Starting phenix.real_space_refine on Fri Mar 6 08:42:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oca_12802/03_2026/7oca_12802.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oca_12802/03_2026/7oca_12802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oca_12802/03_2026/7oca_12802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oca_12802/03_2026/7oca_12802.map" model { file = "/net/cci-nas-00/data/ceres_data/7oca_12802/03_2026/7oca_12802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oca_12802/03_2026/7oca_12802.cif" } resolution = 3.4 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= 0.000 sd= 0.004 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 150 5.16 5 C 19268 2.51 5 N 4660 2.21 5 O 5216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 268 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29294 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5637 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 747} Chain breaks: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 659 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 12, 'GLN:plan1': 12, 'ARG:plan': 16, 'GLU:plan': 22, 'ASP:plan': 19, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 333 Chain: "B" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5815 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 3 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 6, 'GLN:plan1': 6, 'ARG:plan': 7, 'ASP:plan': 12, 'GLU:plan': 22} Unresolved non-hydrogen planarities: 201 Chain: "G" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1248 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "I" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1284 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5815 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 3 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 6, 'GLN:plan1': 6, 'ARG:plan': 7, 'ASP:plan': 12, 'GLU:plan': 22} Unresolved non-hydrogen planarities: 201 Chain: "J" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1284 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5637 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 747} Chain breaks: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 659 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 12, 'GLN:plan1': 12, 'ARG:plan': 16, 'GLU:plan': 22, 'ASP:plan': 19, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 333 Chain: "E" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1248 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 170 Unusual residues: {'E2Q': 1, 'NAG': 2, 'PC1': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PC1:plan-2': 5, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 216 Unusual residues: {'E2Q': 1, 'NAG': 1, 'PC1': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'CLR': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PC1': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 216 Unusual residues: {'E2Q': 1, 'NAG': 1, 'PC1': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PC1': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 170 Unusual residues: {'E2Q': 1, 'NAG': 2, 'PC1': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PC1:plan-2': 5, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'CLR': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 6.70, per 1000 atoms: 0.23 Number of scatterers: 29294 At special positions: 0 Unit cell: (133.75, 126.26, 224.7, 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 150 16.00 O 5216 8.00 N 4660 7.00 C 19268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.05 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.05 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 F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 902 " - " ASN A 231 " " NAG A 903 " - " ASN A 239 " " NAG B2903 " - " ASN B 349 " " NAG C2703 " - " ASN C 231 " " NAG C2704 " - " ASN C 239 " " NAG D 902 " - " ASN D 349 " " NAG F 1 " - " ASN A 45 " " NAG H 1 " - " ASN A 345 " " NAG K 1 " - " ASN B 235 " " NAG L 1 " - " ASN D 235 " " NAG M 1 " - " ASN C 45 " " NAG N 1 " - " ASN C 345 " Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 37 sheets defined 53.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.676A pdb=" N LEU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 Processing helix chain 'A' and resid 72 through 86 removed outlier: 4.779A pdb=" N ASN A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N MET A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.734A pdb=" N ARG A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.656A pdb=" N LYS A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 4.002A pdb=" N ASN A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 242 through 259 Processing helix chain 'A' and resid 269 through 293 removed outlier: 3.554A pdb=" N VAL A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.871A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 4.080A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 626 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.523A pdb=" N GLN A 638 " --> pdb=" O ASP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.547A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 739 through 753 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 820 removed outlier: 3.623A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 31 removed outlier: 4.177A pdb=" N TYR B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.535A pdb=" N GLU B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'B' and resid 166 through 181 removed outlier: 3.817A pdb=" N THR B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 removed outlier: 4.106A