Starting phenix.real_space_refine on Sun Feb 8 05:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bne_44725/02_2026/9bne_44725.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bne_44725/02_2026/9bne_44725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bne_44725/02_2026/9bne_44725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bne_44725/02_2026/9bne_44725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bne_44725/02_2026/9bne_44725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bne_44725/02_2026/9bne_44725.map" } resolution = 3.43 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 194 5.16 5 C 25567 2.51 5 N 6593 2.21 5 O 7717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40071 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5276 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 618} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7825 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5266 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 618} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 7801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7801 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5268 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 618} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7837 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 8.74, per 1000 atoms: 0.22 Number of scatterers: 40071 At special positions: 0 Unit cell: (164.736, 154.752, 233.792, 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 194 16.00 O 7717 8.00 N 6593 7.00 C 25567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A1133 " - pdb=" SG CYS A1141 " distance=2.03 Simple disulfide: pdb=" SG CYS A1344 " - pdb=" SG CYS A1361 " distance=2.03 Simple disulfide: pdb=" SG CYS A1530 " - pdb=" SG CYS A1542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C1133 " - pdb=" SG CYS C1141 " distance=2.03 Simple disulfide: pdb=" SG CYS C1344 " - pdb=" SG CYS C1361 " distance=2.03 Simple disulfide: pdb=" SG CYS C1530 " - pdb=" SG CYS C1542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E1133 " - pdb=" SG CYS E1141 " distance=2.03 Simple disulfide: pdb=" SG CYS E1344 " - pdb=" SG CYS E1361 " distance=2.03 Simple disulfide: pdb=" SG CYS E1530 " - pdb=" SG CYS E1542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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-ASN " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1134 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 165 " " NAG D1304 " - " ASN D 234 " " NAG D1305 " - " ASN D 282 " " NAG D1306 " - " ASN D 331 " " NAG D1307 " - " ASN D 343 " " NAG D1308 " - " ASN D 616 " " NAG D1309 " - " ASN D 657 " " NAG D1310 " - " ASN D 709 " " NAG D1311 " - " ASN D1074 " " NAG D1312 " - " ASN D1134 " " NAG F1301 " - " ASN F 61 " " NAG F1302 " - " ASN F 122 " " NAG F1303 " - " ASN F 165 " " NAG F1304 " - " ASN F 234 " " NAG F1305 " - " ASN F 282 " " NAG F1306 " - " ASN F 616 " " NAG F1307 " - " ASN F 657 " " NAG F1308 " - " ASN F 709 " " NAG F1309 " - " ASN F1074 " " NAG F1310 " - " ASN F1098 " " NAG F1311 " - " ASN F1134 " " NAG G 1 " - " ASN B 331 " " NAG H 1 " - " ASN B 343 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN D 717 " " NAG M 1 " - " ASN D 801 " " NAG N 1 " - " ASN D1098 " " NAG O 1 " - " ASN F 331 " " NAG P 1 " - " ASN F 343 " " NAG Q 1 " - " ASN F 717 " " NAG R 1 " - " ASN F 801 " Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.5 seconds 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9310 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 59 sheets defined 41.5% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 3.551A pdb=" N MET A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1053 removed outlier: 3.518A pdb=" N GLU A1035 " --> pdb=" O LYS A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1081 Processing helix chain 'A' and resid 1090 through 1101 Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'A' and resid 1109 through 1130 Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1157 through 1194 removed outlier: 3.758A pdb=" N GLN A1175 " --> pdb=" O GLU A1171 " (cutoff:3.500A) Proline residue: A1178 - end of helix Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1218 through 1252 removed outlier: 3.585A pdb=" N LEU A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A1223 " --> pdb=" O ARG A1219 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A1224 " --> pdb=" O GLY A1220 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A1232 " --> pdb=" O HIS A1228 " (cutoff:3.500A) Proline residue: A1235 - end of helix removed outlier: 3.618A pdb=" N HIS A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A1250 " --> pdb=" O ALA A1246 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A1251 " --> pdb=" O LYS A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1268 removed outlier: 4.146A pdb=" N GLY A1268 " --> pdb=" O HIS A1265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1265 through 1268' Processing helix chain 'A' and resid 1275 through 1280 Processing helix chain 'A' and resid 1293 through 1300 Processing helix chain 'A' and resid 1303 through 1318 Processing helix chain 'A' and resid 1324 through 1331 removed outlier: 4.184A pdb=" N TRP A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1385 removed outlier: 3.548A pdb=" N HIS A1378 " --> pdb=" O HIS A1374 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1414 Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1431 through 1446 Processing helix chain 'A' and resid 1448 through 1466 removed outlier: 4.367A pdb=" N PHE A1452 " --> pdb=" O GLY A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1471 No H-bonds generated for 'chain 'A' and resid 1469 through 1471' Processing helix chain 'A' and resid 1472 through 1484 Processing helix chain 'A' and resid 1498 through 1502 Processing helix chain 'A' and resid 1503 through 1508 Processing helix chain 'A' and resid 1512 through 1533 removed outlier: 4.289A pdb=" N TYR A1516 " --> pdb=" O PHE A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1542 Processing helix chain 'A' and resid 1547 through 1561 removed outlier: 3.655A pdb=" N GLY A1551 " --> pdb=" O SER A1547 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET A1557 " --> pdb=" O LYS A1553 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A1560 " --> pdb=" O ASN A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1575 Processing helix chain 'A' and resid 1581 through 1588 Processing helix chain 'A' and resid 1588 through 1599 Processing helix chain 'A' and resid 1600 through 1602 No H-bonds generated for 'chain 'A' and resid 1600 through 1602' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.168A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.258A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.615A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.070A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.205A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.558A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.319A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 1020 through 1053 removed outlier: 3.621A pdb=" N HIS C1034 " --> pdb=" O ASP C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1081 Processing helix chain 'C' and resid 1090 through 1102 removed outlier: 3.576A pdb=" N LEU C1097 " --> pdb=" O VAL C1093 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C1102 " --> pdb=" O GLN C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1108 removed outlier: 3.675A pdb=" N LEU C1108 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1129 removed outlier: 3.591A pdb=" N ILE C1119 " --> pdb=" O ARG C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1146 through 1154 Processing helix chain 'C' and resid 1157 through 1194 removed outlier: 3.535A pdb=" N GLY C1173 " --> pdb=" O ARG C1169 " (cutoff:3.500A) Proline residue: C1178 - end of helix Processing helix chain 'C' and resid 1198 through 1208 removed outlier: 4.084A pdb=" N ASP C1206 " --> pdb=" O TYR C1202 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR C1207 " --> pdb=" O TRP C1203 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1252 removed outlier: 3.663A pdb=" N LEU C1222 " --> pdb=" O SER C1218 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE C1223 " --> pdb=" O ARG C1219 " (cutoff:3.500A) Proline residue: C1235 - end of helix removed outlier: 3.667A pdb=" N HIS C1239 " --> pdb=" O PRO C1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 1265 through 1268 removed outlier: 3.932A pdb=" N GLY C1268 " --> pdb=" O HIS C1265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1265 through 1268' Processing helix chain 'C' and resid 1275 through 1277 No H-bonds generated for 'chain 'C' and resid 1275 through 1277' Processing helix chain 'C' and resid 1278 through 1283 Processing helix chain 'C' and resid 1293 through 1300 Processing helix chain 'C' and resid 1303 through 1318 Processing helix chain 'C' and resid 1324 through 1331 removed outlier: 4.239A pdb=" N TRP C1328 " --> pdb=" O THR C1324 " (cutoff:3.500A) Processing helix chain 'C' and resid 1365 through 1385 removed outlier: 3.504A pdb=" N HIS C1373 " --> pdb=" O PHE C1369 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR C1385 " --> pdb=" O TYR C1381 " (cutoff:3.500A) Processing helix chain 'C' and resid 1386 through 1388 No H-bonds generated for 'chain 'C' and resid 1386 through 1388' Processing helix chain 'C' and resid 1399 through 1414 Processing helix chain 'C' and resid 1414 through 1421 Processing helix chain 'C' and resid 1431 through 1446 Processing helix chain 'C' and resid 1448 through 1466 removed outlier: 4.372A pdb=" N PHE C1452 " --> pdb=" O GLY C1448 " (cutoff:3.500A) Processing helix chain 'C' and resid 1469 through 1471 No H-bonds generated for 'chain 'C' and resid 1469 through 1471' Processing helix chain 'C' and resid 1472 through 1484 Processing helix chain 'C' and resid 1498 through 1503 removed outlier: 4.226A pdb=" N LEU C1503 " --> pdb=" O PRO C1500 " (cutoff:3.500A) Processing helix chain 'C' and resid 1505 through 1509 removed outlier: 4.007A pdb=" N ASP C1509 " --> pdb=" O VAL C1506 " (cutoff:3.500A) Processing helix chain 'C' and resid 1512 through 1534 removed outlier: 4.040A pdb=" N TYR C1516 " --> pdb=" O PHE C1512 " (cutoff:3.500A) Processing helix chain 'C' and resid 1538 through 1542 Processing helix chain 'C' and resid 1547 through 1561 removed outlier: 3.547A pdb=" N GLY C1551 " --> pdb=" O SER C1547 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C1560 " --> pdb=" O ASN C1556 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY C1561 " --> pdb=" O MET C1557 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1574 Processing helix chain 'C' and resid 1581 through 1588 Processing helix chain 'C' and resid 1588 through 1600 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.663A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 364 through 370 removed outlier: 3.981A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.699A pdb=" N ASN D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP D 389 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.063A pdb=" N ARG D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.622A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.715A pdb=" N GLU D 619 " --> pdb=" O ASN D 616 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 620 " --> pdb=" O CYS D 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 620' Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.549A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 783 removed outlier: 4.463A pdb=" N CYS D 760 " --> pdb=" O TYR D 756 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.907A pdb=" N GLY D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 910 Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.698A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 945 through 968 removed outlier: 3.696A pdb=" N GLN D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 966 " --> pdb=" O LEU D 962 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER D 967 " --> pdb=" O VAL D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.292A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 17 Processing helix chain 'E' and resid 1020 through 1053 removed outlier: 3.534A pdb=" N GLU E1035 " --> pdb=" O LYS E1031 " (cutoff:3.500A) Processing helix chain 'E' and resid 1055 through 1083 removed outlier: 3.603A pdb=" N TYR E1083 " --> pdb=" O LEU E1079 " (cutoff:3.500A) Processing helix chain 'E' and resid 1084 through 1088 removed outlier: 3.620A pdb=" N GLU E1087 " --> pdb=" O PRO E1084 " (cutoff:3.500A) Processing helix chain 'E' and resid 1090 through 1102 Processing helix chain 'E' and resid 1103 through 1108 Processing helix chain 'E' and resid 1109 through 1129 Processing helix chain 'E' and resid 1146 through 1154 Processing helix chain 'E' and resid 1157 through 1172 Processing helix chain 'E' and resid 1172 through 1194 Proline residue: E1178 - end of helix removed outlier: 3.538A pdb=" N VAL E1185 " --> pdb=" O GLU E1181 " (cutoff:3.500A) Processing helix chain 'E' and resid 1198 through 1205 Processing helix chain 'E' and resid 1218 through 1252 removed outlier: 3.551A pdb=" N LEU E1222 " --> pdb=" O SER E1218 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E1223 " --> pdb=" O ARG E1219 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU E1232 " --> pdb=" O HIS E1228 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E1233 " --> pdb=" O THR E1229 " (cutoff:3.500A) Proline residue: E1235 - end of helix Processing helix chain 'E' and resid 1275 through 1280 removed outlier: 4.093A pdb=" N SER E1280 " --> pdb=" O ASN E1277 " (cutoff:3.500A) Processing helix chain 'E' and resid 1293 through 1300 Processing helix chain 'E' and resid 1303 through 1318 Processing helix chain 'E' and resid 1324 through 1331 removed outlier: 4.240A pdb=" N TRP E1328 " --> pdb=" O THR E1324 " (cutoff:3.500A) Processing helix chain 'E' and resid 1365 through 1385 removed outlier: 3.588A pdb=" N HIS E1378 " --> pdb=" O HIS E1374 " (cutoff:3.500A) Processing helix chain 'E' and resid 1399 through 1413 Processing helix chain 'E' and resid 1414 through 1421 Processing helix chain 'E' and resid 1431 through 1446 Processing helix chain 'E' and resid 1449 through 1466 Processing helix chain 'E' and resid 1469 through 1471 No H-bonds generated for 'chain 'E' and resid 1469 through 1471' Processing helix chain 'E' and resid 1472 through 1484 Processing helix chain 'E' and resid 1498 through 1502 Processing helix chain 'E' and resid 1503 through 1508 Processing helix chain 'E' and resid 1512 through 1534 removed outlier: 3.949A pdb=" N TYR E1516 " --> pdb=" O PHE E1512 " (cutoff:3.500A) Processing helix chain 'E' and resid 1538 through 1542 Processing helix chain 'E' and resid 1547 through 1561 removed outlier: 3.542A pdb=" N GLY E1551 " --> pdb=" O SER E1547 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E1560 " --> pdb=" O ASN E1556 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E1561 " --> pdb=" O MET E1557 " (cutoff:3.500A) Processing helix chain 'E' and resid 1565 through 1575 Processing helix chain 'E' and resid 1581 through 1588 Processing helix chain 'E' and resid 1588 through 1600 Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 337 through 343 removed outlier: 3.802A pdb=" N VAL F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 383 through 389 removed outlier: 3.838A pdb=" N ASN F 388 " --> pdb=" O PRO F 384 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP F 389 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 408 Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.585A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 620 removed outlier: 3.776A pdb=" N GLU F 619 " --> pdb=" O ASN F 616 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F 620 " --> pdb=" O CYS F 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 616 through 620' Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 756 removed outlier: 3.590A pdb=" N TYR F 756 " --> pdb=" O LEU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.556A pdb=" N GLN F 762 " --> pdb=" O SER F 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 886 through 891 removed outlier: 4.188A pdb=" N GLY F 891 " --> pdb=" O PHE F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 918 removed outlier: 4.148A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 Processing helix chain 'F' and resid 945 through 968 removed outlier: 3.502A pdb=" N GLN F 949 " --> pdb=" O LEU F 945 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 966 " --> pdb=" O LEU F 962 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER F 967 " --> pdb=" O VAL F 963 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER F 968 " --> pdb=" O LYS F 964 " (cutoff:3.500A) Processing helix chain 'F' and resid 976 through 982 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 1116 through 1118 No H-bonds generated for 'chain 'F' and resid 1116 through 1118' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.822A pdb=" N ARG A 5 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 27 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 34 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 41 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1131 through 1133 Processing sheet with id=AA3, first strand: chain 'A' and resid 1262 through 1263 removed outlier: 5.354A pdb=" N LEU A1262 " --> pdb=" O VAL A1488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1347 through 1350 Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.001A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.890A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.537A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.240A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.396A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AB2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.605A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.696A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.661A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 721 through 728 removed outlier: 3.674A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 721 through 728 Processing sheet with id=AC1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.838A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.761A pdb=" N LEU C 34 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C 41 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1132 through 1133 Processing sheet with id=AC5, first strand: chain 'C' and resid 1262 through 1263 removed outlier: 5.210A pdb=" N LEU C1262 " --> pdb=" O VAL C1488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 1347 through 1350 Processing sheet with id=AC7, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.180A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR D 95 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 91 " --> pdb=" O GLY D 268 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.037A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.162A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.543A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 311 through 319 removed outlier: 6.688A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AD4, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AD6, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.987A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.782A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.782A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'D' and resid 789 through 790 Processing sheet with id=AE2, first strand: chain 'D' and resid 1081 through 1082 Processing sheet with id=AE3, first strand: chain 'D' and resid 1086 through 1090 removed outlier: 4.680A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1094 through 1096 Processing sheet with id=AE5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.535A pdb=" N PHE E 27 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 33 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY E 41 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 1131 through 1133 Processing sheet with id=AE7, first strand: chain 'E' and resid 1262 through 1263 removed outlier: 5.799A pdb=" N LEU E1262 " --> pdb=" O VAL E1488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 1347 through 1352 removed outlier: 5.783A pdb=" N ASP E1355 " --> pdb=" O LEU E1351 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 47 through 55 removed outlier: 4.126A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 63 through 66 removed outlier: 5.817A pdb=" N ALA F 264 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR F 95 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AF3, first strand: chain 'F' and resid 128 through 129 Processing sheet with id=AF4, first strand: chain 'F' and resid 311 through 319 removed outlier: 3.640A pdb=" N TYR F 313 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL F 595 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN F 317 " --> pdb=" O GLY F 593 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY F 593 " --> pdb=" O ASN F 317 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 324 through 325 removed outlier: 6.536A pdb=" N GLU F 324 " --> pdb=" O ASN F 540 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.703A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.260A pdb=" N ALA F 672 " --> pdb=" O PRO F 665 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 711 through 728 removed outlier: 5.986A pdb=" N GLN F1071 " --> pdb=" O THR F 716 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE F 718 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 720 " --> pdb=" O TYR F1067 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR F1067 " --> pdb=" O ILE F 720 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 722 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL F1065 " --> pdb=" O VAL F 722 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR F 724 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU F1063 " --> pdb=" O THR F 724 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE F 726 " --> pdb=" O VAL F1061 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL F1061 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY F1059 " --> pdb=" O PRO F 728 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 1047 through 1050 removed outlier: 7.182A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'F' and resid 1081 through 1082 Processing sheet with id=AG5, first strand: chain 'F' and resid 1086 through 1090 removed outlier: 4.701A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER F1123 " --> pdb=" O ALA F1087 " (cutoff:3.500A) 1864 hydrogen bonds defined for protein. 