Starting phenix.real_space_refine on Tue Aug 26 09:08:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elf_48147/08_2025/9elf_48147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elf_48147/08_2025/9elf_48147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9elf_48147/08_2025/9elf_48147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elf_48147/08_2025/9elf_48147.map" model { file = "/net/cci-nas-00/data/ceres_data/9elf_48147/08_2025/9elf_48147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elf_48147/08_2025/9elf_48147.cif" } resolution = 2.88 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 22486 2.51 5 N 5747 2.21 5 O 6821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35225 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4821 Classifications: {'peptide': 591} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 1 Chain: "C" Number of atoms: 4785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4785 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 561} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8243 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8249 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 6 Chain: "G" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8249 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 6 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 9.27, per 1000 atoms: 0.26 Number of scatterers: 35225 At special positions: 0 Unit cell: (126.368, 141.446, 252.736, 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 171 16.00 O 6821 8.00 N 5747 7.00 C 22486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.01 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.04 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.04 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.02 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.04 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.06 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.04 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.04 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.04 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.02 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.01 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.04 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.02 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.02 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.02 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.04 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.02 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=2, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 432 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 103 " " NAG B 1 " - " ASN A 546 " " NAG C 701 " - " ASN C 53 " " NAG C 702 " - " ASN C 432 " " NAG D 1 " - " ASN E 717 " " NAG E1301 " - " ASN E 616 " " NAG E1302 " - " ASN E 709 " " NAG E1303 " - " ASN E1074 " " NAG E1304 " - " ASN E 331 " " NAG E1306 " - " ASN E 30 " " NAG F1301 " - " ASN F 616 " " NAG F1302 " - " ASN F 709 " " NAG F1303 " - " ASN F1074 " " NAG F1304 " - " ASN F 331 " " NAG F1305 " - " ASN F 354 " " NAG F1306 " - " ASN F 343 " " NAG F1308 " - " ASN F 30 " " NAG G1301 " - " ASN G 616 " " NAG G1302 " - " ASN G 709 " " NAG G1303 " - " ASN G1074 " " NAG G1304 " - " ASN G 331 " " NAG G1306 " - " ASN G 30 " " NAG H 1 " - " ASN E1098 " " NAG I 1 " - " ASN E1134 " " NAG J 1 " - " ASN E 282 " " NAG K 1 " - " ASN E 801 " " NAG L 1 " - " ASN F 717 " " NAG M 1 " - " ASN F1098 " " NAG N 1 " - " ASN F1134 " " NAG O 1 " - " ASN F 282 " " NAG P 1 " - " ASN F 801 " " NAG Q 1 " - " ASN G 717 " " NAG R 1 " - " ASN G1098 " " NAG S 1 " - " ASN G1134 " " NAG T 1 " - " ASN G 282 " " NAG U 1 " - " ASN G 801 " NAG-THR " NAG E1305 " - " THR E 236 " " NAG F1307 " - " THR F 236 " " NAG G1305 " - " THR G 236 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.4 microseconds 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8144 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 44 sheets defined 39.1% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 91 through 102 removed outlier: 4.266A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.203A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.563A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.564A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.645A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 387 through 388 No H-bonds generated for 'chain 'A' and resid 387 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.324A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 486 removed outlier: 4.363A pdb=" N LYS A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 534 removed outlier: 3.971A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.015A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.880A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.352A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.541A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'C' and resid 20 through 53 Processing helix chain 'C' and resid 55 through 81 Processing helix chain 'C' and resid 82 through 83 No H-bonds generated for 'chain 'C' and resid 82 through 83' Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.593A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.535A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 157 through 194 removed outlier: 3.658A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 198 through 208 Processing helix chain 'C' and resid 218 through 252 Proline residue: C 235 - end of helix removed outlier: 4.091A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 268 removed outlier: 3.791A pdb=" N GLY C 268 " --> pdb=" O HIS C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 301 Processing helix chain 'C' and resid 303 through 319 Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 365 through 386 Processing helix chain 'C' and resid 387 through 388 No H-bonds generated for 'chain 'C' and resid 387 through 388' Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 397 through 414 removed outlier: 3.891A pdb=" N HIS C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 Processing helix chain 'C' and resid 431 through 447 Processing helix chain 'C' and resid 448 through 466 removed outlier: 4.252A pdb=" N PHE C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 512 through 534 removed outlier: 3.885A pdb=" N TYR C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 Processing helix chain 'C' and resid 565 through 575 Processing helix chain 'C' and resid 581 through 600 Proline residue: C 590 - end of helix Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 4.078A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 4.251A pdb=" N SER E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 404 through 408' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 616 through 626 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.801A pdb=" N LEU E 752 " --> pdb=" O GLU E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.028A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.585A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.396A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1139 through 1148 Processing helix chain 'F' and resid 69 through 72 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.519A pdb=" N PHE F 342 " --> pdb=" O PHE F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 4.094A pdb=" N TRP F 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 372 removed outlier: 3.825A pdb=" N TYR F 369 " --> pdb=" O TYR F 365 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 408 removed outlier: 4.473A pdb=" N SER F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 404 through 408' Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 616 through 626 Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 886 through 890 Processing helix chain 'F' and resid 897 through 909 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.047A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 Processing helix chain 'F' and resid 942 through 944 No H-bonds generated for 'chain 'F' and resid 942 through 944' Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.717A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 Processing helix chain 'F' and resid 1139 through 1147 Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 337 through 344 Processing helix chain 'G' and resid 365 through 371 Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.596A pdb=" N SER G 408 " --> pdb=" O ASN G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 737 through 744 Processing helix chain 'G' and resid 746 through 754 removed outlier: 3.608A pdb=" N LEU G 752 " --> pdb=" O GLU G 748 " (cutoff:3.500A) Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.592A pdb=" N ASP G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 826 Processing helix chain 'G' and resid 866 through 885 Processing helix chain 'G' and resid 886 through 891 removed outlier: 3.697A pdb=" N ALA G 890 " --> pdb=" O TRP G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 909 Processing helix chain 'G' and resid 912 through 919 removed outlier: 4.054A pdb=" N LEU G 916 " --> pdb=" O THR G 912 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 941 Processing helix chain 'G' and resid 942 through 944 No H-bonds generated for 'chain 'G' and resid 942 through 944' Processing helix chain 'G' and resid 945 through 965 removed outlier: 3.609A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) Processing helix chain 'G' and resid 966 through 968 No H-bonds generated for 'chain 'G' and resid 966 through 968' Processing helix chain 'G' and resid 976 through 984 Processing helix chain 'G' and resid 985 through 1033 Processing helix chain 'G' and resid 1139 through 1149 removed outlier: 3.511A pdb=" N LEU G1143 " --> pdb=" O ASP G1139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.654A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.209A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.050A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 347 through 352 removed outlier: 5.821A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 26 through 32 removed outlier: 3.902A pdb=" N TRP E 64 " --> pdb=" O GLN E 26 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR E 28 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL E 62 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN E 30 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N SER E 60 " --> pdb=" O ASN E 30 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 42 through 43 removed outlier: 5.848A pdb=" N GLY F 566 " --> pdb=" O ASP F 574 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE F 326 " --> pdb=" O ASN F 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 48 through 55 removed outlier: 7.526A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.546A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU E 132 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS E 166 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 311 through 319 removed outlier: 7.094A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 325 through 328 removed outlier: 5.347A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE E 565 " --> pdb=" O PHE G 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 354 through 359 removed outlier: 3.792A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.598A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 701 through 704 removed outlier: 6.166A pdb=" N ALA E 701 " --> pdb=" O ILE G 788 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LYS G 790 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASN E 703 " --> pdb=" O LYS G 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.562A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.562A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN E1106 " --> pdb=" O GLU E1111 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU E1111 " --> pdb=" O GLN E1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.570A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 787 through 790 Processing sheet with id=AC2, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.687A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 26 through 32 removed outlier: 4.257A pdb=" N TRP F 64 " --> pdb=" O GLN F 26 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR F 28 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL F 62 " --> pdb=" O TYR F 28 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN F 30 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER F 60 " --> pdb=" O ASN F 30 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 42 through 43 removed outlier: 5.384A pdb=" N ASP G 574 " --> pdb=" O ILE G 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 48 through 55 removed outlier: 7.608A pdb=" N THR F 274 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP F 290 " --> pdb=" O THR F 274 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU F 276 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA F 288 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 163 through 172 removed outlier: 3.634A pdb=" N ASN F 164 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N CYS F 166 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL F 130 " --> pdb=" O CYS F 166 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE F 168 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE F 128 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR F 170 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL F 126 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG F 102 " --> pdb=" O ASN F 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 311 through 319 removed outlier: 7.237A pdb=" N VAL F 595 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN F 317 " --> pdb=" O GLY F 593 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY F 593 " --> pdb=" O ASN F 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.633A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.780A pdb=" N GLN F1071 " --> pdb=" O THR F 716 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE F 718 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE F 720 " --> pdb=" O TYR F1067 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR F1067 " --> pdb=" O ILE F 720 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 722 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL F1065 " --> pdb=" O VAL F 722 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR F 724 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F1063 " --> pdb=" O THR F 724 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE F 726 " --> pdb=" O VAL F1061 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL F1061 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY F1059 " --> pdb=" O PRO F 728 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY F1059 " --> pdb=" O SER F1055 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER F1055 " --> pdb=" O GLY F1059 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F1061 " --> pdb=" O PRO F1053 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU F1063 " --> pdb=" O SER F1051 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER F1051 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.780A pdb=" N GLN F1071 " --> pdb=" O THR F 716 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE F 718 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE F 720 " --> pdb=" O TYR F1067 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR F1067 " --> pdb=" O ILE F 720 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 722 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL F1065 " --> pdb=" O VAL F 722 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR F 724 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F1063 " --> pdb=" O THR F 724 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE F 726 " --> pdb=" O VAL F1061 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL F1061 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY F1059 " --> pdb=" O PRO F 728 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN F1106 " --> pdb=" O GLU F1111 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU F1111 " --> pdb=" O GLN F1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.607A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 787 through 790 removed outlier: 3.555A pdb=" N LYS F 790 " --> pdb=" O ASN G 703 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.590A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 26 through 32 removed outlier: 4.238A pdb=" N TRP G 64 " --> pdb=" O GLN G 26 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR G 28 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL G 62 " --> pdb=" O TYR G 28 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN G 30 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER G 60 " --> pdb=" O ASN G 30 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE G 201 " --> pdb=" O ASP G 228 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP G 228 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE G 203 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 48 through 55 removed outlier: 7.602A pdb=" N THR G 274 " --> pdb=" O ASP G 290 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP G 290 " --> pdb=" O THR G 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU G 276 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA G 288 " --> pdb=" O LEU G 276 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS G 278 " --> pdb=" O THR G 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 163 through 172 removed outlier: 5.644A pdb=" N ASN G 165 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU G 132 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL G 130 " --> pdb=" O THR G 167 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU G 169 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE G 128 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL G 171 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL G 126 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ARG G 102 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 311 through 319 removed outlier: 7.153A pdb=" N VAL G 595 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN G 317 " --> pdb=" O GLY G 593 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY G 593 " --> pdb=" O ASN G 317 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY G 594 " --> pdb=" O GLN G 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 354 through 359 Processing sheet with id=AE2, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.573A pdb=" N ILE G 670 " --> pdb=" O ILE G 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 711 through 714 removed outlier: 3.960A pdb=" N ALA G1078 " --> pdb=" O PHE G1095 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE G1095 " --> pdb=" O ALA G1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 717 through 728 removed outlier: 7.167A pdb=" N GLY G1059 " --> pdb=" O SER G1055 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N SER G1055 " --> pdb=" O GLY G1059 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G1061 " --> pdb=" O PRO G1053 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU G1063 " --> pdb=" O SER G1051 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER G1051 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL G1065 " --> pdb=" O LEU G1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.527A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA G1087 " --> pdb=" O SER G1123 " (cutoff:3.500A) 1631 hydrogen bonds defined for protein. 4629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.84 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5801 1.32 - 1.46: 13827 1.46 - 1.60: 16207 1.60 - 1.75: 4 1.75 - 1.89: 241 Bond restraints: 36080 Sorted by residual: bond pdb=" N PRO E 809 " pdb=" CD PRO E 809 " ideal model delta sigma weight residual 1.473 1.745 -0.272 1.40e-02 5.10e+03 3.76e+02 bond pdb=" C LYS F1028 " pdb=" O LYS F1028 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.29e-02 6.01e+03 2.03e+01 bond pdb=" N ILE E 233 " pdb=" CA ILE E 233 " ideal model delta sigma weight residual 1.455 1.514 -0.059 1.32e-02 5.74e+03 1.98e+01 bond pdb=" N ILE F 235 " pdb=" CA ILE F 235 " ideal model delta sigma weight residual 1.459 1.514 -0.055 1.25e-02 6.40e+03 1.91e+01 bond pdb=" N LEU E 390 " pdb=" CA LEU E 390 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.18e-02 7.18e+03 1.68e+01 ... (remaining 36075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 48096 3.74 - 7.47: 883 7.47 - 11.21: 64 11.21 - 14.94: 9 14.94 - 18.68: 4 Bond angle restraints: 49056 Sorted by residual: angle pdb=" C PHE E 855 " pdb=" CA PHE E 855 " pdb=" CB PHE E 855 " ideal model delta sigma weight residual 110.42 92.89 17.53 1.99e+00 2.53e-01 7.76e+01 angle pdb=" N LYS G 786 " pdb=" CA LYS G 786 " pdb=" CB LYS G 786 " ideal model delta sigma weight residual 110.28 96.69 13.59 1.55e+00 4.16e-01 7.69e+01 angle pdb=" CA PHE G 888 " pdb=" CB PHE G 888 " pdb=" CG PHE G 888 " ideal model delta sigma weight residual 113.80 121.78 -7.98 1.00e+00 1.00e+00 6.37e+01 angle pdb=" N PHE G 238 " pdb=" CA PHE G 238 " pdb=" CB PHE G 238 " ideal model delta sigma weight residual 111.13 96.97 14.16 1.81e+00 3.05e-01 6.12e+01 angle pdb=" CA PHE E 888 " pdb=" CB PHE E 888 " pdb=" CG PHE E 888 " ideal model delta sigma weight residual 113.80 121.09 -7.29 1.00e+00 1.00e+00 5.31e+01 ... (remaining 49051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.35: 21121 21.35 - 42.70: 824 42.70 - 64.04: 220 64.04 - 85.39: 85 85.39 - 106.74: 33 Dihedral angle restraints: 22283 sinusoidal: 9634 harmonic: 12649 Sorted by residual: dihedral pdb=" CB CYS F 538 " pdb=" SG CYS F 538 " pdb=" SG CYS F 590 " pdb=" CB CYS F 590 " ideal model delta sinusoidal sigma weight residual -86.00 -5.68 -80.32 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS F 480 " pdb=" SG CYS F 480 " pdb=" SG CYS F 488 " pdb=" CB CYS F 488 " ideal model delta sinusoidal sigma weight residual 93.00 169.71 -76.71 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" C PHE E 855 " pdb=" N PHE E 855 " pdb=" CA PHE E 855 " pdb=" CB PHE E 855 " ideal model delta harmonic sigma weight residual -122.60 -102.75 -19.85 0 2.50e+00 1.60e-01 6.31e+01 ... (remaining 22280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.358: 5614 0.358 - 0.717: 4 0.717 - 1.075: 1 1.075 - 1.433: 0 1.433 - 1.791: 1 Chirality restraints: 5620 Sorted by residual: chirality pdb=" C1 NAG G1303 " pdb=" ND2 ASN G1074 " pdb=" C2 NAG G1303 " pdb=" O5 NAG G1303 " both_signs ideal model delta sigma weight residual False -2.40 -0.61 -1.79 2.00e-01 2.50e+01 8.02e+01 chirality pdb=" CG LEU G 176 " pdb=" CB LEU G 176 " pdb=" CD1 LEU G 176 " pdb=" CD2 LEU G 176 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CB THR A 519 " pdb=" CA THR A 519 " pdb=" OG1 THR A 519 " pdb=" CG2 THR A 519 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.30e+00 ... (remaining 5617 not shown) Planarity restraints: 6277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 331 " 0.088 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" CG ASN F 331 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN F 331 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN F 331 " -0.239 2.00e-02 2.50e+03 pdb=" C1 NAG F1304 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 331 " 0.075 2.00e-02 2.50e+03 8.42e-02 8.86e+01 pdb=" CG ASN E 331 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN E 331 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN E 331 " -0.136 2.00e-02 2.50e+03 pdb=" C1 NAG E1304 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 237 " 0.749 9.50e-02 1.11e+02 3.36e-01 6.87e+01 pdb=" NE ARG F 237 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG F 237 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 237 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 237 " 0.021 2.00e-02 2.50e+03 ... (remaining 6274 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 5 1.81 - 2.59: 273 2.59 - 3.36: 44400 3.36 - 4.13: 89109 4.13 - 4.90: 159767 Nonbonded interactions: 293554 Sorted by model distance: nonbonded pdb=" O THR C 20 " pdb=" OE1 GLN C 24 " model vdw 1.043 3.040 nonbonded pdb=" CD1 LEU C 91 " pdb=" O GLY C 211 " model vdw 1.285 3.460 nonbonded pdb=" OD1 ASN G1074 " pdb=" C1 NAG G1303 " model vdw 1.580 2.776 nonbonded pdb=" CD1 ILE A 407 " pdb=" OE1 GLN A 526 " model vdw 1.748 3.460 nonbonded pdb=" CD2 TYR C 381 " pdb=" CE1 HIS C 401 " model vdw 1.807 3.560 ... (remaining 293549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 133 or resid 143 through 182 or (resid 183 and \ (name N or name CA or name C or name O or name CB )) or resid 184 through 702)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 24 through 391 or (resid 392 and (name N or name CA or nam \ e C or name O or name CB )) or resid 393 through 1306)) selection = (chain 'G' and (resid 24 through 391 or (resid 392 and (name N or name CA or nam \ e C or name O or name CB )) or resid 393 through 1306)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.560 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: 0.030 Extract box with map and model: 0.970 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 38.330 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.150 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.010 1.255 36190 Z= 0.552 Angle : 1.319 57.206 49333 Z= 0.745 Chirality : 0.071 1.791 5620 Planarity : 0.011 0.336 6238 Dihedral : 13.686 106.738 14007 Min Nonbonded Distance : 1.043 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.13 % Allowed : 6.95 % Favored : 92.92 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.91 % 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 aren not related in a simple way. whole: 0.62 (0.12), residues: 4284 helix: 0.64 (0.12), residues: 1462 sheet: 0.88 (0.19), residues: 597 loop : 0.26 (0.12), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 190 TYR 0.049 0.004 TYR C 385 PHE 0.067 0.004 PHE G 400 TRP 0.039 0.005 TRP C 69 HIS 0.032 0.003 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00736 (36080) covalent geometry : angle 1.23194 (49056) SS BOND : bond 0.00812 ( 44) SS BOND : angle 2.93254 ( 88) hydrogen bonds : bond 0.14822 ( 1614) hydrogen bonds : angle 7.36951 ( 4629) Misc. bond : bond 0.32646 ( 2) link_BETA1-4 : bond 0.00597 ( 22) link_BETA1-4 : angle 4.32436 ( 66) link_NAG-ASN : bond 0.20111 ( 39) link_NAG-ASN : angle 8.79329 ( 117) link_NAG-THR : bond 0.03637 ( 3) link_NAG-THR : angle 7.71438 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 409 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PRO cc_start: 0.6705 (Cg_exo) cc_final: 0.6291 (Cg_endo) REVERT: A 219 ARG cc_start: 0.5853 (ppt170) cc_final: 0.5499 (mpp80) REVERT: A 273 ARG cc_start: 0.3476 (ttt180) cc_final: 0.2756 (tpp80) REVERT: A 539 LEU cc_start: 0.2738 (tp) cc_final: 0.2208 (tt) REVERT: A 572 ASN cc_start: 0.6232 (m-40) cc_final: 0.5428 (t0) REVERT: C 360 MET cc_start: 0.5226 (ttt) cc_final: 0.3868 (tmm) REVERT: C 408 MET cc_start: 0.2575 (mmp) cc_final: 0.2333 (mmp) REVERT: C 462 MET cc_start: 0.2008 (mtt) cc_final: 0.0673 (ptm) REVERT: E 153 MET cc_start: 0.2808 (mmm) cc_final: 0.1499 (ppp) REVERT: F 190 ARG cc_start: 0.8029 (mmt-90) cc_final: 0.7799 (mpt180) REVERT: F 239 GLN cc_start: 0.8150 (mt0) cc_final: 0.7365 (mt0) REVERT: F 636 TYR cc_start: 0.7388 (t80) cc_final: 0.7150 (t80) REVERT: G 568 ASP cc_start: 0.7111 (m-30) cc_final: 0.6794 (m-30) outliers start: 5 outliers final: 1 residues processed: 413 average time/residue: 0.5438 time to fit residues: 280.7681 Evaluate side-chains 291 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 210 ASN A 241 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 524 GLN C 228 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN C 401 HIS C 524 GLN E 564 GLN E 779 GLN E1002 GLN E1011 GLN E1135 ASN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 ASN F1119 ASN G 52 GLN G 280 ASN G1002 GLN G1010 GLN G1113 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.236570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145233 restraints weight = 42904.130| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.83 r_work: 0.3358 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 36190 Z= 0.167 Angle : 0.692 13.536 49333 Z= 0.354 Chirality : 0.047 0.444 5620 Planarity : 0.005 0.080 6238 Dihedral : 7.457 66.394 5974 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.35 % Favored : 98.62 % Rotamer: Outliers : 1.76 % Allowed : 7.87 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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 aren not related in a simple way. whole: 0.87 (0.12), residues: 4284 helix: 1.44 (0.13), residues: 1461 sheet: 0.78 (0.19), residues: 586 loop : 0.01 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 190 TYR 0.047 0.002 TYR E 612 PHE 0.045 0.002 PHE G 86 TRP 0.025 0.002 TRP C 69 HIS 0.011 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00369 (36080) covalent geometry : angle 0.66571 (49056) SS BOND : bond 0.00419 ( 44) SS BOND : angle 1.66274 ( 88) hydrogen bonds : bond 0.05772 ( 1614) hydrogen bonds : angle 5.96083 ( 4629) Misc. bond : bond 0.00200 ( 2) link_BETA1-4 : bond 0.00684 ( 22) link_BETA1-4 : angle 3.26158 ( 66) link_NAG-ASN : bond 0.00550 ( 39) link_NAG-ASN : angle 2.76161 ( 117) link_NAG-THR : bond 0.00420 ( 3) link_NAG-THR : angle 3.05306 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 368 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.5806 (t0) cc_final: 0.5373 (p0) REVERT: A 152 MET cc_start: 0.1525 (OUTLIER) cc_final: 0.1075 (mtm) REVERT: A 219 ARG cc_start: 0.6384 (ppt170) cc_final: 0.5672 (mpp80) REVERT: A 238 GLU cc_start: 0.4311 (tp30) cc_final: 0.4029 (pt0) REVERT: A 474 MET cc_start: -0.0426 (OUTLIER) cc_final: -0.0786 (ttt) REVERT: A 475 LYS cc_start: 0.6551 (mttt) cc_final: 0.6289 (tmtt) REVERT: A 557 MET cc_start: 0.7031 (pmt) cc_final: 0.6310 (mpt) REVERT: A 572 ASN cc_start: 0.6344 (m-40) cc_final: 0.5619 (t0) REVERT: C 144 LEU cc_start: 0.4323 (tp) cc_final: 0.4027 (tp) REVERT: C 157 ASP cc_start: 0.4327 (m-30) cc_final: 0.3832 (OUTLIER) REVERT: C 323 MET cc_start: 0.0663 (ptm) cc_final: 0.0158 (tpt) REVERT: C 360 MET cc_start: 0.3028 (ttt) cc_final: 0.2356 (tmm) REVERT: C 366 MET cc_start: 0.3181 (OUTLIER) cc_final: 0.2872 (mmt) REVERT: C 479 GLU cc_start: 0.5700 (tt0) cc_final: 0.5389 (tm-30) REVERT: C 514 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.5180 (ptm160) REVERT: C 515 TYR cc_start: 0.4702 (m-10) cc_final: 0.3721 (m-10) REVERT: E 153 MET cc_start: 0.2219 (mmm) cc_final: 0.1001 (ppp) REVERT: E 271 GLN cc_start: 0.7247 (mt0) cc_final: 0.7000 (pt0) REVERT: E 365 TYR cc_start: 0.7160 (m-10) cc_final: 0.6898 (m-80) REVERT: E 569 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8077 (tp) REVERT: F 740 MET cc_start: 0.8421 (ttt) cc_final: 0.8215 (ttt) REVERT: F 1038 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8639 (mttp) REVERT: G 205 SER cc_start: 0.8984 (p) cc_final: 0.8513 (m) REVERT: G 281 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: G 400 PHE cc_start: 0.6265 (p90) cc_final: 0.5705 (p90) REVERT: G 574 ASP cc_start: 0.8077 (p0) cc_final: 0.7779 (p0) REVERT: G 985 ASP cc_start: 0.7514 (p0) cc_final: 0.7293 (p0) outliers start: 67 outliers final: 19 residues processed: 404 average time/residue: 0.5058 time to fit residues: 256.1774 Evaluate side-chains 321 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 296 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1038 LYS Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1142 GLN Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 747 THR Chi-restraints excluded: chain G residue 994 ASP Chi-restraints excluded: chain G residue 1117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 138 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 chunk 35 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 353 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 328 optimal weight: 0.9990 chunk 373 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 58 ASN C 76 GLN C 210 ASN ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN E 613 GLN E 677 GLN E 703 ASN E 804 GLN E 935 GLN F 125 ASN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 360 ASN F1005 GLN G 52 GLN G 280 ASN G 901 GLN G1002 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.234367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143877 restraints weight = 42803.016| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.01 r_work: 0.3369 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36190 Z= 0.159 Angle : 0.629 11.051 49333 Z= 0.318 Chirality : 0.046 0.662 5620 Planarity : 0.004 0.058 6238 Dihedral : 5.865 47.140 5972 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.73 % Favored : 98.25 % Rotamer: Outliers : 2.26 % Allowed : 8.42 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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 aren not related in a simple way. whole: 0.80 (0.12), residues: 4284 helix: 1.47 (0.13), residues: 1473 sheet: 0.64 (0.19), residues: 612 loop : -0.07 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 582 TYR 0.046 0.002 TYR C 385 PHE 0.047 0.002 PHE G 238 TRP 0.023 0.002 TRP C 461 HIS 0.014 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00358 (36080) covalent geometry : angle 0.60080 (49056) SS BOND : bond 0.00430 ( 44) SS BOND : angle 1.45563 ( 88) hydrogen bonds : bond 0.05098 ( 1614) hydrogen bonds : angle 5.63644 ( 4629) Misc. bond : bond 0.00456 ( 2) link_BETA1-4 : bond 0.00576 ( 22) link_BETA1-4 : angle 2.91825 ( 66) link_NAG-ASN : bond 0.00568 ( 39) link_NAG-ASN : angle 2.97012 ( 117) link_NAG-THR : bond 0.00306 ( 3) link_NAG-THR : angle 2.92507 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 341 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.5778 (t0) cc_final: 0.5355 (p0) REVERT: A 196 TYR cc_start: 0.3808 (OUTLIER) cc_final: 0.3530 (m-10) REVERT: A 219 ARG cc_start: 0.6332 (ppt170) cc_final: 0.5766 (mpp80) REVERT: A 222 LEU cc_start: 0.4044 (OUTLIER) cc_final: 0.3786 (tp) REVERT: A 227 GLU cc_start: 0.6431 (mt-10) cc_final: 0.5715 (pm20) REVERT: A 238 GLU cc_start: 0.4250 (tp30) cc_final: 0.3922 (pt0) REVERT: A 273 ARG cc_start: 0.4193 (ttt180) cc_final: 0.3244 (ttm-80) REVERT: A 398 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5647 (mp0) REVERT: A 475 LYS cc_start: 0.6639 (mttt) cc_final: 0.6358 (tmtt) REVERT: A 557 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6385 (mpt) REVERT: A 572 ASN cc_start: 0.6335 (m-40) cc_final: 0.5480 (t0) REVERT: C 144 LEU cc_start: 0.4552 (tp) cc_final: 0.4122 (pt) REVERT: C 157 ASP cc_start: 0.4289 (m-30) cc_final: 0.3735 (t0) REVERT: C 198 ASP cc_start: 0.3844 (m-30) cc_final: 0.3417 (p0) REVERT: C 222 LEU cc_start: 0.3386 (mt) cc_final: 