7290 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 59 sheets defined 22.0% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.536A pdb=" N VAL C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 154' Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.754A pdb=" N LEU C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 495 through 501 removed outlier: 3.839A pdb=" N VAL C 500 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 501 " --> pdb=" O THR C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 754 removed outlier: 3.737A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 4.034A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 824 Processing helix chain 'C' and resid 847 through 852 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.539A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.329A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 removed outlier: 3.577A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 965 removed outlier: 3.504A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.597A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU C 981 " --> pdb=" O ILE C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.859A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1142 removed outlier: 3.671A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.801A pdb=" N LEU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.533A pdb=" N ASN A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 495 through 500 removed outlier: 4.597A pdb=" N VAL A 500 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.614A pdb=" N GLY A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 824 removed outlier: 3.575A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.301A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.593A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 964 removed outlier: 4.040A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.185A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1142 removed outlier: 3.783A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.589A pdb=" N VAL E 154 " --> pdb=" O SER E 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 150 through 154' Processing helix chain 'E' and resid 291 through 301 Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 361 through 368 removed outlier: 4.112A pdb=" N LEU E 365 " --> pdb=" O ASP E 361 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN E 367 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.616A pdb=" N LEU E 384 " --> pdb=" O PRO E 381 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN E 385 " --> pdb=" O THR E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 removed outlier: 3.513A pdb=" N ALA E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 419 Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.948A pdb=" N GLN E 503 " --> pdb=" O GLY E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 740 removed outlier: 3.623A pdb=" N TYR E 738 " --> pdb=" O ASP E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 754 removed outlier: 3.754A pdb=" N GLY E 754 " --> pdb=" O LEU E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 780 Processing helix chain 'E' and resid 813 through 824 Processing helix chain 'E' and resid 845 through 852 Processing helix chain 'E' and resid 863 through 881 Processing helix chain 'E' and resid 883 through 888 Processing helix chain 'E' and resid 894 through 907 Processing helix chain 'E' and resid 909 through 916 removed outlier: 4.226A pdb=" N LEU E 913 " --> pdb=" O THR E 909 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR E 914 " --> pdb=" O GLN E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 937 removed outlier: 3.681A pdb=" N GLN E 932 " --> pdb=" O ILE E 928 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP E 933 " --> pdb=" O GLY E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 965 removed outlier: 3.629A pdb=" N LEU E 963 " --> pdb=" O LEU E 959 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 964 " --> pdb=" O VAL E 960 " (cutoff:3.500A) Processing helix chain 'E' and resid 973 through 981 Processing helix chain 'E' and resid 982 through 1029 Processing helix chain 'E' and resid 1137 through 1142 Processing helix chain 'G' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.463A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 63 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 264 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.802A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.830A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.376A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 240 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE C 99 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.595A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 322 through 323 removed outlier: 6.889A pdb=" N ILE C 323 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE C 562 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.972A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.972A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.126A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 450 through 451 Processing sheet with id=AB3, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.529A pdb=" N TYR C 486 " --> pdb=" O TYR C 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.975A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 698 through 701 removed outlier: 3.581A pdb=" N LYS E 787 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.690A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.690A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 