5232 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: 9.95 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12829 1.34 - 1.46: 10003 1.46 - 1.58: 17928 1.58 - 1.70: 0 1.70 - 1.82: 283 Bond restraints: 41043 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1 NAG D1310 " pdb=" O5 NAG D1310 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 41038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 54796 1.70 - 3.41: 899 3.41 - 5.11: 108 5.11 - 6.82: 21 6.82 - 8.52: 1 Bond angle restraints: 55825 Sorted by residual: angle pdb=" N ILE D 666 " pdb=" CA ILE D 666 " pdb=" C ILE D 666 " ideal model delta sigma weight residual 111.45 107.95 3.50 9.30e-01 1.16e+00 1.41e+01 angle pdb=" N SER B 884 " pdb=" CA SER B 884 " pdb=" C SER B 884 " ideal model delta sigma weight residual 112.93 108.67 4.26 1.33e+00 5.65e-01 1.03e+01 angle pdb=" N GLY B 889 " pdb=" CA GLY B 889 " pdb=" C GLY B 889 " ideal model delta sigma weight residual 115.32 111.28 4.04 1.31e+00 5.83e-01 9.50e+00 angle pdb=" C VAL D 83 " pdb=" N LEU D 84 " pdb=" CA LEU D 84 " ideal model delta sigma weight residual 122.38 113.86 8.52 2.90e+00 1.19e-01 8.63e+00 angle pdb=" CA GLY B1035 " pdb=" C GLY B1035 " pdb=" N GLN B1036 " ideal model delta sigma weight residual 114.58 116.90 -2.32 8.60e-01 1.35e+00 7.27e+00 ... (remaining 55820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.92: 23882 24.92 - 49.84: 875 49.84 - 74.77: 143 74.77 - 99.69: 93 99.69 - 124.61: 106 Dihedral angle restraints: 25099 sinusoidal: 10646 harmonic: 14453 Sorted by residual: dihedral pdb=" C2 NAG G 2 " pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " pdb=" C5 NAG G 2 " ideal model delta sinusoidal sigma weight residual -62.96 61.65 -124.61 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C2 NAG B1307 " pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " pdb=" C5 NAG B1307 " ideal model delta sinusoidal sigma weight residual -62.96 61.23 -124.19 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " pdb=" C5 NAG J 2 " ideal model delta sinusoidal sigma weight residual -62.96 61.20 -124.16 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 25096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 6250 0.117 - 0.233: 74 0.233 - 0.350: 3 0.350 - 0.467: 0 0.467 - 0.583: 1 Chirality restraints: 6328 Sorted by residual: chirality pdb=" C1 NAG F1311 " pdb=" ND2 ASN F1134 " pdb=" C2 NAG F1311 " pdb=" O5 NAG F1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 5.02e+00 chirality pdb=" C4 NAG Q 1 " pdb=" C3 NAG Q 1 " pdb=" C5 NAG Q 1 " pdb=" O4 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 6325 not shown) Planarity restraints: 7197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO D 987 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 294 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO F 295 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 295 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 295 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 462 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO D 463 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " 0.022 5.00e-02 4.00e+02 ... (remaining 7194 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1143 2.66 - 3.22: 42135 3.22 - 3.78: 71006 3.78 - 4.34: 93866 4.34 - 4.90: 146619 Nonbonded interactions: 354769 Sorted by model distance: nonbonded pdb=" O GLU D 780 " pdb=" NE2 GLN D 784 " model vdw 2.098 3.120 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR D1027 " pdb=" OE2 GLU D1031 " model vdw 2.144 3.040 nonbonded pdb=" O ASN B 81 " pdb=" NE2 GLN B 239 " model vdw 2.157 3.120 nonbonded pdb=" NE2 GLN F 115 " pdb=" O VAL F 130 " model vdw 2.166 3.120 ... (remaining 354764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 4 or (resid 5 through 6 and (name N or name CA o \ r name C or name O or name CB )) or resid 7 through 17 or (resid 18 and (name N \ or name CA or name C or name O or name CB )) or resid 19 through 1019 or (resid \ 1020 and (name N or name CA or name C or name O or name CB )) or resid 1021 thro \ ugh 1110 or (resid 1111 and (name N or name CA or name C or name O or name CB )) \ or resid 1112 through 1257 or (resid 1258 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1259 through 1508 or (resid 1509 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1510 through 1614)) selection = (chain 'C' and (resid 1 through 4 or (resid 5 through 6 and (name N or name CA o \ r name C or name O or name CB )) or resid 7 through 1019 or (resid 1020 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1021 through 1479 or ( \ resid 1480 and (name N or name CA or name C or name O or name CB )) or resid 148 \ 1 through 1614)) selection = (chain 'E' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 1110 or (resid 1111 and (name N or \ name CA or name C or name O or name CB )) or resid 1112 through 1257 or (resid 1 \ 258 and (name N or name CA or name C or name O or name CB )) or resid 1259 throu \ gh 1479 or (resid 1480 and (name N or name CA or name C or name O or name CB )) \ or resid 1481 through 1508 or (resid 1509 and (name N or name CA or name C or na \ me O or name CB )) or resid 1510 through 1614)) } ncs_group { reference = (chain 'B' and (resid 27 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 331 or (resid 332 and (name N or n \ ame CA or name C or name O or name CB )) or resid 333 through 438 or (resid 439 \ and (name N or name CA or name C or name O or name CB )) or resid 440 through 51 \ 8 or resid 524 through 527 or (resid 528 and (name N or name CA or name C or nam \ e O or name CB )) or resid 529 through 579 or (resid 580 and (name N or name CA \ or name C or name O or name CB )) or resid 581 through 802 or (resid 803 and (na \ me N or name CA or name C or name O or name CB )) or resid 804 through 883 or (r \ esid 884 and (name N or name CA or name C or name O or name CB )) or resid 885 t \ hrough 911 or (resid 912 and (name N or name CA or name C or name O or name CB ) \ ) or resid 913 through 1310)) selection = (chain 'D' and (resid 27 through 214 or (resid 215 and (name N or name CA or nam \ e C or name O or name CB )) or resid 216 through 407 or (resid 408 and (name N o \ r name CA or name C or name O or name CB )) or resid 409 through 492 or (resid 4 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 494 through \ 579 or (resid 580 and (name N or name CA or name C or name O or name CB )) or r \ esid 581 through 710 or (resid 711 and (name N or name CA or name C or name O or \ name CB )) or resid 712 through 911 or (resid 912 and (name N or name CA or nam \ e C or name O or name CB )) or resid 913 through 1040 or (resid 1041 and (name N \ or name CA or name C or name O or name CB )) or resid 1042 through 1126 or (res \ id 1127 and (name N or name CA or name C or name O or name CB )) or resid 1128 t \ hrough 1144 or resid 1303 through 1312)) selection = (chain 'F' and (resid 27 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 214 or (resid 215 and (name N or n \ ame CA or name C or name O or name CB )) or resid 216 through 280 or (resid 281 \ and (name N or name CA or name C or name O or name CB )) or resid 282 through 40 \ 7 or (resid 408 and (name N or name CA or name C or name O or name CB )) or resi \ d 409 through 438 or (resid 439 and (name N or name CA or name C or name O or na \ me CB )) or resid 440 through 442 or (resid 443 and (name N or name CA or name C \ or name O or name CB )) or resid 444 through 518 or resid 524 through 527 or (r \ esid 528 and (name N or name CA or name C or name O or name CB )) or resid 529 t \ hrough 710 or (resid 711 and (name N or name CA or name C or name O or name CB ) \ ) or resid 712 through 802 or (resid 803 and (name N or name CA or name C or nam \ e O or name CB )) or resid 804 through 883 or (resid 884 and (name N or name CA \ or name C or name O or name CB )) or resid 885 through 1040 or (resid 1041 and ( \ name N or name CA or name C or name O or name CB )) or resid 1042 through 1099 o \ r (resid 1100 and (name N or name CA or name C or name O or name CB )) or resid \ 1101 through 1126 or (resid 1127 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1128 through 1310)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 37.120 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.004 0.076 41145 Z= 0.206 Angle : 0.558 10.116 56086 Z= 0.278 Chirality : 0.043 0.583 6328 Planarity : 0.003 0.048 7152 Dihedral : 16.685 124.610 15654 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.33 % Allowed : 8.01 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.12), residues: 