pdb=" N GLN B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.681A pdb=" N THR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 297 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.774A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.607A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 822 removed outlier: 3.720A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 40 removed outlier: 3.846A pdb=" N ALA G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN G 40 " --> pdb=" O THR G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 67 Processing helix chain 'G' and resid 67 through 85 removed outlier: 4.228A pdb=" N GLU G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 108 Proline residue: G 96 - end of helix removed outlier: 4.054A pdb=" N ARG G 108 " --> pdb=" O ARG G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 159 Processing helix chain 'I' and resid 17 through 41 Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 128 through 149 Processing helix chain 'I' and resid 157 through 184 removed outlier: 3.596A pdb=" N GLY I 162 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA I 184 " --> pdb=" O ILE I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 240 removed outlier: 3.543A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 31 removed outlier: 4.178A pdb=" N TYR D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 75 through 87 Processing helix chain 'D' and resid 111 through 122 removed outlier: 3.535A pdb=" N GLU D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 151 Processing helix chain 'D' and resid 166 through 181 removed outlier: 3.818A pdb=" N THR D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 removed outlier: 4.107A pdb=" N GLN D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 removed outlier: 3.680A pdb=" N THR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 297 Processing helix chain 'D' and resid 319 through 329 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.774A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.606A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 822 removed outlier: 3.721A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 41 Processing helix chain 'J' and resid 116 through 128 Processing helix chain 'J' and resid 128 through 149 Processing helix chain 'J' and resid 157 through 184 removed outlier: 3.597A pdb=" N GLY J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA J 184 " --> pdb=" O ILE J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 240 removed outlier: 3.543A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.676A pdb=" N LEU C 28 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 63 Processing helix chain 'C' and resid 72 through 86 removed outlier: 4.779A pdb=" N ASN C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N MET C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.735A pdb=" N ARG C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 3.657A pdb=" N LYS C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 201 removed outlier: 4.002A pdb=" N ASN C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 201 " --> pdb=" O GLN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 242 through 259 Processing helix chain 'C' and resid 269 through 293 removed outlier: 3.554A pdb=" N VAL C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 326 Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.871A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 484 removed outlier: 4.079A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 626 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.524A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 removed outlier: 3.547A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 670 Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 739 through 753 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 788 through 820 removed outlier: 3.622A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 40 removed outlier: 3.846A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 67 Processing helix chain 'E' and resid 67 through 85 removed outlier: 4.228A pdb=" N GLU E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 108 Proline residue: E 96 - end of helix removed outlier: 4.054A pdb=" N ARG E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 159 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.062A pdb=" N LYS A 36 " --> pdb=" O ILE A 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.639A pdb=" N ILE A 67 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 158 removed outlier: 7.237A pdb=" N PHE A 127 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL A 157 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR A 129 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR A 126 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL A 183 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 128 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASP A 185 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE A 130 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN A 231 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 235 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 232 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 348 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR A 363 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 350 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 357 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 329 removed outlier: 3.580A pdb=" N PHE A 328 