730 through 732 removed outlier: 4.494A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 785 through 786 removed outlier: 5.924A pdb=" N ILE C 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AC2, first strand: chain 'H' and resid 57 through 60 removed outlier: 5.928A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.508A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.430A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.290A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.304A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AC9, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.515A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 240 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 99 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.472A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.665A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 432 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.245A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD5, first strand: chain 'A' and resid 651 through 657 removed outlier: 5.880A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL A 653 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.785A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AD8, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.892A pdb=" N ILE A 785 " --> pdb=" O ASN E 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AE1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AE2, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AE3, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.752A pdb=" N VAL B 114 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 34 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.713A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.415A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 27 through 30 removed outlier: 3.604A pdb=" N VAL E 88 " --> pdb=" O PHE E 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL E 224 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER E 200 " --> pdb=" O PRO E 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 48 through 55 removed outlier: 4.243A pdb=" N ASP E 284 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.333A pdb=" N GLY E 101 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N ILE E 126 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR E 162 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL E 128 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASN E 160 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLU E 130 " --> pdb=" O ALA E 158 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA E 158 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN E 132 " --> pdb=" O SER E 156 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 308 through 316 removed outlier: 5.554A pdb=" N ILE E 309 " --> pdb=" O THR E 596 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR E 596 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN E 311 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL E 594 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER E 313 " --> pdb=" O VAL E 592 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY E 591 " --> pdb=" O GLN E 610 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 321 through 325 removed outlier: 3.908A pdb=" N GLU E 321 " --> pdb=" O CYS E 535 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASP E 571 " --> pdb=" O ILE E 584 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 351 through 354 removed outlier: 4.834A pdb=" N ASN E 391 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU E 513 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 351 through 354 Processing sheet with id=AF5, first strand: chain 'E' and resid 449 through 451 Processing sheet with id=AF6, first strand: chain 'E' and resid 651 through 653 removed outlier: 4.449A pdb=" N THR E 693 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 667 " --> pdb=" O ILE E 663 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 708 through 725 removed outlier: 6.756A pdb=" N SER E 708 " --> pdb=" O THR E1073 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR E1073 " --> pdb=" O SER E 708 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA E 710 " --> pdb=" O ASN E1071 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E1071 " --> pdb=" O ALA E 710 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU E1069 " --> pdb=" O PRO E 712 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY E1056 " --> pdb=" O SER E1052 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER E1052 " --> pdb=" O GLY E1056 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL E1058 " --> pdb=" O PRO E1050 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU E1060 " --> pdb=" O SER E1048 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER E1048 " --> pdb=" O LEU E1060 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E1062 " --> pdb=" O LEU E1046 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 708 through 725 removed outlier: 6.756A pdb=" N SER E 708 " --> pdb=" O THR E1073 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR E1073 " --> pdb=" O SER E 708 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA E 710 " --> pdb=" O ASN E1071 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E1071 " --> pdb=" O ALA E 710 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU E1069 " --> pdb=" O PRO E 712 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E1075 " --> pdb=" O PHE E1092 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE E1092 " --> pdb=" O ALA E1075 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 730 through 733 removed outlier: 4.389A pdb=" N LYS E 730 " --> pdb=" O LEU E 858 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 1117 through 1122 removed outlier: 4.291A pdb=" N ALA E1084 " --> pdb=" O SER E1120 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.230A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 86 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.612A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3213 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: 15.81 Time building geometry restraints manager: 15.