4893 helix: 2.03 (0.13), residues: 1755 sheet: -0.84 (0.20), residues: 661 loop : -0.52 (0.13), residues: 2477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1000 TYR 0.018 0.001 TYR F1067 PHE 0.012 0.001 PHE B 92 TRP 0.008 0.001 TRP D1102 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00424 (41043) covalent geometry : angle 0.54302 (55825) SS BOND : bond 0.00238 ( 45) SS BOND : angle 0.70907 ( 90) hydrogen bonds : bond 0.19763 ( 1849) hydrogen bonds : angle 6.64136 ( 5232) link_BETA1-4 : bond 0.00601 ( 12) link_BETA1-4 : angle 2.59330 ( 36) link_NAG-ASN : bond 0.00447 ( 45) link_NAG-ASN : angle 2.30426 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 205 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1172 VAL cc_start: 0.1127 (OUTLIER) cc_final: 0.0140 (m) REVERT: B 242 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8975 (mp) REVERT: B 663 ASP cc_start: 0.8836 (m-30) cc_final: 0.8470 (m-30) REVERT: B 780 GLU cc_start: 0.8993 (tt0) cc_final: 0.8539 (tp30) REVERT: B 919 ASN cc_start: 0.9145 (m-40) cc_final: 0.8917 (t0) REVERT: B 1019 ARG cc_start: 0.8898 (tpt170) cc_final: 0.8684 (tpt-90) REVERT: C 13 MET cc_start: -0.2849 (tmm) cc_final: -0.3121 (ttp) REVERT: C 1152 MET cc_start: 0.0043 (ptp) cc_final: -0.0548 (mtt) REVERT: C 1270 MET cc_start: 0.4588 (ptp) cc_final: 0.4273 (ptp) REVERT: C 1360 MET cc_start: 0.3820 (ttm) cc_final: 0.3405 (ttm) REVERT: C 1579 MET cc_start: 0.5402 (mmt) cc_final: 0.4975 (mmt) REVERT: D 551 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.8951 (p) REVERT: D 762 GLN cc_start: 0.9176 (tp40) cc_final: 0.8830 (tp40) REVERT: D 1001 LEU cc_start: 0.9721 (tp) cc_final: 0.9411 (pp) REVERT: D 1106 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: E 13 MET cc_start: -0.2847 (mmt) cc_final: -0.3651 (ttm) REVERT: E 1332 MET cc_start: 0.9254 (ptt) cc_final: 0.7938 (ppp) REVERT: E 1366 MET cc_start: 0.8603 (mmp) cc_final: 0.8396 (mmm) REVERT: E 1462 MET cc_start: 0.8732 (ptp) cc_final: 0.8522 (ptm) REVERT: E 1480 MET cc_start: 0.8811 (ptt) cc_final: 0.8517 (ptp) REVERT: F 118 LEU cc_start: 0.9593 (tt) cc_final: 0.9294 (mp) REVERT: F 198 ASP cc_start: 0.9605 (m-30) cc_final: 0.9403 (t70) REVERT: F 297 SER cc_start: 0.8921 (m) cc_final: 0.8401 (p) REVERT: F 298 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.8957 (mm-30) REVERT: F 495 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6326 (m-80) REVERT: F 560 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9016 (mm) REVERT: F 663 ASP cc_start: 0.8575 (m-30) cc_final: 0.8361 (m-30) REVERT: F 786 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8600 (mmmt) REVERT: F 823 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: F 1010 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.8997 (mp10) REVERT: F 1017 GLU cc_start: 0.9178 (tt0) cc_final: 0.8974 (tm-30) outliers start: 187 outliers final: 83 residues processed: 383 average time/residue: 0.2225 time to fit residues: 146.3186 Evaluate side-chains 243 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 150 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 1031 LYS Chi-restraints excluded: chain C residue 1331 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 676 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 936 ASP Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1106 GLN Chi-restraints excluded: chain E residue 1206 ASP Chi-restraints excluded: chain E residue 1227 GLU Chi-restraints excluded: chain E residue 1331 SER Chi-restraints excluded: chain E residue 1339 VAL Chi-restraints excluded: chain E residue 1400 PHE Chi-restraints excluded: chain E residue 1485 VAL Chi-restraints excluded: chain E residue 1499 ASP Chi-restraints excluded: chain E residue 1555 PHE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 165 ASN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 449 TYR Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 710 ASN Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 823 PHE Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 950 ASP Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1039 ARG Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 50.0000 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 0.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 50.0000 chunk 470 optimal weight: 0.9990 overall best weight: 3.0128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 ASN A1175 GLN A1194 ASN A1250 ASN A1330 ASN ** A1378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1106 GLN C 31 GLN C1061 ASN ** C1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 437 ASN D 935 GLN D1005 GLN D1023 ASN D1142 GLN E1058 ASN E1089 GLN ** E1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN F1002 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.077774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.051376 restraints weight = 301698.815| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 7.71 r_work: 0.2971 rms_B_bonded: 6.89 restraints_weight: 2.0000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41145 Z= 0.161 Angle : 0.641 10.157 56086 Z= 0.312 Chirality : 0.046 0.481 6328 Planarity : 0.004 0.075 7152 Dihedral : 15.548 114.144 6663 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.15 % Allowed : 9.98 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.12), residues: 4893 helix: 1.75 (0.12), residues: 1805 sheet: -0.81 (0.19), residues: 702 loop : -0.49 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1177 TYR 0.022 0.001 TYR C1183 PHE 0.017 0.001 PHE E1504 TRP 0.016 0.001 TRP E1477 HIS 0.008 0.001 HIS E1374 Details of bonding type rmsd covalent geometry : bond 0.00340 (41043) covalent geometry : angle 0.62910 (55825) SS BOND : bond 0.00266 ( 45) SS BOND : angle 0.96984 ( 90) hydrogen bonds : bond 0.04952 ( 1849) hydrogen bonds : angle 5.47556 ( 5232) link_BETA1-4 : bond 0.00575 ( 12) link_BETA1-4 : angle 2.38165 ( 36) link_NAG-ASN : bond 0.00447 ( 45) link_NAG-ASN : angle 2.22140 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 173 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1172 VAL cc_start: 0.4469 (OUTLIER) cc_final: 0.4034 (m) REVERT: A 1297 MET cc_start: 0.6716 (mmm) cc_final: 0.6342 (mtt) REVERT: B 242 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8810 (mp) REVERT: B 663 ASP cc_start: 0.9151 (m-30) cc_final: 0.8659 (m-30) REVERT: B 740 MET cc_start: 0.8731 (tpt) cc_final: 0.7884 (tpp) REVERT: B 780 GLU cc_start: 0.9437 (tt0) cc_final: 0.9043 (tp30) REVERT: B 900 MET cc_start: 0.9016 (mmm) cc_final: 0.8680 (mmt) REVERT: B 919 ASN cc_start: 0.9315 (m-40) cc_final: 0.9026 (t0) REVERT: B 1029 MET cc_start: 0.9149 (tpp) cc_final: 0.8623 (ttp) REVERT: B 1031 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: C 1123 MET cc_start: 0.3357 (ptt) cc_final: 0.3080 (ptt) REVERT: C 1152 MET cc_start: 0.1450 (ptp) cc_final: 0.0731 (mtt) REVERT: C 1270 MET cc_start: 0.5130 (ptp) cc_final: 0.4874 (ptp) REVERT: C 1360 MET cc_start: 0.3918 (ttm) cc_final: 0.3683 (ttm) REVERT: C 1579 MET cc_start: 0.5804 (mmt) cc_final: 0.5404 (mmt) REVERT: D 129 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8257 (ptpt) REVERT: D 707 TYR cc_start: 0.8698 (t80) cc_final: 0.8497 (t80) REVERT: D 740 MET cc_start: 0.9537 (OUTLIER) cc_final: 0.9287 (ttm) REVERT: D 762 GLN cc_start: 0.9544 (tp40) cc_final: 0.9202 (tp40) REVERT: D 1001 LEU cc_start: 0.9778 (tp) cc_final: 0.9492 (pp) REVERT: D 1106 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8823 (mp10) REVERT: D 1111 GLU cc_start: 0.9446 (tt0) cc_final: 0.8602 (tm-30) REVERT: E 13 MET cc_start: -0.2766 (mmt) cc_final: -0.3475 (ttt) REVERT: E 1123 MET cc_start: 0.8574 (mmm) cc_final: 0.8340 (mmm) REVERT: E 1332 MET cc_start: 0.9394 (ptt) cc_final: 0.7835 (ppp) REVERT: E 1376 MET cc_start: 0.9567 (tpt) cc_final: 0.9122 (ttm) REVERT: E 1462 MET cc_start: 