0.3047 (tp) REVERT: C 360 MET cc_start: 0.3266 (ttt) cc_final: 0.2584 (tmm) REVERT: C 366 MET cc_start: 0.2989 (OUTLIER) cc_final: 0.2280 (mmt) REVERT: C 369 PHE cc_start: 0.1729 (OUTLIER) cc_final: 0.1424 (t80) REVERT: C 429 GLN cc_start: 0.0497 (tp40) cc_final: 0.0252 (mt0) REVERT: C 479 GLU cc_start: 0.5831 (tt0) cc_final: 0.5386 (tm-30) REVERT: E 153 MET cc_start: 0.2214 (mmm) cc_final: 0.1042 (ppp) REVERT: E 569 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8053 (tp) REVERT: E 618 THR cc_start: 0.8146 (m) cc_final: 0.7856 (p) REVERT: E 964 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7658 (mptt) REVERT: E 1084 ASP cc_start: 0.7151 (p0) cc_final: 0.6806 (p0) REVERT: F 200 TYR cc_start: 0.7753 (m-80) cc_final: 0.7312 (m-80) REVERT: F 314 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: F 636 TYR cc_start: 0.7603 (t80) cc_final: 0.6994 (t80) REVERT: F 740 MET cc_start: 0.8555 (ttt) cc_final: 0.8330 (ttt) REVERT: F 1114 ILE cc_start: 0.9023 (mm) cc_final: 0.8818 (mp) REVERT: G 205 SER cc_start: 0.8993 (p) cc_final: 0.8610 (m) REVERT: G 400 PHE cc_start: 0.6607 (p90) cc_final: 0.6036 (p90) REVERT: G 574 ASP cc_start: 0.8089 (p0) cc_final: 0.7781 (p0) outliers start: 86 outliers final: 30 residues processed: 390 average time/residue: 0.5055 time to fit residues: 246.5753 Evaluate side-chains 325 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1142 GLN Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 565 PHE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 724 THR Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain G residue 1117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 298 optimal weight: 0.7980 chunk 345 optimal weight: 0.8980 chunk 341 optimal weight: 0.8980 chunk 343 optimal weight: 0.0000 chunk 157 optimal weight: 0.8980 chunk 353 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 294 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 96 GLN ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 703 ASN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 360 ASN F1005 GLN F1119 ASN G 52 GLN G 280 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.234464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143657 restraints weight = 42568.860| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.83 r_work: 0.3369 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36190 Z= 0.138 Angle : 0.590 12.010 49333 Z= 0.297 Chirality : 0.045 0.663 5620 Planarity : 0.004 0.058 6238 Dihedral : 5.051 42.884 5972 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.20 % Rotamer: Outliers : 2.49 % Allowed : 9.16 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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 aren not related in a simple way. whole: 0.77 (0.12), residues: 4284 helix: 1.55 (0.13), residues: 1478 sheet: 0.56 (0.19), residues: 619 loop : -0.17 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 582 TYR 0.021 0.001 TYR C 385 PHE 0.030 0.002 PHE C 369 TRP 0.024 0.001 TRP A 461 HIS 0.011 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00305 (36080) covalent geometry : angle 0.56688 (49056) SS BOND : bond 0.00372 ( 44) SS BOND : angle 1.14711 ( 88) hydrogen bonds : bond 0.04646 ( 1614) hydrogen bonds : angle 5.46293 ( 4629) Misc. bond : bond 0.01249 ( 2) link_BETA1-4 : bond 0.00573 ( 22) link_BETA1-4 : angle 2.62290 ( 66) link_NAG-ASN : bond 0.00478 ( 39) link_NAG-ASN : angle 2.60524 ( 117) link_NAG-THR : bond 0.00361 ( 3) link_NAG-THR : angle 2.58924 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 339 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.5773 (t0) cc_final: 0.5366 (p0) REVERT: A 166 GLU cc_start: 0.5598 (tp30) cc_final: 0.4951 (mm-30) REVERT: A 183 TYR cc_start: 0.2597 (t80) cc_final: 0.2315 (t80) REVERT: A 196 TYR cc_start: 0.3688 (OUTLIER) cc_final: 0.3380 (m-10) REVERT: A 219 ARG cc_start: 0.6337 (ppt170) cc_final: 0.5829 (mpp80) REVERT: A 238 GLU cc_start: 0.4185 (tp30) cc_final: 0.3961 (pt0) REVERT: A 273 ARG cc_start: 0.4323 (ttt180) cc_final: 0.3465 (ttm-80) REVERT: A 398 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5557 (mp0) REVERT: A 475 LYS cc_start: 0.6685 (mttt) cc_final: 0.6374 (tmtt) REVERT: A 557 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6171 (mpt) REVERT: A 572 ASN cc_start: 0.6403 (m-40) cc_final: 0.5535 (t0) REVERT: A 579 MET cc_start: 0.4384 (OUTLIER) cc_final: 0.3240 (ppp) REVERT: C 144 LEU cc_start: 0.4218 (tp) cc_final: 0.3937 (pt) REVERT: C 157 ASP cc_start: 0.4133 (m-30) cc_final: 0.3517 (t0) REVERT: C 198 ASP cc_start: 0.3869 (m-30) cc_final: 0.3434 (p0) REVERT: C 222 LEU cc_start: 0.3344 (mt) cc_final: 0.2973 (tm) REVERT: C 357 ARG cc_start: 0.3619 (OUTLIER) cc_final: 0.3400 (ttp-170) REVERT: C 360 MET cc_start: 0.3264 (ttt) cc_final: 0.2592 (tmm) REVERT: C 366 MET cc_start: 0.2823 (OUTLIER) cc_final: 0.2306 (mmt) REVERT: C 369 PHE cc_start: 0.1759 (OUTLIER) cc_final: 0.1390 (t80) REVERT: C 429 GLN cc_start: 0.0509 (tp40) cc_final: 0.0244 (mt0) REVERT: C 479 GLU cc_start: 0.5717 (tt0) cc_final: 0.5380 (tm-30) REVERT: E 153 MET cc_start: 0.2182 (mmm) cc_final: 0.0913 (ppp) REVERT: E 364 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7233 (p0) REVERT: E 569 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8024 (tp) REVERT: E 964 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7630 (mptt) REVERT: E 1084 ASP cc_start: 0.7350 (p0) cc_final: 0.6946 (p0) REVERT: F 189 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7015 (tt) REVERT: F 200 TYR cc_start: 0.7787 (m-80) cc_final: 0.7325 (m-80) REVERT: F 547 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7524 (p) REVERT: F 636 TYR cc_start: 0.7634 (t80) cc_final: 0.6954 (t80) REVERT: F 740 MET cc_start: 0.8493 (ttt) cc_final: 0.8224 (ttt) REVERT: F 1038 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8643 (mttp) REVERT: G 205 SER cc_start: 0.8851 (p) cc_final: 0.8513 (m) REVERT: G 400 PHE cc_start: 0.6634 (p90) cc_final: 0.6103 (p90) REVERT: G 568 ASP cc_start: 0.7250 (m-30) cc_final: 0.6684 (m-30) REVERT: G 574 ASP cc_start: 0.7975 (p0) cc_final: 0.7677 (p0) REVERT: G 1084 ASP cc_start: 0.7664 (p0) cc_final: 0.7385 (p0) REVERT: G 1092 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7666 (mt-10) outliers start: 95 outliers final: 34 residues processed: 395 average time/residue: 0.6034 time to fit residues: 297.1616 Evaluate side-chains 339 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 292 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 565 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 353 TRP Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1038 LYS Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 565 PHE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 724 THR Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain G residue 1117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 250 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 245 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 340 optimal weight: 0.8980 chunk 341 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 367 optimal weight: 0.8980 chunk 233 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN C 58 ASN C 76 GLN C 300 GLN C 330 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 334 ASN E 703 ASN E1002 GLN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 360 ASN F1005 GLN F1119 ASN G 52 GLN G1010 GLN G1125 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.239568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.166440 restraints weight = 44035.097| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.61 r_work: 0.3454 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36190 Z= 0.142 Angle : 0.594 12.028 49333 Z= 0.296 Chirality : 0.045 0.617 5620 Planarity : 0.004 0.057 6238 Dihedral : 4.896 40.868 5972 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.89 % Favored : 98.09 % Rotamer: Outliers : 2.31 % Allowed : 10.02 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 aren not related in a simple way. whole: 0.75 (0.12), residues: 4284 helix: 1.60 (0.13), residues: 1479 sheet: 0.49 (0.19), residues: 618 loop : -0.21 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 582 TYR 0.025 0.001 TYR A 41 PHE 0.032 0.001 PHE C 369 TRP 0.029 0.001 TRP C 461 HIS 0.010 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00321 (36080) covalent geometry : angle 0.57210 (49056) SS BOND : bond 0.00372 ( 44) SS BOND : angle 1.13007 ( 88) hydrogen bonds : bond 0.04600 ( 1614) hydrogen bonds : angle 5.41031 ( 4629) Misc. bond : bond 0.00777 ( 2) link_BETA1-4 : bond 0.00487 ( 22) link_BETA1-4 : angle 2.54690 ( 66) link_NAG-ASN : bond 0.00555 ( 39) link_NAG-ASN : angle 2.56846 ( 117) link_NAG-THR : bond 0.00305 ( 3) link_NAG-THR : angle 2.41753 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 314 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.5552 (t0) cc_final: 0.5226 (p0) REVERT: A 183 TYR cc_start: 0.2560 (t80) cc_final: 0.2286 (t80) REVERT: A 196 TYR cc_start: 0.3788 (OUTLIER) cc_final: 0.3249 (m-10) REVERT: A 219 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5731 (mpp80) REVERT: A 238 GLU cc_start: 0.4084 (tp30) cc_final: 0.3849 (pt0) REVERT: A 273 ARG cc_start: 0.4177 (ttt180) cc_final: 0.3363 (ttm-80) REVERT: A 307 ILE cc_start: 0.5325 (pt) cc_final: 0.4927 (mp) REVERT: A 398 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5593 (mp0) REVERT: A 475 LYS cc_start: 0.6691 (mttt) cc_final: 0.6337 (tmtt) REVERT: A 557 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6137 (mpt) REVERT: A 572 ASN cc_start: 0.6403 (m-40) cc_final: 0.5860 (m110) REVERT: A 579 MET cc_start: 0.4589 (OUTLIER) cc_final: 0.3349 (ppp) REVERT: C 144 LEU cc_start: 0.4173 (tp) cc_final: 0.3710 (pt) REVERT: C 157 ASP cc_start: 0.4189 (m-30) cc_final: 0.3468 (t0) REVERT: C 198 ASP cc_start: 0.3943 (m-30) cc_final: 0.3479 (p0) REVERT: C 360 MET cc_start: 0.3685 (ttt) cc_final: 0.2886 (tmm) REVERT: C 366 MET cc_start: 0.2600 (OUTLIER) cc_final: 0.2125 (mmt) REVERT: C 369 PHE cc_start: 0.1724 (OUTLIER) cc_final: 0.1260 (t80) REVERT: C 429 GLN cc_start: 0.0519 (tp40) cc_final: 0.0254 (mt0) REVERT: C 462 MET cc_start: 0.1846 (mtt) cc_final: 0.0841 (ptt) REVERT: C 480 MET cc_start: 0.2548 (mmm) cc_final: 0.2168 (mtm) REVERT: E 153 MET cc_start: 0.2352 (mmm) cc_final: 0.0932 (ppp) REVERT: E 364 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7098 (p0) REVERT: E 964 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7869 (mptt) REVERT: E 1084 ASP cc_start: 0.7392 (p0) cc_final: 0.6962 (p0) REVERT: F 189 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7346 (tt) REVERT: F 190 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.8044 (mtm-85) REVERT: F 200 TYR cc_start: 0.8036 (m-80) cc_final: 0.7639 (m-80) REVERT: F 547 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7808 (p) REVERT: F 636 TYR cc_start: 0.7623 (t80) cc_final: 0.7058 (t80) REVERT: F 740 MET cc_start: 0.8610 (ttt) cc_final: 0.8379 (ttt) REVERT: F 1038 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8713 (mttp) REVERT: G 205 SER cc_start: 0.8909 (p) cc_final: 0.8699 (m) REVERT: G 269 TYR cc_start: 0.8382 (m-80) cc_final: 0.8156 (m-80) REVERT: G 400 PHE cc_start: 0.7020 (p90) cc_final: 0.6575 (p90) REVERT: G 554 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7952 (tttp) REVERT: G 586 ASP cc_start: 0.8591 (m-30) cc_final: 0.8372 (m-30) REVERT: G 820 ASP cc_start: 0.8190 (t70) cc_final: 0.7898 (m-30) REVERT: G 1010 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7685 (mp-120) REVERT: G 1084 ASP cc_start: 0.7683 (p0) cc_final: 0.7419 (p0) REVERT: G 1092 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7732 (mt-10) outliers start: 88 outliers final: 36 residues processed: 372 average time/residue: 0.6193 time to fit residues: 287.7571 Evaluate side-chains 340 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 565 PHE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 353 TRP Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1038 LYS Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1142 GLN Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 554 LYS Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 724 THR Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain G residue 994 ASP Chi-restraints excluded: chain G residue 1010 GLN Chi-restraints excluded: chain G residue 1117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 81 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 399 optimal weight: 0.0020 chunk 245 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 388 optimal weight: 0.7980 chunk 419 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 201 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN C 76 GLN C 277 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 703 ASN E1002 GLN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 360 ASN F1005 GLN F1119 ASN G 52 GLN G 280 ASN G1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.240240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166484 restraints weight = 44057.697| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.71 r_work: 0.3449 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 36190 Z= 0.135 Angle : 0.590 12.183 49333 Z= 0.294 Chirality : 0.044 0.613 5620 Planarity : 0.004 0.086 6238 Dihedral : 4.797 42.299 5972 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.05 % Favored : 97.92 % Rotamer: Outliers : 2.55 % Allowed : 10.15 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.74 (0.12), residues: 4284 helix: 1.63 (0.13), residues: 1486 sheet: 0.42 (0.19), residues: 630 loop : -0.24 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 357 TYR 0.045 0.001 TYR E 612 PHE 0.032 0.001 PHE C 369 TRP 0.031 0.002 TRP A 461 HIS 0.012 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00304 (36080) covalent geometry : angle 0.56901 (49056) SS BOND : bond 0.00406 ( 44) SS BOND : angle 1.25845 ( 88) hydrogen bonds : bond 0.04456 ( 1614) hydrogen bonds : angle 5.37522 ( 4629) Misc. bond : bond 0.01167 ( 2) link_BETA1-4 : bond 0.00469 ( 22) link_BETA1-4 : angle 2.42769 ( 66) link_NAG-ASN : bond 0.00490 ( 39) link_NAG-ASN : angle 2.46233 ( 117) link_NAG-THR : bond 0.00297 ( 3) link_NAG-THR : angle 2.28266 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 313 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7342 (mt) cc_final: 0.6496 (tm) REVERT: A 111 ASP cc_start: 0.5711 (t0) cc_final: 0.5326 (p0) REVERT: A 112 LYS cc_start: 0.4901 (mmtt) cc_final: 0.4700 (mmtt) REVERT: A 183 TYR cc_start: 0.2520 (t80) cc_final: 0.2234 (t80) REVERT: A 196 TYR cc_start: 0.3793 (OUTLIER) cc_final: 0.3257 (m-10) REVERT: A 219 ARG cc_start: 0.6312 (ppt170) cc_final: 0.5715 (mpp80) REVERT: A 225 ASP cc_start: 0.4028 (t0) cc_final: 0.3650 (t0) REVERT: A 273 ARG cc_start: 0.4214 (ttt180) cc_final: 0.3392 (ttm-80) REVERT: A 307 ILE cc_start: 0.5479 (pt) cc_final: 0.5109 (mp) REVERT: A 475 LYS cc_start: 0.6736 (mttt) cc_final: 0.6497 (mmtp) REVERT: A 557 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6121 (mpt) REVERT: A 572 ASN cc_start: 0.6472 (m-40) cc_final: 0.5418 (t0) REVERT: A 579 MET cc_start: 0.4629 (OUTLIER) cc_final: 0.3411 (ppp) REVERT: C 144 LEU cc_start: 0.4157 (tp) cc_final: 0.3775 (pt) REVERT: C 157 ASP cc_start: 0.4056 (m-30) cc_final: 0.3359 (t0) REVERT: C 198 ASP cc_start: 0.3930 (m-30) cc_final: 0.3484 (p0) REVERT: C 222 LEU cc_start: 0.3325 (mt) cc_final: 0.3036 (tm) REVERT: C 360 MET cc_start: 0.3651 (ttt) cc_final: 0.3043 (tmm) REVERT: C 366 MET cc_start: 0.2604 (OUTLIER) cc_final: 0.2026 (mmt) REVERT: C 369 PHE cc_start: 0.1716 (OUTLIER) cc_final: 0.1353 (t80) REVERT: C 429 GLN cc_start: 0.0386 (tp40) cc_final: 0.0112 (mt0) REVERT: C 442 GLN cc_start: 0.4691 (tm-30) cc_final: 0.2924 (mm-40) REVERT: C 462 MET cc_start: 0.2117 (mtt) cc_final: 0.1166 (ptt) REVERT: C 480 MET cc_start: 0.2747 (mmm) cc_final: 0.2377 (mtm) REVERT: E 153 MET cc_start: 0.2330 (mmm) cc_final: 0.0968 (ppp) REVERT: E 364 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7187 (p0) REVERT: E 755 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: E 964 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.7870 (mptt) REVERT: E 1084 ASP cc_start: 0.7414 (p0) cc_final: 0.6936 (p0) REVERT: E 1142 GLN cc_start: 0.7110 (tp40) cc_final: 0.6541 (tm-30) REVERT: F 189 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7398 (tt) REVERT: F 190 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.8045 (mtm-85) REVERT: F 200 TYR cc_start: 0.8095 (m-80) cc_final: 0.7698 (m-80) REVERT: F 235 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7572 (mt) REVERT: F 281 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8187 (pp20) REVERT: F 547 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7824 (p) REVERT: F 740 MET cc_start: 0.8606 (ttt) cc_final: 0.8356 (ttt) REVERT: G 269 TYR cc_start: 0.8386 (m-80) cc_final: 0.8177 (m-80) REVERT: G 400 PHE cc_start: 0.7129 (p90) cc_final: 0.6677 (p90) REVERT: G 554 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8055 (tttp) REVERT: G 586 ASP cc_start: 0.8599 (m-30) cc_final: 0.8296 (m-30) REVERT: G 820 ASP cc_start: 0.8175 (t70) cc_final: 0.7845 (m-30) REVERT: G 1084 ASP cc_start: 0.7748 (p0) cc_final: 0.7443 (p0) REVERT: G 1092 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7716 (mt-10) outliers start: 97 outliers final: 44 residues processed: 374 average time/residue: 0.6167 time to fit residues: 288.4483 Evaluate side-chains 344 