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9947 1.35 - 1.47: 8137 1.47 - 1.59: 13937 1.59 - 1.71: 2 1.71 - 1.83: 177 Bond restraints: 32200 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.426 1.504 -0.078 3.20e-02 9.77e+02 5.99e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.426 1.502 -0.076 3.20e-02 9.77e+02 5.65e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.426 1.355 0.071 3.20e-02 9.77e+02 4.96e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.426 1.496 -0.070 3.20e-02 9.77e+02 4.75e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.426 1.489 -0.063 3.20e-02 9.77e+02 3.88e+00 ... (remaining 32195 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.79: 773 105.79 - 112.88: 17224 112.88 - 119.97: 10426 119.97 - 127.05: 15031 127.05 - 134.14: 320 Bond angle restraints: 43774 Sorted by residual: angle pdb=" C2 NAG Y 1 " pdb=" C3 NAG Y 1 " pdb=" C4 NAG Y 1 " ideal model delta sigma weight residual 110.39 115.68 -5.29 1.16e+00 7.50e-01 2.10e+01 angle pdb=" C GLY A 479 " pdb=" N VAL A 480 " pdb=" CA VAL A 480 " ideal model delta sigma weight residual 121.97 129.57 -7.60 1.80e+00 3.09e-01 1.78e+01 angle pdb=" C ASN E 85 " pdb=" CA ASN E 85 " pdb=" CB ASN E 85 " ideal model delta sigma weight residual 115.89 110.53 5.36 1.32e+00 5.74e-01 1.65e+01 angle pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " pdb=" C5 NAG Q 1 " ideal model delta sigma weight residual 113.34 119.76 -6.42 1.74e+00 3.30e-01 1.36e+01 angle pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " pdb=" C5 NAG A1302 " ideal model delta sigma weight residual 113.34 119.73 -6.39 1.74e+00 3.30e-01 1.35e+01 ... (remaining 43769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 16838 22.35 - 44.71: 1829 44.71 - 67.06: 263 67.06 - 89.42: 98 89.42 - 111.77: 38 Dihedral angle restraints: 19066 sinusoidal: 7708 harmonic: 11358 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 5.88 87.12 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS A 837 " pdb=" SG CYS A 837 " pdb=" SG CYS A 848 " pdb=" CB CYS A 848 " ideal model delta sinusoidal sigma weight residual -86.00 -169.27 83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CA SER L 95 " pdb=" C SER L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual -180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 19063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 5011 0.128 - 0.256: 43 0.256 - 0.384: 12 0.384 - 0.512: 4 0.512 - 0.640: 1 Chirality restraints: 5071 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C1095 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 600 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 5068 not shown) Planarity restraints: 5607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 95 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO F 96 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO F 96 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 96 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " 0.084 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO L 96 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 95 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO D 96 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO D 96 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 96 " -0.063 5.00e-02 4.00e+02 ... (remaining 5604 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 777 2.67 - 3.22: 32294 3.22 - 3.78: 55179 3.78 - 4.34: 73829 4.34 - 4.90: 113978 Nonbonded interactions: 276057 Sorted by model distance: nonbonded pdb=" OH TYR E 652 " pdb=" OG1 THR E 693 " model vdw 2.107 2.440 nonbonded pdb=" O ALA E 289 " pdb=" OG1 THR E 629 " model vdw 2.117 2.440 nonbonded pdb=" OG SER C 491 " pdb=" OG SER C 493 " model vdw 2.136 2.440 nonbonded pdb=" OG1 THR A 107 " pdb=" OD2 ASP A 109 " model vdw 2.143 2.440 nonbonded pdb=" OG SER G 17 " pdb=" OE1 GLN G 82 " model vdw 2.147 2.440 ... (remaining 276052 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 'A' and (resid 25 through 69 or resid 74 through 142 or resid 149 through \ 174 or resid 180 through 826 or resid 831 through 833 or (resid 834 and (name N \ or name CA or name C or name O or name CB )) or resid 835 through 837 or resid \ 845 through 1144 or resid 1301 through 1305)) selection = (chain 'C' and (resid 25 through 142 or resid 149 through 174 or resid 180 throu \ gh 244 or resid 254 through 621 or resid 629 through 826 or resid 831 through 83 \ 3 or (resid 834 and (name N or name CA or name C or name O or name CB )) or resi \ d 835 through 837 or resid 845 through 1144 or resid 1301 through 1305)) selection = (chain 'E' and (resid 25 through 174 or resid 180 through 244 or resid 254 throu \ gh 621 or resid 629 through 837 or resid 845 through 1144 or resid 1301 through \ 1305)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 20037 2.51 5 N 5161 2.21 5 O 6134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.840 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.270 Process input model: 86.830 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 32200 Z= 0.213 Angle : 0.660 