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.868A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.868A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.497A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 36 through 44 removed outlier: 3.896A pdb=" N ILE B 6 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N ALA B 66 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN B 7 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N PHE B 68 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY B 9 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 67 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE B 90 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 158 removed outlier: 7.739A pdb=" N LYS B 126 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ILE B 187 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA B 128 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP B 189 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 130 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B 239 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL B 236 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 366 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU B 356 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS B 364 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS B 358 " --> pdb=" O PRO B 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.993A pdb=" N LYS B 340 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.610A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB8, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.844A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.408A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 100 through 102 removed outlier: 3.632A pdb=" N LEU I 45 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 36 through 44 removed outlier: 3.897A pdb=" N ILE D 6 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N ALA D 66 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN D 7 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N PHE D 68 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY D 9 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE D 67 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE D 90 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 158 removed outlier: 7.741A pdb=" N LYS D 126 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ILE D 187 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA D 128 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP D 189 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU D 130 " --> pdb=" O ASP D 189 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE D 239 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL D 236 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D 366 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU D 356 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS D 364 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS D 358 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 332 through 333 removed outlier: 3.995A pdb=" N LYS D 340 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC6, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.610A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC8, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.844A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.405A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 100 through 102 removed outlier: 3.633A pdb=" N LEU J 45 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 6 through 8 removed outlier: 6.063A pdb=" N LYS C 36 " --> pdb=" O ILE C 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AD4, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.639A pdb=" N ILE C 67 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 153 through 158 removed outlier: 7.239A pdb=" N PHE C 127 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL C 157 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 129 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR C 126 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL C 183 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 128 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASP C 185 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE C 130 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN C 231 " --> pdb=" O TYR C 208 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE C 235 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 232 " --> pdb=" O MET C 353 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 348 " --> pdb=" O TYR C 363 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR C 363 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL C 350 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 357 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 328 through 329 removed outlier: 3.582A pdb=" N PHE C 328 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 436 through 438 removed outlier: 4.867A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 436 through 438 removed outlier: 4.867A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AE1, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.496A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) 1661 hydrogen bonds defined for protein. 