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 287 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 755 GLN Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 353 TRP Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1038 LYS Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain F residue 1123 SER Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1142 GLN Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain G residue 554 LYS Chi-restraints excluded: chain G residue 565 PHE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 724 THR Chi-restraints excluded: chain G residue 747 THR Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain G residue 1081 ILE Chi-restraints excluded: chain G residue 1117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 286 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 424 optimal weight: 0.6980 chunk 322 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 302 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 396 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 423 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 239 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 703 ASN E1002 GLN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 360 ASN F1119 ASN G 52 GLN G 658 ASN G 675 GLN G 955 ASN G1125 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.245079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.179206 restraints weight = 43896.141| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.75 r_work: 0.3407 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36190 Z= 0.149 Angle : 0.598 13.467 49333 Z= 0.298 Chirality : 0.045 0.665 5620 Planarity : 0.004 0.055 6238 Dihedral : 4.753 40.189 5972 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.08 % Favored : 97.85 % Rotamer: Outliers : 2.55 % Allowed : 10.47 % Favored : 86.99 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.69 (0.12), residues: 4284 helix: 1.63 (0.13), residues: 1486 sheet: 0.37 (0.19), residues: 646 loop : -0.31 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 582 TYR 0.039 0.001 TYR E 612 PHE 0.040 0.002 PHE G 238 TRP 0.040 0.002 TRP A 461 HIS 0.011 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00346 (36080) covalent geometry : angle 0.57717 (49056) SS BOND : bond 0.00560 ( 44) SS BOND : angle 1.42375 ( 88) hydrogen bonds : bond 0.04473 ( 1614) hydrogen bonds : angle 5.39801 ( 4629) Misc. bond : bond 0.00736 ( 2) link_BETA1-4 : bond 0.00503 ( 22) link_BETA1-4 : angle 2.36683 ( 66) link_NAG-ASN : bond 0.00432 ( 39) link_NAG-ASN : angle 2.44763 ( 117) link_NAG-THR : bond 0.00305 ( 3) link_NAG-THR : angle 2.15432 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 313 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7411 (mt) cc_final: 0.6569 (tm) REVERT: A 111 ASP cc_start: 0.5792 (t0) cc_final: 0.5371 (p0) REVERT: A 183 TYR cc_start: 0.2612 (t80) cc_final: 0.2359 (t80) REVERT: A 196 TYR cc_start: 0.3855 (OUTLIER) cc_final: 0.3409 (m-10) REVERT: A 219 ARG cc_start: 0.6318 (ppt170) cc_final: 0.5741 (mpp80) REVERT: A 225 ASP cc_start: 0.4168 (t0) cc_final: 0.3721 (t0) REVERT: A 273 ARG cc_start: 0.4240 (ttt180) cc_final: 0.3500 (ttm-80) REVERT: A 475 LYS cc_start: 0.6669 (mttt) cc_final: 0.6448 (mmtp) REVERT: A 557 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6043 (mpt) REVERT: A 572 ASN cc_start: 0.6625 (m-40) cc_final: 0.5555 (t0) REVERT: A 579 MET cc_start: 0.4601 (OUTLIER) cc_final: 0.3456 (ppp) REVERT: C 76 GLN cc_start: 0.4867 (OUTLIER) cc_final: 0.4601 (mp-120) REVERT: C 144 LEU cc_start: 0.4179 (tp) cc_final: 0.3784 (pt) REVERT: C 157 ASP cc_start: 0.3930 (m-30) cc_final: 0.3246 (t0) REVERT: C 198 ASP cc_start: 0.3857 (m-30) cc_final: 0.3459 (p0) REVERT: C 222 LEU cc_start: 0.3381 (mt) cc_final: 0.3071 (tm) REVERT: C 306 ARG cc_start: 0.5739 (tpt-90) cc_final: 0.5450 (ttm-80) REVERT: C 360 MET cc_start: 0.3506 (ttt) cc_final: 0.3008 (tmm) REVERT: C 366 MET cc_start: 0.2646 (OUTLIER) cc_final: 0.2124 (mmt) REVERT: C 369 PHE cc_start: 0.1677 (OUTLIER) cc_final: 0.1320 (t80) REVERT: C 376 MET cc_start: 0.2074 (ttm) cc_final: 0.1820 (ptm) REVERT: C 442 GLN cc_start: 0.4470 (tm-30) cc_final: 0.2931 (mm-40) REVERT: C 462 MET cc_start: 0.2321 (mtt) cc_final: 0.1455 (ptt) REVERT: C 480 MET cc_start: 0.2930 (mmm) cc_final: 0.2544 (mtm) REVERT: C 566 TRP cc_start: 0.1788 (OUTLIER) cc_final: 0.0375 (p90) REVERT: E 153 MET cc_start: 0.2266 (mmm) cc_final: 0.0965 (ppp) REVERT: E 364 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7182 (p0) REVERT: E 755 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: E 964 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7935 (mptt) REVERT: E 1084 ASP cc_start: 0.7595 (p0) cc_final: 0.7119 (p0) REVERT: E 1142 GLN cc_start: 0.7219 (tp40) cc_final: 0.6575 (tm-30) REVERT: F 189 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7495 (tt) REVERT: F 200 TYR cc_start: 0.8090 (m-80) cc_final: 0.7736 (m-80) REVERT: F 281 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8274 (pp20) REVERT: F 547 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7872 (p) REVERT: F 740 MET cc_start: 0.8574 (ttt) cc_final: 0.8316 (ttt) REVERT: F 936 ASP cc_start: 0.7477 (m-30) cc_final: 0.7227 (m-30) REVERT: G 269 TYR cc_start: 0.8420 (m-80) cc_final: 0.8196 (m-80) REVERT: G 400 PHE cc_start: 0.7176 (p90) cc_final: 0.6705 (p90) REVERT: G 554 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8067 (tttp) REVERT: G 586 ASP cc_start: 0.8657 (m-30) cc_final: 0.8380 (m-30) REVERT: G 820 ASP cc_start: 0.8323 (t70) cc_final: 0.7995 (m-30) REVERT: G 1084 ASP cc_start: 0.7885 (p0) cc_final: 0.7560 (p0) REVERT: G 1092 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7859 (mt-10) outliers start: 97 outliers final: 45 residues processed: 377 average time/residue: 0.5721 time to fit residues: 270.2514 Evaluate side-chains 351 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 292 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 566 TRP Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 755 GLN Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 353 TRP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1038 LYS Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain F residue 1123 SER Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1142 GLN Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain G residue 554 LYS Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 724 THR Chi-restraints excluded: chain G residue 747 THR Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain G residue 994 ASP Chi-restraints excluded: chain G residue 1081 ILE Chi-restraints excluded: chain G residue 1117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 115 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 406 optimal weight: 0.4980 chunk 307 optimal weight: 0.7980 chunk 249 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 364 optimal weight: 4.9990 chunk 419 optimal weight: 0.6980 chunk 245 optimal weight: 0.4980 chunk 158 optimal weight: 0.8980 chunk 32 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 76 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 ASN E 239 GLN E 703 ASN E1002 GLN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 360 ASN F 448 ASN F1005 GLN G 52 GLN G 280 ASN G 675 GLN G1002 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.243365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3947 r_free = 0.3947 target = 0.157619 restraints weight = 42956.273| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.75 r_work: 0.3392 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 36190 Z= 0.133 Angle : 0.600 22.338 49333 Z= 0.297 Chirality : 0.045 0.682 5620 Planarity : 0.004 0.056 6238 Dihedral : 4.663 37.844 5972 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.08 % Favored : 97.83 % Rotamer: Outliers : 1.94 % Allowed : 11.62 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 aren not related in a simple way. whole: 0.69 (0.12), residues: 4284 helix: 1.69 (0.13), residues: 1480 sheet: 0.35 (0.19), residues: 624 loop : -0.32 (0.13), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 357 TYR 0.032 0.001 TYR E 612 PHE 0.037 0.001 PHE C 315 TRP 0.046 0.001 TRP A 461 HIS 0.015 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00301 (36080) covalent geometry : angle 0.58104 (49056) SS BOND : bond 0.00375 ( 44) SS BOND : angle 1.31059 ( 88) hydrogen bonds : bond 0.04321 ( 1614) hydrogen bonds : angle 5.36183 ( 4629) Misc. bond : bond 0.00220 ( 2) link_BETA1-4 : bond 0.00479 ( 22) link_BETA1-4 : angle 2.29579 ( 66) link_NAG-ASN : bond 0.00431 ( 39) link_NAG-ASN : angle 2.37764 ( 117) link_NAG-THR : bond 0.00375 ( 3) link_NAG-THR : angle 2.02693 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 320 