12.382 43774 Z= 0.367 Chirality : 0.049 0.640 5071 Planarity : 0.006 0.127 5566 Dihedral : 18.879 111.770 11632 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 3850 helix: 2.30 (0.19), residues: 706 sheet: -0.01 (0.17), residues: 830 loop : -0.67 (0.12), residues: 2314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.4345 time to fit residues: 43.2423 Evaluate side-chains 48 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 3.761 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.3468 time to fit residues: 9.0601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 325 optimal weight: 10.0000 chunk 292 optimal weight: 30.0000 chunk 162 optimal weight: 0.0030 chunk 99 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 302 optimal weight: 20.0000 chunk 117 optimal weight: 50.0000 chunk 183 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 overall best weight: 7.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS C 484 ASN C 502 HIS ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN C 604 GLN C 610 GLN C 700 ASN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 989 GLN ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 357 ASN A 434 ASN A 436 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 610 GLN A 638 ASN A 954 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 HIS ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN ** E 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN E 484 ASN E 503 GLN ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 687 GLN E 748 ASN E 759 GLN E 801 GLN ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 917 GLN E 922 ASN ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN E1008 GLN ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 32200 Z= 0.346 Angle : 0.646 9.447 43774 Z= 0.356 Chirality : 0.048 0.494 5071 Planarity : 0.006 0.126 5566 Dihedral : 13.056 112.925 4598 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.95 % Favored : 95.87 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 3850 helix: 2.34 (0.19), residues: 737 sheet: -0.05 (0.17), residues: 853 loop : -0.66 (0.13), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 41 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 71 residues processed: 183 average time/residue: 0.3991 time to fit residues: 124.8776 Evaluate side-chains 111 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 40 time to evaluate : 3.867 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 3 residues processed: 71 average time/residue: 0.3112 time to fit residues: 44.5627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 194 optimal weight: 5.9990 chunk 108 optimal weight: 50.0000 chunk 291 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 351 optimal weight: 6.9990 chunk 379 optimal weight: 6.9990 chunk 312 optimal weight: 0.8980 chunk 348 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN C 850 GLN C 916 ASN ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1020 ASN C1098 HIS ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 752 GLN E 759 GLN E 801 GLN ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 932 GLN ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1033 GLN ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 32200 Z= 0.302 Angle : 0.614 9.176 43774 Z= 0.337 Chirality : 0.048 0.483 5071 Planarity : 0.006 0.124 5566 Dihedral : 13.051 112.610 4598 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.05 % Favored : 95.77 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 3850 helix: 2.24 (0.19), residues: 736 sheet: -0.24 (0.17), residues: 856 loop : -0.70 (0.13), residues: 2258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 40 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 54 residues processed: 144 average time/residue: 0.3838 time to fit residues: 98.1736 Evaluate side-chains 94 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 40 time to evaluate : 3.859 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 3 residues processed: 54 average time/residue: 0.3280 time to fit residues: 36.4621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 346 optimal weight: 9.9990 chunk 264 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 167 optimal weight: 30.0000 chunk 235 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 373 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 334 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 957 ASN ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 32200 Z= 0.325 Angle : 0.616 7.903 43774 Z= 0.337 Chirality : 0.048 0.458 5071 Planarity : 0.006 0.123 5566 Dihedral : 13.097 113.006 4598 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.52 % Favored : 95.30 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 3850 helix: 2.22 (0.19), residues: 734 sheet: -0.29 (0.17), residues: 859 loop : -0.69 (0.13), residues: 2257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 40 time to evaluate : 3.776 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 outliers start: 104 outliers final: 55 residues processed: 140 average time/residue: 0.4390 time to fit residues: 102.8157 Evaluate side-chains 95 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 40 time to evaluate : 3.796 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 3 residues processed: 55 average time/residue: 0.3435 time to fit residues: 38.8288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 310 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 5 optimal weight: 0.0770 chunk 277 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 318 optimal weight: 8.9990 chunk 257 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 190 optimal weight: 3.9990 chunk 334 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 overall best weight: 4.