4881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4498 1.31 - 1.45: 8491 1.45 - 1.58: 16685 1.58 - 1.71: 8 1.71 - 1.84: 222 Bond restraints: 29904 Sorted by residual: bond pdb=" C09 E2Q C2702 " pdb=" S11 E2Q C2702 " ideal model delta sigma weight residual 1.799 1.691 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C09 E2Q D 901 " pdb=" S11 E2Q D 901 " ideal model delta sigma weight residual 1.799 1.691 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C09 E2Q A 901 " pdb=" S11 E2Q A 901 " ideal model delta sigma weight residual 1.799 1.692 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C09 E2Q B2902 " pdb=" S11 E2Q B2902 " ideal model delta sigma weight residual 1.799 1.692 0.107 2.00e-02 2.50e+03 2.88e+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 1.29e+01 ... (remaining 29899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.08: 40435 6.08 - 12.16: 53 12.16 - 18.24: 0 18.24 - 24.32: 0 24.32 - 30.40: 2 Bond angle restraints: 40490 Sorted by residual: angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 143.10 -30.40 3.00e+00 1.11e-01 1.03e+02 angle pdb=" CB MET A 52 " pdb=" CG MET A 52 " pdb=" SD MET A 52 " ideal model delta sigma weight residual 112.70 143.05 -30.35 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C32 PC1 C2709 " pdb=" C31 PC1 C2709 " pdb=" O31 PC1 C2709 " ideal model delta sigma weight residual 111.44 120.99 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C32 PC1 A 908 " pdb=" C31 PC1 A 908 " pdb=" O31 PC1 A 908 " ideal model delta sigma weight residual 111.44 120.96 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C22 PC1 D 904 " pdb=" C21 PC1 D 904 " pdb=" O21 PC1 D 904 " ideal model delta sigma weight residual 111.12 120.41 -9.29 3.00e+00 1.11e-01 9.59e+00 ... (remaining 40485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 16549 23.04 - 46.07: 1035 46.07 - 69.11: 152 69.11 - 92.14: 61 92.14 - 115.18: 49 Dihedral angle restraints: 17846 sinusoidal: 6862 harmonic: 10984 Sorted by residual: dihedral pdb=" CB CYS I 52 " pdb=" SG CYS I 52 " pdb=" SG CYS I 91 " pdb=" CB CYS I 91 " ideal model delta sinusoidal sigma weight residual -86.00 -163.21 77.21 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CB CYS J 52 " pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " pdb=" CB CYS J 91 " ideal model delta sinusoidal sigma weight residual -86.00 -163.18 77.18 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual -86.00 -34.84 -51.16 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 17843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3628 0.052 - 0.105: 906 0.105 - 0.157: 116 0.157 - 0.210: 0 0.210 - 0.262: 6 Chirality restraints: 4656 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.98e+00 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.81e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 4653 not shown) Planarity restraints: 4998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 152 " -0.021 2.00e-02 2.50e+03 1.69e-02 7.14e+00 pdb=" CG TRP C 152 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 152 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 152 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 152 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 152 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 152 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 152 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 152 " 0.021 2.00e-02 2.50e+03 1.68e-02 7.03e+00 pdb=" CG TRP A 152 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 152 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 152 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 152 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 152 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 152 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 152 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 702 " 0.016 2.00e-02 2.50e+03 1.51e-02 4.56e+00 pdb=" CG TYR B 702 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 702 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 702 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 702 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 702 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 702 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 702 " 0.001 2.00e-02 2.50e+03 ... (remaining 4995 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 305 2.64 - 3.21: 27768 3.21 - 3.77: 43244 3.77 - 4.34: 59857 4.34 - 4.90: 101582 Nonbonded interactions: 232756 Sorted by model distance: nonbonded pdb=" OG1 THR D 398 " pdb=" OE2 GLU D 466 " model vdw 2.080 3.040 nonbonded pdb=" N LYS B 716 " pdb=" OE1 GLU B 772 " model vdw 2.101 3.120 nonbonded pdb=" N LYS D 716 " pdb=" OE1 GLU D 772 " model vdw 2.101 3.120 nonbonded pdb=" OG SER B 635 " pdb=" OD1 ASP B 638 " model vdw 2.121 3.040 nonbonded pdb=" OG SER D 635 " pdb=" OD1 ASP D 638 " model vdw 2.121 3.040 ... (remaining 232751 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 820 or resid 903 or (resid 905 through 907 and ( \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C2A or name C2B or name C2C or name C2D or name \ C2E or name C2F or name C2G or name O21 or name O22)))) selection = (chain 'C' and (resid 3 through 820 or resid 2703 or (resid 2705 through 2707 an \ d (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C2A or name C2B or name C2C or name C2D or n \ ame C2E or name C2F or name C2G or name O21 or name O22)))) } ncs_group { reference = (chain 'B' and (resid 4 through 823 or resid 2904 through 2907 or (resid 2908 an \ d (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C2A or name C2B or name C2C or name C2D or n \ ame C2E or name C2F or name C2G or name O21 or name O22)) or resid 2911)) selection = (chain 'D' and (resid 4 through 823 or (resid 904 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name O21 or name \ O22)) or resid 905 through 908 or resid 911)) } ncs_group { reference = (chain 'E' and (resid 2 through 3101 or (resid 3102 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or nam \ e C2G or name O21 or name O22)) or