0.8632 (ptp) cc_final: 0.8386 (ptm) REVERT: F 117 LEU cc_start: 0.9290 (tp) cc_final: 0.8880 (mm) REVERT: F 118 LEU cc_start: 0.9573 (tt) cc_final: 0.9141 (mp) REVERT: F 297 SER cc_start: 0.9092 (m) cc_final: 0.8590 (p) REVERT: F 298 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.9062 (mm-30) REVERT: F 319 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7781 (tpp80) REVERT: F 449 TYR cc_start: 0.9358 (OUTLIER) cc_final: 0.9109 (m-80) REVERT: F 495 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: F 762 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: F 786 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8633 (mmmt) REVERT: F 823 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8859 (m-80) REVERT: F 984 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8234 (mm) REVERT: F 1001 LEU cc_start: 0.9745 (tt) cc_final: 0.9530 (pp) REVERT: F 1010 GLN cc_start: 0.9608 (OUTLIER) cc_final: 0.9294 (mp10) REVERT: F 1017 GLU cc_start: 0.9666 (tt0) cc_final: 0.9424 (tm-30) REVERT: F 1039 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8183 (ptm160) outliers start: 136 outliers final: 73 residues processed: 298 average time/residue: 0.2085 time to fit residues: 107.8949 Evaluate side-chains 238 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 149 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 1031 LYS Chi-restraints excluded: chain C residue 1331 SER Chi-restraints excluded: chain C residue 1367 ASP Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 676 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1106 GLN Chi-restraints excluded: chain D residue 1142 GLN Chi-restraints excluded: chain E residue 1227 GLU Chi-restraints excluded: chain E residue 1324 THR Chi-restraints excluded: chain E residue 1331 SER Chi-restraints excluded: chain E residue 1339 VAL Chi-restraints excluded: chain E residue 1400 PHE Chi-restraints excluded: chain E residue 1485 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 165 ASN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 319 ARG Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 449 TYR Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 762 GLN Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 823 PHE Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 950 ASP Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1039 ARG Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 172 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 384 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 203 optimal weight: 40.0000 chunk 25 optimal weight: 8.9990 chunk 319 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 chunk 446 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 901 GLN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 ASN C1063 ASN D 69 HIS ** D1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1250 ASN ** E1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.076374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.049564 restraints weight = 304713.524| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 7.14 r_work: 0.2917 rms_B_bonded: 6.70 restraints_weight: 2.0000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 41145 Z= 0.276 Angle : 0.689 10.456 56086 Z= 0.337 Chirality : 0.045 0.448 6328 Planarity : 0.004 0.049 7152 Dihedral : 12.989 112.664 6613 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.59 % Allowed : 10.90 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 4893 helix: 1.46 (0.12), residues: 1810 sheet: -0.98 (0.19), residues: 712 loop : -0.58 (0.13), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1177 TYR 0.016 0.002 TYR F1067 PHE 0.017 0.002 PHE B 92 TRP 0.018 0.001 TRP E1165 HIS 0.007 0.001 HIS E1374 Details of bonding type rmsd covalent geometry : bond 0.00579 (41043) covalent geometry : angle 0.67672 (55825) SS BOND : bond 0.00342 ( 45) SS BOND : angle 0.93609 ( 90) hydrogen bonds : bond 0.04645 ( 1849) hydrogen bonds : angle 5.51681 ( 5232) link_BETA1-4 : bond 0.00595 ( 12) link_BETA1-4 : angle 2.22439 ( 36) link_NAG-ASN : bond 0.00533 ( 45) link_NAG-ASN : angle 2.43886 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 145 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1172 VAL cc_start: 0.4035 (OUTLIER) cc_final: 0.3558 (m) REVERT: A 1297 MET cc_start: 0.6228 (mmm) cc_final: 0.5772 (mtt) REVERT: A 1376 MET cc_start: 0.8420 (ttt) cc_final: 0.7956 (ptp) REVERT: B 242 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8883 (mp) REVERT: B 495 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.5944 (m-10) REVERT: B 560 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8299 (mm) REVERT: B 663 ASP cc_start: 0.9222 (m-30) cc_final: 0.8751 (m-30) REVERT: B 740 MET cc_start: 0.8791 (tpt) cc_final: 0.7971 (tpp) REVERT: B 780 GLU cc_start: 0.9497 (tt0) cc_final: 0.9089 (tp30) REVERT: B 900 MET cc_start: 0.9119 (mmm) cc_final: 0.8854 (mmp) REVERT: B 919 ASN cc_start: 0.9370 (m-40) cc_final: 0.9065 (t0) REVERT: B 948 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9141 (mt) REVERT: B 1001 LEU cc_start: 0.9794 (OUTLIER) cc_final: 0.9528 (pp) REVERT: C 1123 MET cc_start: 0.3386 (ptt) cc_final: 0.2989 (ptt) REVERT: C 1152 MET cc_start: 0.0668 (OUTLIER) cc_final: -0.0019 (mtt) REVERT: C 1297 MET cc_start: 0.3930 (mtt) cc_final: 0.2471 (mtp) REVERT: C 1360 MET cc_start: 0.3783 (ttm) cc_final: 0.3367 (ttm) REVERT: C 1579 MET cc_start: 0.5587 (mmt) cc_final: 0.5085 (mmt) REVERT: D 773 GLU cc_start: 0.9361 (tp30) cc_final: 0.8978 (tp30) REVERT: D 1002 GLN cc_start: 0.9726 (tt0) cc_final: 0.9277 (tm-30) REVERT: D 1106 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8753 (mp10) REVERT: D 1111 GLU cc_start: 0.9432 (tt0) cc_final: 0.8590 (tm-30) REVERT: E 13 MET cc_start: -0.2777 (mmt) cc_final: -0.3348 (ttt) REVERT: E 1062 MET cc_start: 0.9825 (mmm) cc_final: 0.9624 (mmm) REVERT: E 1123 MET cc_start: 0.8751 (mmm) cc_final: 0.8413 (mmm) REVERT: E 1332 MET cc_start: 0.9450 (ptt) cc_final: 0.7813 (ppp) REVERT: E 1462 MET cc_start: 0.8589 (ptp) cc_final: 0.8328 (ptm) REVERT: E 1579 MET cc_start: 0.6960 (pmm) cc_final: 0.6504 (pmm) REVERT: F 117 LEU cc_start: 0.9365 (tp) cc_final: 0.8930 (mm) REVERT: F 118 LEU cc_start: 0.9609 (tt) cc_final: 0.9180 (mp) REVERT: F 297 SER cc_start: 0.9151 (m) cc_final: 0.8675 (p) REVERT: F 449 TYR cc_start: 0.9361 (OUTLIER) cc_final: 0.9115 (m-80) REVERT: F 495 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.6954 (m-80) REVERT: F 560 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9047 (mm) REVERT: F 786 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8670 (mmmt) REVERT: F 823 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: F 900 MET cc_start: 0.9393 (mmm) cc_final: 0.9131 (mmt) REVERT: F 957 GLN cc_start: 0.9455 (tp-100) cc_final: 0.9206 (tm-30) REVERT: F 984 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8240 (mm) REVERT: F 1010 GLN cc_start: 0.9660 (OUTLIER) cc_final: 0.9343 (mp10) REVERT: F 1017 GLU cc_start: 0.9626 (tt0) cc_final: 0.9392 (tm-30) REVERT: F 1031 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8575 (pm20) REVERT: F 1039 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8252 (ptm160) outliers start: 155 outliers final: 100 residues processed: 289 average time/residue: 0.2162 time to fit residues: 106.6545 Evaluate side-chains 253 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 136 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1203 TRP Chi-restraints excluded: chain A residue 1327 PHE Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1498 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 1031 LYS Chi-restraints excluded: chain C residue 1091 LEU Chi-restraints excluded: chain C residue 1152 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1106 GLN Chi-restraints excluded: chain D residue 1130 ILE Chi-restraints excluded: chain D