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 784 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 32200 Z= 0.250 Angle : 0.587 10.561 43774 Z= 0.318 Chirality : 0.047 0.445 5071 Planarity : 0.005 0.124 5566 Dihedral : 13.040 112.165 4598 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.34 % Favored : 95.48 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 3850 helix: 2.31 (0.19), residues: 737 sheet: -0.39 (0.17), residues: 858 loop : -0.67 (0.13), residues: 2255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 40 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 33 residues processed: 110 average time/residue: 0.4218 time to fit residues: 79.9572 Evaluate side-chains 73 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 40 time to evaluate : 3.686 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 3 residues processed: 33 average time/residue: 0.3512 time to fit residues: 24.8640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 125 optimal weight: 0.0030 chunk 336 optimal weight: 0.1980 chunk 73 optimal weight: 0.0770 chunk 219 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 373 optimal weight: 5.9990 chunk 310 optimal weight: 30.0000 chunk 172 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 overall best weight: 2.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 GLN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 32200 Z= 0.206 Angle : 0.577 10.748 43774 Z= 0.309 Chirality : 0.047 0.453 5071 Planarity : 0.005 0.124 5566 Dihedral : 12.979 111.584 4598 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.92 % Favored : 95.90 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3850 helix: 2.41 (0.19), residues: 737 sheet: -0.40 (0.17), residues: 881 loop : -0.71 (0.13), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 41 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 28 residues processed: 98 average time/residue: 0.4197 time to fit residues: 72.7121 Evaluate side-chains 68 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 40 time to evaluate : 3.755 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 3 residues processed: 28 average time/residue: 0.2831 time to fit residues: 20.1220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 360 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 372 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 801 GLN ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 32200 Z= 0.317 Angle : 0.614 10.288 43774 Z= 0.330 Chirality : 0.047 0.441 5071 Planarity : 0.005 0.123 5566 Dihedral : 13.062 113.007 4598 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.52 % Favored : 95.30 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.13), residues: 3850 helix: 2.34 (0.19), residues: 740 sheet: -0.44 (0.17), residues: 914 loop : -0.76 (0.13), residues: 2196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 40 time to evaluate : 3.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 85 average time/residue: 0.4143 time to fit residues: 63.2930 Evaluate side-chains 61 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 40 time to evaluate : 4.100 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 3 residues processed: 21 average time/residue: 0.3196 time to fit residues: 17.4903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7545 > 50: distance: 71 - 189: 30.125 distance: 74 - 186: 33.064 distance: 83 - 174: 34.595 distance: 86 - 171: 28.934 distance: 119 - 128: 22.908 distance: 128 - 129: 25.465 distance: 129 - 130: 9.500 distance: 129 - 132: 22.688 distance: 130 - 131: 57.898 distance: 130 - 134: 40.521 distance: 132 - 133: 63.142 distance: 134 - 135: 29.346 distance: 135 - 136: 26.636 distance: 135 - 138: 44.790 distance: 136 - 137: 20.068 distance: 136 - 139: 20.428 distance: 139 - 140: 10.084 distance: 140 - 141: 26.167 distance: 140 - 143: 36.773 distance: 141 - 142: 44.216 distance: 141 - 147: 22.367 distance: 143 - 144: 23.629 distance: 144 - 145: 17.929 distance: 144 - 146: 22.145 distance: 147 - 148: 40.886 distance: 148 - 149: 22.918 distance: 148 - 151: 28.808 distance: 149 - 150: 24.789 distance: 149 - 156: 15.253 distance: 151 - 152: 28.162 distance: 152 - 153: 8.556 distance: 153 - 154: 21.862 distance: 153 - 155: 37.024 distance: 156 - 157: 48.132 distance: 156 - 162: 27.480 distance: 157 - 158: 15.690 distance: 157 - 160: 18.961 distance: 158 - 159: 48.013 distance: 158 - 163: 52.705 distance: 160 - 161: 54.958 distance: 161 - 162: 31.623 distance: 163 - 164: 56.187 distance: 164 - 165: 21.079 distance: 164 - 167: 32.190 distance: 165 - 171: 45.478 distance: 167 - 168: 17.214 distance: 168 - 169: 45.259 distance: 168 - 170: 40.559 distance: 171 - 172: 46.841 distance: 172 - 173: 40.390 distance: 172 - 175: 50.428 distance: 173 - 174: 30.078 distance: 173 - 178: 4.052 distance: 175 - 176: 40.873 distance: 175 - 177: 49.416 distance: 178 - 179: 22.708 distance: 179 - 180: 31.374 distance: 179 - 182: 25.185 distance: 180 - 181: 30.144 distance: 180 - 186: 23.420 distance: 182 - 183: 23.548 distance: 183 - 184: 25.104 distance: 183 - 185: 40.932 distance: 186 - 187: 19.312 distance: 187 - 188: 21.410 distance: 187 - 190: 19.116 distance: 188 - 189: 36.515 distance: 188 - 194: 26.517 distance: 190 - 191: 56.293 distance: 191 - 192: 51.798 distance: 191 - 193: 48.162 distance: 194 - 195: 13.642 distance: 194 - 200: 16.295 distance: 195 - 196: 5.214 distance: 195 - 198: 27.124 distance: 196 - 197: 9.556 distance: 196 - 201: 21.948 distance: 198 - 199: 16.393 distance: 199 - 200: 21.802