resid 3103 through 3104)) selection = (chain 'G' and (resid 2 through 159 or (resid 3101 through 3102 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or nam \ e C2F or name C2G or name O21 or name O22)) or resid 3103 through 3104)) } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = (chain 'I' and (resid 16 through 3003 or (resid 3004 through 3005 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or n \ ame C2F or name C2G or name O21 or name O22)))) selection = (chain 'J' and (resid 16 through 240 or (resid 2501 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or nam \ e C2G or name O21 or name O22)) or resid 2502 through 2505)) } 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.660 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.009 0.108 29936 Z= 0.358 Angle : 0.891 30.396 40574 Z= 0.396 Chirality : 0.044 0.262 4656 Planarity : 0.004 0.049 4986 Dihedral : 16.989 115.180 10778 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.15 % Allowed : 0.61 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.20 (0.14), residues: 3746 helix: 1.49 (0.12), residues: 1926 sheet: -1.07 (0.26), residues: 380 loop : -1.41 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 14 TYR 0.037 0.002 TYR B 702 PHE 0.033 0.002 PHE C 82 TRP 0.046 0.002 TRP C 152 HIS 0.016 0.002 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00859 (29904) covalent geometry : angle 0.88596 (40490) SS BOND : bond 0.00795 ( 12) SS BOND : angle 2.09395 ( 24) hydrogen bonds : bond 0.13613 ( 1647) hydrogen bonds : angle 5.45186 ( 4881) link_BETA1-4 : bond 0.00777 ( 8) link_BETA1-4 : angle 2.42353 ( 24) link_NAG-ASN : bond 0.00860 ( 12) link_NAG-ASN : angle 2.15702 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 346 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 GLU cc_start: 0.7103 (tp30) cc_final: 0.6877 (tp30) REVERT: B 463 MET cc_start: 0.8264 (mtm) cc_final: 0.8045 (mtp) REVERT: C 482 GLU cc_start: 0.7133 (tp30) cc_final: 0.6894 (tp30) outliers start: 4 outliers final: 3 residues processed: 346 average time/residue: 0.1867 time to fit residues: 102.3936 Evaluate side-chains 256 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain C residue 52 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS B 284 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN D 106 GLN D 284 GLN D 329 GLN D 756 GLN C 209 HIS E 27 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127479 restraints weight = 40443.525| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.45 r_work: 0.3109 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29936 Z= 0.122 Angle : 0.552 10.251 40574 Z= 0.277 Chirality : 0.042 0.220 4656 Planarity : 0.004 0.042 4986 Dihedral : 13.023 84.778 5413 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.80 % Allowed : 5.28 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.24 (0.14), residues: 3746 helix: 2.38 (0.12), residues: 1938 sheet: -0.64 (0.24), residues: 412 loop : -0.99 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 65 TYR 0.020 0.001 TYR A 363 PHE 0.014 0.001 PHE C 217 TRP 0.031 0.001 TRP A 152 HIS 0.006 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00251 (29904) covalent geometry : angle 0.54499 (40490) SS BOND : bond 0.00350 ( 12) SS BOND : angle 0.75875 ( 24) hydrogen bonds : bond 0.03984 ( 1647) hydrogen bonds : angle 3.99244 ( 4881) link_BETA1-4 : bond 0.00630 ( 8) link_BETA1-4 : angle 2.38857 ( 24) link_NAG-ASN : bond 0.00448 ( 12) link_NAG-ASN : angle 2.22458 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8569 (mt) cc_final: 0.8348 (mt) REVERT: A 482 GLU cc_start: 0.7385 (tp30) cc_final: 0.7176 (tp30) REVERT: B 36 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.7076 (ptt180) REVERT: B 355 MET cc_start: 0.8339 (mtp) cc_final: 0.8103 (mtt) REVERT: C 482 GLU cc_start: 0.7393 (tp30) cc_final: 0.7184 (tp30) REVERT: C 499 MET cc_start: 0.8872 (ttm) cc_final: 0.8607 (ttp) outliers start: 21 outliers final: 13 residues processed: 291 average time/residue: 0.1841 time to fit residues: 85.2716 Evaluate side-chains 268 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 255 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain C residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 230 optimal weight: 10.0000 chunk 357 optimal weight: 8.9990 chunk 196 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 18 GLN B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 HIS ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN C 141 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113800 restraints weight = 41280.261| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.71 r_work: 0.2914 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29936 Z= 0.225 Angle : 0.604 11.846 40574 Z= 0.302 Chirality : 0.044 0.225 4656 Planarity : 0.004 0.050 4986 Dihedral : 11.350 74.483 5404 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.48 % Allowed : 8.24 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.11 (0.14), residues: 3746 helix: 2.17 (0.11), residues: 1964 sheet: -0.46 (0.24), residues: 420 loop : -1.04 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 65 TYR 0.025 0.002 TYR B 71 PHE 0.016 0.002 PHE A 127 TRP 0.032 0.002 TRP C 152 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00542 (29904) covalent geometry : angle 0.59605 (40490) SS BOND : bond 0.00451 ( 12) SS BOND : angle 0.77685 ( 24) hydrogen bonds : bond 0.04612 ( 1647) hydrogen bonds : angle 3.93031 ( 4881) link_BETA1-4 : bond 0.00418 ( 8) link_BETA1-4 : angle 2.31209 ( 24) link_NAG-ASN : bond 0.00660 ( 12) link_NAG-ASN : angle 2.83792 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.7993 (tmm) cc_final: 