residue 1142 GLN Chi-restraints excluded: chain E residue 1032 PHE Chi-restraints excluded: chain E residue 1227 GLU Chi-restraints excluded: chain E residue 1324 THR Chi-restraints excluded: chain E residue 1331 SER Chi-restraints excluded: chain E residue 1339 VAL Chi-restraints excluded: chain E residue 1400 PHE Chi-restraints excluded: chain E residue 1401 HIS Chi-restraints excluded: chain E residue 1485 VAL Chi-restraints excluded: chain E residue 1555 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 165 ASN Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 449 TYR Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 823 PHE Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 948 LEU Chi-restraints excluded: chain F residue 950 ASP Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain F residue 1031 GLU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1039 ARG Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 446 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 208 optimal weight: 30.0000 chunk 199 optimal weight: 40.0000 chunk 87 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 304 optimal weight: 0.4980 chunk 370 optimal weight: 9.9990 chunk 7 optimal weight: 50.0000 chunk 268 optimal weight: 10.0000 chunk 203 optimal weight: 30.0000 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1250 ASN ** A1378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.077098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.050572 restraints weight = 298295.101| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 6.74 r_work: 0.2928 rms_B_bonded: 6.44 restraints_weight: 2.0000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41145 Z= 0.187 Angle : 0.623 10.566 56086 Z= 0.302 Chirality : 0.044 0.320 6328 Planarity : 0.004 0.049 7152 Dihedral : 11.549 109.376 6606 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.54 % Allowed : 11.92 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 4893 helix: 1.58 (0.12), residues: 1810 sheet: -0.95 (0.19), residues: 708 loop : -0.56 (0.13), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 319 TYR 0.013 0.001 TYR E1385 PHE 0.014 0.001 PHE A1230 TRP 0.017 0.001 TRP A1165 HIS 0.007 0.001 HIS E1374 Details of bonding type rmsd covalent geometry : bond 0.00395 (41043) covalent geometry : angle 0.60862 (55825) SS BOND : bond 0.00271 ( 45) SS BOND : angle 1.19658 ( 90) hydrogen bonds : bond 0.04165 ( 1849) hydrogen bonds : angle 5.32941 ( 5232) link_BETA1-4 : bond 0.00638 ( 12) link_BETA1-4 : angle 2.44287 ( 36) link_NAG-ASN : bond 0.00449 ( 45) link_NAG-ASN : angle 2.37059 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 145 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1297 MET cc_start: 0.5061 (mmm) cc_final: 0.4424 (mtt) REVERT: B 242 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8914 (mp) REVERT: B 495 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.5753 (m-10) REVERT: B 560 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8281 (mm) REVERT: B 663 ASP cc_start: 0.9193 (m-30) cc_final: 0.8729 (m-30) REVERT: B 740 MET cc_start: 0.8809 (tpt) cc_final: 0.7989 (tpp) REVERT: B 773 GLU cc_start: 0.9212 (tt0) cc_final: 0.8834 (tp30) REVERT: B 780 GLU cc_start: 0.9470 (tt0) cc_final: 0.9087 (tp30) REVERT: B 900 MET cc_start: 0.9053 (mmm) cc_final: 0.8799 (mmt) REVERT: B 919 ASN cc_start: 0.9340 (m-40) cc_final: 0.9037 (t0) REVERT: B 1001 LEU cc_start: 0.9795 (OUTLIER) cc_final: 0.9519 (pp) REVERT: C 1123 MET cc_start: 0.2949 (ptt) cc_final: 0.2497 (ptt) REVERT: C 1360 MET cc_start: 0.3451 (ttm) cc_final: 0.3240 (ttm) REVERT: C 1579 MET cc_start: 0.5209 (mmt) cc_final: 0.4581 (mmt) REVERT: D 1001 LEU cc_start: 0.9785 (tt) cc_final: 0.9541 (pp) REVERT: D 1029 MET cc_start: 0.9194 (tpp) cc_final: 0.8994 (tpp) REVERT: D 1106 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8758 (mp10) REVERT: D 1111 GLU cc_start: 0.9413 (tt0) cc_final: 0.8511 (tm-30) REVERT: E 13 MET cc_start: -0.2558 (mmt) cc_final: -0.2972 (ttt) REVERT: E 1123 MET cc_start: 0.8750 (mmm) cc_final: 0.8302 (mmm) REVERT: E 1332 MET cc_start: 0.9387 (ptt) cc_final: 0.7656 (ppp) REVERT: E 1366 MET cc_start: 0.8775 (mmm) cc_final: 0.8520 (mmm) REVERT: E 1462 MET cc_start: 0.8571 (ptp) cc_final: 0.8316 (ptm) REVERT: E 1557 MET cc_start: 0.9466 (ppp) cc_final: 0.9125 (ppp) REVERT: F 63 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7028 (m) REVERT: F 117 LEU cc_start: 0.9414 (tp) cc_final: 0.8965 (mm) REVERT: F 118 LEU cc_start: 0.9670 (tt) cc_final: 0.9235 (mp) REVERT: F 223 LEU cc_start: 0.8686 (tp) cc_final: 0.8421 (tp) REVERT: F 297 SER cc_start: 0.9124 (m) cc_final: 0.8622 (p) REVERT: F 449 TYR cc_start: 0.9419 (OUTLIER) cc_final: 0.9167 (m-80) REVERT: F 495 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: F 560 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9069 (mm) REVERT: F 786 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8532 (mmmt) REVERT: F 823 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: F 900 MET cc_start: 0.9372 (mmm) cc_final: 0.9142 (mmt) REVERT: F 984 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8330 (mm) REVERT: F 1010 GLN cc_start: 0.9667 (OUTLIER) cc_final: 0.9364 (mp10) REVERT: F 1017 GLU cc_start: 0.9640 (tt0) cc_final: 0.9400 (tm-30) REVERT: F 1031 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8549 (pm20) REVERT: F 1039 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8181 (ptm160) outliers start: 153 outliers final: 101 residues processed: 289 average time/residue: 0.2056 time to fit residues: 104.2032 Evaluate side-chains 252 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 136 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1203 TRP Chi-restraints excluded: chain A residue 1327 PHE Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1498 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 1031 LYS Chi-restraints excluded: chain C residue 1091 LEU Chi-restraints excluded: chain C residue 1203 TRP Chi-restraints excluded: chain C residue 1359 LEU Chi-restraints excluded: chain C residue 1367 ASP Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 379 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 676 THR Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1106 GLN Chi-restraints excluded: chain D residue 1130 ILE Chi-restraints excluded: chain E residue 1227 GLU Chi-restraints excluded: chain E residue 1231 GLU Chi-restraints excluded: chain E residue 1324 THR Chi-restraints excluded: chain E residue 1331 SER Chi-restraints excluded: chain E residue 1339 VAL Chi-restraints excluded: chain E residue 1400 PHE Chi-restraints excluded: chain E residue 1401 HIS Chi-restraints excluded: chain E residue 1485 VAL Chi-restraints excluded: chain E residue 1555 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 165 ASN Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 449 TYR Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 823 PHE Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 950 ASP Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain F residue 1031 GLU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1039 ARG Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 225 optimal weight: 4.9990 chunk 295 optimal weight: 0.9980 chunk 231 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 367 optimal weight: 30.0000 chunk 213 optimal weight: 20.0000 chunk 460 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN ** E1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 957 GLN ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.077591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.050745 restraints weight = 298776.228| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 7.04 r_work: 0.2976 rms_B_bonded: 6.31 restraints_weight: 2.0000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41145 Z= 0.141 Angle : 0.599 10.987 56086 Z= 0.289 Chirality : 0.043 0.317 6328 Planarity : 0.004 0.049 7152 Dihedral : 10.902 106.918 6604 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.15 % Allowed : 12.85 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.12), residues: 4893 helix: 1.66 (0.12), residues: 1805 sheet: -0.90 (0.19), residues: 692 loop : -0.55 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1582 TYR 0.018 0.001 TYR A1050 PHE 0.015 0.001 PHE A1369 TRP 0.017 0.001 TRP E1165 HIS 0.007 0.001 HIS E1374 Details of bonding type rmsd covalent geometry : bond 0.00302 (41043) covalent geometry : angle 0.58376 (55825) SS BOND : bond 0.00321 ( 45) SS BOND : angle 1.25567 ( 90) hydrogen bonds : bond 0.03943 ( 1849) hydrogen bonds : angle 5.18850 ( 5232) link_BETA1-4 : bond 0.00704 ( 12) link_BETA1-4 : angle 2.46796 ( 36) link_NAG-ASN : bond 0.00377 ( 45) link_NAG-ASN : angle 2.33599 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 151 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1297 MET cc_start: 0.5469 (mmm) cc_final: 0.4755 (mtt) REVERT: B 242 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8788 (mp) REVERT: B 495 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.5804 (m-10) REVERT: B 560 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 663 ASP cc_start: 0.9150 (m-30) cc_final: 0.8681 (m-30) REVERT: B 740 MET cc_start: 0.8731 (tpt) cc_final: 0.7963 (tpp) REVERT: B 773 GLU cc_start: 0.9184 (tt0) cc_final: 0.8807 (tp30) REVERT: B 780 GLU cc_start: 0.9465 (tt0) cc_final: 0.9074 (tp30) REVERT: B 900 MET cc_start: 0.8970 (mmm) cc_final: 0.8752 (mmt) REVERT: B 902 MET cc_start: 0.9332 (tpp) cc_final: 0.9119 (mmt) REVERT: B 919 ASN cc_start: 0.9335 (m-40) cc_final: 0.8999 (t0) REVERT: B 1029 MET cc_start: 0.9165 (tpp) cc_final: 0.8720 (ttp) REVERT: C 1123 MET cc_start: 0.2779 (ptt) cc_final: 0.2342 (ptt) REVERT: C 1360 MET cc_start: 0.3702 (ttm) cc_final: 0.3330 (ttm) REVERT: C 1579 MET cc_start: 0.5439 (mmt) cc_final: 0.4826 (mmt) REVERT: D 762 GLN cc_start: 0.9571 (tp40) cc_final: 0.9201 (tp40) REVERT: D 773 GLU cc_start: 0.9326 (tp30) cc_final: 0.8962 (tp30) REVERT: D 1001 LEU cc_start: 0.9775 (tt) cc_final: 0.9527 (pp) REVERT: D 1111 GLU cc_start: 0.9408 (tt0) cc_final: 0.8623 (tm-30) REVERT: E 13 MET cc_start: -0.2544 (mmt) cc_final: -0.3034 (ttt) REVERT: E 1062 MET cc_start: 0.9779 (mmm) cc_final: 0.9544 (mmm) REVERT: E 1123 MET cc_start: 0.8816 (mmm) cc_final: 0.8328 (mmm) REVERT: E 1197 GLU cc_start: 0.9424 (pt0) cc_final: 0.9153 (tm-30) REVERT: E 1332 MET cc_start: 0.9491 (ptt) cc_final: 0.7825 (ppp) REVERT: E 1462 MET cc_start: 0.8518 (ptp) cc_final: 0.8219 (ptm) REVERT: E 1557 MET cc_start: 0.9485 (ppp) cc_final: 0.9226 (ppp) REVERT: E 1579 MET cc_start: 0.6557 (pmm) cc_final: 0.6184 (pmm) REVERT: F 63 THR cc_start: 0.7621 (OUTLIER) cc_final: 0.7334 (p) REVERT: F 117 LEU cc_start: 0.9286 (tp) cc_final: 0.8862 (mm) REVERT: F 118 LEU cc_start: 0.9569 (tt) cc_final: 0.9106 (mp) REVERT: F 223 LEU cc_start: 0.8479 (tp) cc_final: 0.8238 (tp) REVERT: F 297 SER cc_start: 0.9080 (m) cc_final: 0.8586 (p) REVERT: F 449 TYR cc_start: 0.9429 (OUTLIER) cc_final: 0.9208 (m-80) REVERT: F 495 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: F 560 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9073 (mm) REVERT: F 786 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8552 (mmmt) REVERT: F 823 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8783 (m-80) REVERT: F 900 MET cc_start: 0.9337 (mmm) cc_final: 0.9099 (mmt) REVERT: F 984 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8221 (mm) REVERT: F 1010 GLN cc_start: 0.9598 (OUTLIER) cc_final: 0.9309 (mp10) REVERT: F 1017 GLU cc_start: 0.9608 (tt0) cc_final: 0.9360 (tm-30) REVERT: F 1031 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: F 1039 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8092 (ptm160) outliers start: 136 outliers final: 86 residues processed: 276 average time/residue: 0.2167 time to fit residues: 104.4519 Evaluate side-chains 247 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 148 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1203 TRP Chi-restraints excluded: chain A residue 1327 PHE Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1498 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 1031 LYS Chi-restraints excluded: chain C residue 1055 THR Chi-restraints excluded: chain C residue 1203 TRP Chi-restraints excluded: chain C residue 1283 VAL Chi-restraints excluded: chain C residue 1359 LEU Chi-restraints excluded: chain C residue 1367 ASP Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 379 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 676 THR Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1130 ILE Chi-restraints excluded: chain E residue 1227 GLU Chi-restraints excluded: chain E residue 1324 THR Chi-restraints excluded: chain E residue 1331 SER Chi-restraints excluded: chain E residue 1339 VAL Chi-restraints excluded: chain E residue 1400 PHE Chi-restraints excluded: chain E residue 1401 HIS Chi-restraints excluded: chain E residue 1485 VAL Chi-restraints excluded: chain E residue 1555 PHE Chi-restraints excluded: chain E residue 1604 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 165 ASN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 449 TYR Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 823 PHE Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 950 ASP Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain F residue 1031 GLU Chi-restraints excluded: chain F residue 1039 ARG Chi-restraints excluded: chain F residue 1065 VAL Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3886 > 50: distance: 14 - 18: 8.648 distance: 18 - 19: 7.718 distance: 19 - 20: 9.617 distance: 19 - 22: 11.373 distance: 20 - 21: 18.444 distance: 20 - 26: 32.911 distance: 22 - 23: 7.646 distance: 23 - 24: 9.780 distance: 23 - 25: 5.264 distance: 26 - 27: 3.105 distance: 27 - 28: 10.209 distance: 27 - 30: 16.879 distance: 28 - 29: 11.893 distance: 28 - 37: 12.405 distance: 30 - 31: 18.306 distance: 31 - 32: 8.908 distance: 31 - 33: 6.876 distance: 32 - 34: 19.122 distance: 33 - 35: 11.268 distance: 34 - 36: 7.055 distance: 35 - 36: 6.865 distance: 37 - 38: 4.692 distance: 38 - 41: 8.506 distance: 39 - 40: 11.559 distance: 39 - 48: 22.591 distance: 41 - 42: 15.310 distance: 42 - 43: 25.529 distance: 43 - 44: 14.267 distance: 44 - 45: 15.098 distance: 45 - 46: 22.517 distance: 45 - 47: 4.243 distance: 48 - 49: 11.306 distance: 49 - 50: 11.120 distance: 49 - 52: 14.103 distance: 50 - 51: 17.076 distance: 50 - 55: 11.949 distance: 52 - 53: 30.425 distance: 52 - 54: 15.967 distance: 55 - 56: 34.304 distance: 56 - 57: 23.135 distance: 56 - 59: 7.611 distance: 57 - 58: 5.178 distance: 57 - 64: 14.510 distance: 59 - 60: 15.106 distance: 60 - 61: 37.472 distance: 61 - 62: 18.083 distance: 61 - 63: 22.054 distance: 64 - 65: 8.516 distance: 64 - 70: 22.515 distance: 65 - 66: 12.915 distance: 65 - 68: 12.603 distance: 66 - 67: 10.260 distance: 66 - 71: 8.345 distance: 68 - 69: 14.378 distance: 69 - 70: 19.766 distance: 71 - 72: 3.816 distance: 72 - 73: 8.951 distance: 72 - 75: 13.230 distance: 73 - 74: 29.152 distance: 73 - 78: 6.629 distance: 75 - 76: 32.140 distance: 75 - 77: 33.649 distance: 78 - 79: 15.501 distance: 79 - 80: 21.876 distance: 79 - 82: 28.083 distance: 80 - 81: 11.474 distance: 80 - 87: 16.639 distance: 82 - 83: 16.645 distance: 83 - 84: 9.674 distance: 84 - 85: 25.938 distance: 84 - 86: 14.688 distance: 87 - 88: 8.978 distance: 88 - 89: 12.686 distance: 88 - 91: 12.295 distance: 89 - 90: 7.202 distance: 89 - 93: 9.203 distance: 91 - 92: 14.888 distance: 93 - 94: 8.768 distance: 93 - 141: 6.655 distance: 94 - 95: 4.061 distance: 94 - 97: 3.258 distance: 95 - 101: 4.342 distance: 96 - 151: 6.973 distance: 97 - 98: 5.115 distance: 98 - 100: 8.357