0.7658 (tmm) REVERT: A 462 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7795 (mm-30) REVERT: A 499 MET cc_start: 0.8995 (ttm) cc_final: 0.8729 (ttp) REVERT: A 581 MET cc_start: 0.9326 (mmt) cc_final: 0.8957 (mmt) REVERT: B 463 MET cc_start: 0.8720 (mtp) cc_final: 0.8516 (mtp) REVERT: G 65 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7776 (ttm110) REVERT: C 52 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7988 (mtp) REVERT: C 195 LEU cc_start: 0.8327 (mt) cc_final: 0.8024 (mt) REVERT: C 462 GLU cc_start: 0.8062 (mp0) cc_final: 0.7823 (mm-30) REVERT: E 65 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7700 (ttm110) outliers start: 39 outliers final: 31 residues processed: 297 average time/residue: 0.2066 time to fit residues: 95.9327 Evaluate side-chains 278 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 484 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 217 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 375 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 309 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 206 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 257 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 329 GLN ** D 331 GLN ** 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 = 0.3763 r_free = 0.3763 target = 0.147959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117537 restraints weight = 40527.034| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.64 r_work: 0.2970 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29936 Z= 0.112 Angle : 0.500 8.905 40574 Z= 0.250 Chirality : 0.040 0.163 4656 Planarity : 0.003 0.041 4986 Dihedral : 10.191 71.929 5404 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.29 % Allowed : 9.07 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.52 (0.14), residues: 3746 helix: 2.56 (0.12), residues: 1966 sheet: -0.33 (0.25), residues: 414 loop : -0.92 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 815 TYR 0.021 0.001 TYR A 812 PHE 0.013 0.001 PHE A 26 TRP 0.022 0.001 TRP A 152 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00249 (29904) covalent geometry : angle 0.48978 (40490) SS BOND : bond 0.00264 ( 12) SS BOND : angle 0.72408 ( 24) hydrogen bonds : bond 0.03619 ( 1647) hydrogen bonds : angle 3.67228 ( 4881) link_BETA1-4 : bond 0.00532 ( 8) link_BETA1-4 : angle 2.15250 ( 24) link_NAG-ASN : bond 0.00391 ( 12) link_NAG-ASN : angle 2.95020 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 MET cc_start: 0.7923 (tmm) cc_final: 0.7553 (tmm) REVERT: A 499 MET cc_start: 0.8941 (ttm) cc_final: 0.8573 (ttp) REVERT: B 527 MET cc_start: 0.8989 (mmm) cc_final: 0.8727 (mmt) REVERT: B 682 PHE cc_start: 0.7606 (m-10) cc_final: 0.7365 (m-10) REVERT: G 35 ARG cc_start: 0.5897 (OUTLIER) cc_final: 0.5687 (tpt170) REVERT: D 527 MET cc_start: 0.8970 (mmm) cc_final: 0.8698 (mmt) REVERT: C 195 LEU cc_start: 0.8302 (mt) cc_final: 0.8018 (mt) REVERT: C 499 MET cc_start: 0.8926 (ttm) cc_final: 0.8625 (ttp) outliers start: 34 outliers final: 20 residues processed: 297 average time/residue: 0.1805 time to fit residues: 86.5247 Evaluate side-chains 273 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain C residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 244 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 300 optimal weight: 10.0000 chunk 351 optimal weight: 7.9990 chunk 345 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 335 optimal weight: 0.9980 chunk 372 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN D 106 GLN D 284 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114885 restraints weight = 41135.220| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.68 r_work: 0.2908 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29936 Z= 0.205 Angle : 0.549 9.842 40574 Z= 0.278 Chirality : 0.041 0.180 4656 Planarity : 0.004 0.044 4986 Dihedral : 10.086 69.373 5404 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.59 % Allowed : 10.29 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.31 (0.14), residues: 3746 helix: 2.33 (0.11), residues: 1970 sheet: -0.37 (0.25), residues: 410 loop : -0.95 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 65 TYR 0.022 0.002 TYR A 812 PHE 0.016 0.002 PHE B 127 TRP 0.023 0.001 TRP C 152 HIS 0.006 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00493 (29904) covalent geometry : angle 0.54032 (40490) SS BOND : bond 0.00338 ( 12) SS BOND : angle 0.81120 ( 24) hydrogen bonds : bond 0.04181 ( 1647) hydrogen bonds : angle 3.76298 ( 4881) link_BETA1-4 : bond 0.00361 ( 8) link_BETA1-4 : angle 2.34067 ( 24) link_NAG-ASN : bond 0.00607 ( 12) link_NAG-ASN : angle 2.80299 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 MET cc_start: 0.8033 (tmm) cc_final: 0.7631 (tmm) REVERT: A 499 MET cc_start: 0.8941 (ttm) cc_final: 0.8584 (ttp) REVERT: G 65 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7787 (ttm110) REVERT: C 499 MET cc_start: 0.8946 (ttm) cc_final: 0.8655 (ttp) outliers start: 42 outliers final: 33 residues processed: 292 average time/residue: 0.1952 time to fit residues: 90.3422 Evaluate side-chains 273 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 120 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 258 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 349 optimal weight: 10.0000 chunk 310 optimal weight: 0.0770 chunk 150 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 329 GLN ** D 331 GLN ** 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 = 0.3758 r_free = 0.3758 target = 0.147526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115169 restraints weight = 40625.201| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.61 r_work: 0.2965 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29936 Z= 0.106 Angle : 0.480 7.578 40574 Z= 0.243 Chirality : 0.039 0.148 4656 Planarity : 0.003 0.040 4986 Dihedral : 9.444 65.508 5404 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.03 % Allowed : 11.58 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.63 (0.14), residues: 3746 helix: 2.63 (0.11), residues: 1970 sheet: -0.29 (0.24), residues: 421 loop : -0.85 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 657 TYR 0.020 0.001 TYR A 812 PHE 0.019 0.001 PHE A 26 TRP 0.017 0.001 TRP A 152 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00233 (29904) covalent geometry : angle 0.47098 (40490) SS BOND : bond 0.00186 ( 12) SS BOND : angle 0.57917 ( 24) hydrogen bonds : bond 0.03483 ( 1647) hydrogen bonds : angle 3.58400 ( 4881) link_BETA1-4 : bond 0.00497 ( 8) link_BETA1-4 : angle 2.19886 ( 24) link_NAG-ASN : bond 0.00299 ( 12) link_NAG-ASN : angle 2.59638 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8428 (t0) cc_final: 0.8159 (t0) REVERT: A 353 MET cc_start: 0.7886 (tmm) cc_final: 0.7477 (tmm) REVERT: A 499 MET cc_start: 0.8950 (ttm) cc_final: 0.8539 (ttp) REVERT: B 682 PHE cc_start: 0.7558 (m-10) cc_final: 0.7220 (m-10) REVERT: G 35 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5674 (tpt170) REVERT: C 499 MET cc_start: 0.8901 (ttm) cc_final: 0.8552 (ttp) outliers start: 27 outliers final: 21 residues processed: 287 average time/residue: 0.1897 time to fit residues: 87.0103 Evaluate side-chains 268 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 365 optimal weight: 0.0770 chunk 65 optimal weight: 3.9990 chunk 348 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN C 349 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114375 restraints weight = 40875.099| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.73 r_work: 0.2929 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29936 Z= 0.143 Angle : 0.496 7.916 40574 Z= 0.251 Chirality : 0.039 0.149 4656 Planarity : 0.003 0.044 4986 Dihedral : 9.278 60.876 5404 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.44 % Allowed : 11.43 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.62 (0.14), residues: 3746 helix: 2.62 (0.11), residues: 1969 sheet: -0.28 (0.24), residues: 423 loop : -0.85 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 65 TYR 0.023 0.001 TYR C 812 PHE 0.029 0.001 PHE A 26 TRP 0.017 0.001 TRP A 152 HIS 0.004 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00335 (29904) covalent geometry : angle 0.48757 (40490) SS BOND : bond 0.00359 ( 12) SS BOND : angle 0.55942 ( 24) hydrogen bonds : bond 0.03682 ( 1647) hydrogen bonds : angle 3.59077 ( 4881) link_BETA1-4 : bond 0.00417 ( 8) link_BETA1-4 : angle 2.26867 ( 24) link_NAG-ASN : bond 0.00425 ( 12) link_NAG-ASN : angle 2.57010 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8473 (t0) cc_final: 0.8187 (t0) REVERT: A 353 MET cc_start: 0.7918 (tmm) cc_final: 0.7506 (tmm) REVERT: A 499 MET cc_start: 0.8958 (ttm) cc_final: 0.8545 (ttp) REVERT: C 499 MET cc_start: 0.8928 (ttm) cc_final: 0.8579 (ttp) outliers start: 38 outliers final: 29 residues processed: 282 average time/residue: 0.1943 time to fit residues: 87.4169 Evaluate side-chains 273 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 332 optimal weight: 0.0870 chunk 234 optimal weight: 0.8980 chunk 293 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 chunk 166 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN D 106 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116151 restraints weight = 40883.337| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.64 r_work: 0.2955 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29936 Z= 0.113 Angle : 0.479 7.794 40574 Z= 0.242 Chirality : 0.039 0.150 4656 Planarity : 0.003 0.042 4986 Dihedral : 8.964 59.562 5404 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.33 % Allowed : 11.58 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.71 (0.14), residues: 3746 helix: 2.71 (0.11), residues: 1972 sheet: -0.28 (0.24), residues: 422 loop : -0.83 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 65 TYR 0.023 0.001 TYR A 812 PHE 0.024 0.001 PHE A 26 TRP 0.016 0.001 TRP A 152 HIS 0.003 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00257 (29904) covalent geometry : angle 0.47039 (40490) SS BOND : bond 0.00396 ( 12) SS BOND : angle 0.52974 ( 24) hydrogen bonds : bond 0.03462 ( 1647) hydrogen bonds : angle 3.53199 ( 4881) link_BETA1-4 : bond 0.00463 ( 8) link_BETA1-4 : angle 2.21432 ( 24) link_NAG-ASN : bond 0.00313 ( 12) link_NAG-ASN : angle 2.48055 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8430 (t0) cc_final: 0.8179 (t0) REVERT: A 353 MET cc_start: 0.7886 (tmm) cc_final: 0.7466 (tmm) REVERT: A 499 MET cc_start: 0.8946 (ttm) cc_final: 0.8496 (ttp) REVERT: A 804 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8798 (tp) REVERT: B 527 MET cc_start: 0.9050 (mmm) cc_final: 0.8832 (mmt) REVERT: D 527 MET cc_start: 0.9026 (mmm) cc_final: 0.8801 (mmt) REVERT: C 499 MET cc_start: 0.8911 (ttm) cc_final: 0.8547 (ttp) REVERT: C 804 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8798 (tp) outliers start: 35 outliers final: 28 residues processed: 287 average time/residue: 0.1877 time to fit residues: 86.8395 Evaluate side-chains 280 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 804 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 327 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 347 optimal weight: 0.2980 chunk 64 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 368 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114770 restraints weight = 40642.618| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.64 r_work: 0.2964 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29936 Z= 0.104 Angle : 0.469 7.695 40574 Z= 0.237 Chirality : 0.039 0.152 4656 Planarity : 0.003 0.044 4986 Dihedral : 8.669 59.901 5404 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.33 % Allowed : 11.54 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.79 (0.14), residues: 3746 helix: 2.78 (0.11), residues: 1975 sheet: -0.26 (0.24), residues: 423 loop : -0.80 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 65 TYR 0.023 0.001 TYR C 812 PHE 0.022 0.001 PHE A 26 TRP 0.021 0.001 TRP D 766 HIS 0.003 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00233 (29904) covalent geometry : angle 0.46054 (40490) SS BOND : bond 0.00279 ( 12) SS BOND : angle 0.59403 ( 24) hydrogen bonds : bond 0.03360 ( 1647) hydrogen bonds : angle 3.48228 ( 4881) link_BETA1-4 : bond 0.00483 ( 8) link_BETA1-4 : angle 2.18501 ( 24) link_NAG-ASN : bond 0.00300 ( 12) link_NAG-ASN : angle 2.41562 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8461 (t0) cc_final: 0.8249 (t0) REVERT: A 499 MET cc_start: 0.8923 (ttm) cc_final: 0.8449 (ttp) REVERT: A 804 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8788 (tp) REVERT: B 527 MET cc_start: 0.9033 (mmm) cc_final: 0.8814 (mmt) REVERT: G 67 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7807 (tt) REVERT: D 527 MET cc_start: 0.9007 (mmm) cc_final: 0.8781 (mmt) REVERT: C 79 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8534 (mm) REVERT: C 499 MET cc_start: 0.8912 (ttm) cc_final: 0.8539 (ttp) REVERT: C 804 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8779 (tp) outliers start: 35 outliers final: 29 residues processed: 289 average time/residue: 0.1781 time to fit residues: 83.3604 Evaluate side-chains 287 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 804 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 293 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 237 optimal weight: 0.3980 chunk 248 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115174 restraints weight = 40777.801| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.67 r_work: 0.2929 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29936 Z= 0.164 Angle : 0.506 8.022 40574 Z= 0.256 Chirality : 0.040 0.163 4656 Planarity : 0.003 0.044 4986 Dihedral : 8.691 59.644 5404 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.52 % Allowed : 11.58 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.66 (0.14), residues: 3746 helix: 2.65 (0.11), residues: 1971 sheet: -0.22 (0.25), residues: 411 loop : -0.85 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 65 TYR 0.024 0.001 TYR C 812 PHE 0.025 0.002 PHE D 546 TRP 0.022 0.001 TRP D 766 HIS 0.005 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00388 (29904) covalent geometry : angle 0.49789 (40490) SS BOND : bond 0.00339 ( 12) SS BOND : angle 0.71399 ( 24) hydrogen bonds : bond 0.03753 ( 1647) hydrogen bonds : angle 3.56685 ( 4881) link_BETA1-4 : bond 0.00381 ( 8) link_BETA1-4 : angle 2.21870 ( 24) link_NAG-ASN : bond 0.00462 ( 12) link_NAG-ASN : angle 2.41692 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8498 (t0) cc_final: 0.8273 (t0) REVERT: A 499 MET cc_start: 0.8954 (ttm) cc_final: 0.8523 (ttp) REVERT: A 804 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8809 (tp) REVERT: B 527 MET cc_start: 0.9079 (mmm) cc_final: 0.8851 (mmt) REVERT: G 67 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7829 (tt) REVERT: G 123 MET cc_start: 0.6684 (mmm) cc_final: 0.6393 (mmm) REVERT: G 129 ASN cc_start: 0.7773 (p0) cc_final: 0.7347 (p0) REVERT: D 527 MET cc_start: 0.9071 (mmm) cc_final: 0.8840 (mmt) REVERT: C 79 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8536 (mm) REVERT: C 499 MET cc_start: 0.8952 (ttm) cc_final: 0.8613 (ttp) REVERT: C 804 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8780 (tp) REVERT: E 123 MET cc_start: 0.6854 (mmm) cc_final: 0.6012 (mmm) outliers start: 40 outliers final: 34 residues processed: 283 average time/residue: 0.1854 time to fit residues: 84.8652 Evaluate side-chains 287 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 355 optimal weight: 0.9980 chunk 268 optimal weight: 4.9990 chunk 359 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 150 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN D 106 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116050 restraints weight = 41024.142| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.67 r_work: 0.2941 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29936 Z= 0.130 Angle : 0.489 9.254 40574 Z= 0.247 Chirality : 0.039 0.156 4656 Planarity : 0.003 0.043 4986 Dihedral : 8.479 59.909 5404 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.48 % Allowed : 11.73 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.73 (0.14), residues: 3746 helix: 2.72 (0.11), residues: 1971 sheet: -0.21 (0.24), residues: 412 loop : -0.82 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 65 TYR 0.023 0.001 TYR C 812 PHE 0.024 0.001 PHE C 95 TRP 0.018 0.001 TRP D 766 HIS 0.004 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00304 (29904) covalent geometry : angle 0.48104 (40490) SS BOND : bond 0.00308 ( 12) SS BOND : angle 0.65886 ( 24) hydrogen bonds : bond 0.03557 ( 1647) hydrogen bonds : angle 3.52245 ( 4881) link_BETA1-4 : bond 0.00421 ( 8) link_BETA1-4 : angle 2.15675 ( 24) link_NAG-ASN : bond 0.00357 ( 12) link_NAG-ASN : angle 2.33964 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6870.16 seconds wall clock time: 118 minutes 16.62 seconds (7096.62 seconds total)