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7411 (mt) cc_final: 0.6591 (tm) REVERT: A 111 ASP cc_start: 0.5897 (t0) cc_final: 0.5474 (p0) REVERT: A 183 TYR cc_start: 0.2660 (t80) cc_final: 0.2307 (t80) REVERT: A 196 TYR cc_start: 0.3826 (OUTLIER) cc_final: 0.3472 (m-10) REVERT: A 219 ARG cc_start: 0.6395 (ppt170) cc_final: 0.5792 (mpp80) REVERT: A 225 ASP cc_start: 0.4367 (t0) cc_final: 0.3958 (t0) REVERT: A 455 MET cc_start: 0.7668 (ptt) cc_final: 0.7454 (pmm) REVERT: A 475 LYS cc_start: 0.6579 (mttt) cc_final: 0.6357 (mmtp) REVERT: A 557 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.5985 (mpt) REVERT: A 572 ASN cc_start: 0.6612 (m-40) cc_final: 0.5655 (t0) REVERT: A 579 MET cc_start: 0.4707 (OUTLIER) cc_final: 0.3519 (ppp) REVERT: C 144 LEU cc_start: 0.4478 (tp) cc_final: 0.3986 (pt) REVERT: C 157 ASP cc_start: 0.3832 (m-30) cc_final: 0.3174 (t0) REVERT: C 198 ASP cc_start: 0.3907 (m-30) cc_final: 0.3498 (p0) REVERT: C 222 LEU cc_start: 0.3382 (mt) cc_final: 0.3077 (tm) REVERT: C 270 MET cc_start: -0.0080 (OUTLIER) cc_final: -0.0575 (ttp) REVERT: C 306 ARG cc_start: 0.5834 (tpt-90) cc_final: 0.5526 (ttm-80) REVERT: C 360 MET cc_start: 0.3579 (ttt) cc_final: 0.3119 (tmm) REVERT: C 442 GLN cc_start: 0.4577 (tm-30) cc_final: 0.3713 (mm-40) REVERT: C 462 MET cc_start: 0.2467 (mtt) cc_final: 0.1732 (ptt) REVERT: C 480 MET cc_start: 0.2988 (mmm) cc_final: 0.2670 (mtm) REVERT: C 514 ARG cc_start: 0.6403 (ptp-170) cc_final: 0.5555 (ptm160) REVERT: C 566 TRP cc_start: 0.1891 (OUTLIER) cc_final: 0.1563 (p90) REVERT: C 587 TYR cc_start: 0.1445 (t80) cc_final: 0.1233 (t80) REVERT: E 153 MET cc_start: 0.2095 (mmm) cc_final: 0.0875 (ppp) REVERT: E 364 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7174 (p0) REVERT: E 755 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: E 820 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: E 964 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7835 (mptt) REVERT: E 1084 ASP cc_start: 0.7529 (p0) cc_final: 0.7127 (p0) REVERT: E 1142 GLN cc_start: 0.7078 (tp40) cc_final: 0.6398 (tm-30) REVERT: F 189 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7380 (tt) REVERT: F 200 TYR cc_start: 0.8013 (m-80) cc_final: 0.7572 (m-80) REVERT: F 281 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8213 (pp20) REVERT: F 547 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7722 (p) REVERT: F 740 MET cc_start: 0.8470 (ttt) cc_final: 0.8180 (ttt) REVERT: F 936 ASP cc_start: 0.7277 (m-30) cc_final: 0.7068 (m-30) REVERT: G 269 TYR cc_start: 0.8425 (m-80) cc_final: 0.8211 (m-80) REVERT: G 400 PHE cc_start: 0.6963 (p90) cc_final: 0.6468 (p90) REVERT: G 554 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7973 (tttp) REVERT: G 574 ASP cc_start: 0.8176 (p0) cc_final: 0.7941 (p0) REVERT: G 586 ASP cc_start: 0.8567 (m-30) cc_final: 0.8236 (m-30) REVERT: G 820 ASP cc_start: 0.8185 (t70) cc_final: 0.7802 (m-30) REVERT: G 1084 ASP cc_start: 0.7795 (p0) cc_final: 0.7525 (p0) REVERT: G 1092 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7802 (mt-10) outliers start: 74 outliers final: 42 residues processed: 366 average time/residue: 0.6194 time to fit residues: 282.9471 Evaluate side-chains 351 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 296 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 566 TRP Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 755 GLN Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 985 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 353 TRP Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1038 LYS Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain F residue 1123 SER Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1142 GLN Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain G residue 554 LYS Chi-restraints excluded: chain G residue 565 PHE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 724 THR Chi-restraints excluded: chain G residue 747 THR Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain G residue 994 ASP Chi-restraints excluded: chain G residue 1081 ILE Chi-restraints excluded: chain G residue 1117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 345 optimal weight: 4.9990 chunk 387 optimal weight: 0.0370 chunk 107 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 382 optimal weight: 0.9990 chunk 291 optimal weight: 0.8980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS C 76 GLN E 505 HIS E 703 ASN E1002 GLN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 360 ASN F1101 HIS F1119 ASN G 52 GLN G 675 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.240260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.169473 restraints weight = 43494.162| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.50 r_work: 0.3405 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36190 Z= 0.139 Angle : 0.600 15.714 49333 Z= 0.297 Chirality : 0.044 0.285 5620 Planarity : 0.004 0.055 6238 Dihedral : 4.649 48.753 5972 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.71 % Rotamer: Outliers : 2.15 % Allowed : 11.86 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 aren not related in a simple way. whole: 0.66 (0.13), residues: 4284 helix: 1.67 (0.13), residues: 1480 sheet: 0.37 (0.19), residues: 614 loop : -0.36 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 582 TYR 0.031 0.001 TYR E 612 PHE 0.031 0.001 PHE C 356 TRP 0.050 0.002 TRP A 461 HIS 0.011 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00317 (36080) covalent geometry : angle 0.57817 (49056) SS BOND : bond 0.00623 ( 44) SS BOND : angle 1.25233 ( 88) hydrogen bonds : bond 0.04332 ( 1614) hydrogen bonds : angle 5.34868 ( 4629) Misc. bond : bond 0.00449 ( 2) link_BETA1-4 : bond 0.00508 ( 22) link_BETA1-4 : angle 2.25546 ( 66) link_NAG-ASN : bond 0.00469 ( 39) link_NAG-ASN : angle 2.68974 ( 117) link_NAG-THR : bond 0.00343 ( 3) link_NAG-THR : angle 2.00125 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 309 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7428 (mt) cc_final: 0.6605 (tm) REVERT: A 111 ASP cc_start: 0.5794 (t0) cc_final: 0.5387 (p0) REVERT: A 112 LYS cc_start: 0.4919 (mmtm) cc_final: 0.4642 (mmtt) REVERT: A 142 LEU cc_start: 0.0019 (tp) cc_final: -0.0292 (mp) REVERT: A 183 TYR cc_start: 0.2480 (t80) cc_final: 0.2176 (t80) REVERT: A 196 TYR cc_start: 0.3866 (OUTLIER) cc_final: 0.3319 (m-10) REVERT: A 219 ARG cc_start: 0.6254 (ppt170) cc_final: 0.5680 (mpp80) REVERT: A 225 ASP cc_start: 0.4495 (t0) cc_final: 0.4075 (t0) REVERT: A 557 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.5912 (mpm) REVERT: A 572 ASN cc_start: 0.6634 (m-40) cc_final: 0.5793 (m-40) REVERT: A 579 MET cc_start: 0.4677 (OUTLIER) cc_final: 0.3506 (ppp) REVERT: C 144 LEU cc_start: 0.4382 (tp) cc_final: 0.4012 (pt) REVERT: C 157 ASP cc_start: 0.3896 (m-30) cc_final: 0.3191 (t0) REVERT: C 198 ASP cc_start: 0.3968 (m-30) cc_final: 0.3503 (p0) REVERT: C 270 MET cc_start: 0.0376 (OUTLIER) cc_final: -0.0625 (ttp) REVERT: C 306 ARG cc_start: 0.5774 (tpt-90) cc_final: 0.5496 (ttm-80) REVERT: C 360 MET cc_start: 0.3641 (ttt) cc_final: 0.2962 (tmm) REVERT: C 442 GLN cc_start: 0.4383 (tm-30) cc_final: 0.3329 (mm110) REVERT: C 446 ILE cc_start: 0.5597 (pt) cc_final: 0.5282 (pp) REVERT: C 462 MET cc_start: 0.2635 (mtt) cc_final: 0.1661 (ptt) REVERT: C 514 ARG cc_start: 0.6425 (ptp-170) cc_final: 0.5519 (ptm160) REVERT: C 566 TRP cc_start: 0.1905 (OUTLIER) cc_final: 0.1489 (p90) REVERT: E 90 VAL cc_start: 0.8214 (t) cc_final: 0.8005 (p) REVERT: E 153 MET cc_start: 0.2157 (mmm) cc_final: 0.0922 (ppp) REVERT: E 364 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7050 (p0) REVERT: E 755 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: E 820 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8473 (m-30) REVERT: E 964 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7873 (mptt) REVERT: E 1084 ASP cc_start: 0.7564 (p0) cc_final: 0.7201 (p0) REVERT: E 1142 GLN cc_start: 0.7175 (tp40) cc_final: 0.6518 (tm-30) REVERT: F 189 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7510 (tt) REVERT: F 190 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.7917 (mtm-85) REVERT: F 200 TYR cc_start: 0.8112 (m-80) cc_final: 0.7699 (m-80) REVERT: F 281 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8217 (pp20) REVERT: F 357 ARG cc_start: 0.7143 (mtp180) cc_final: 0.6810 (ttt180) REVERT: F 740 MET cc_start: 0.8488 (ttt) cc_final: 0.8203 (ttt) REVERT: F 936 ASP cc_start: 0.7361 (m-30) cc_final: 0.7134 (m-30) REVERT: F 1005 GLN cc_start: 0.8880 (mt0) cc_final: 0.8670 (mt0) REVERT: G 269 TYR cc_start: 0.8427 (m-80) cc_final: 0.8183 (m-80) REVERT: G 281 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8277 (pp20) REVERT: G 319 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7483 (ttp-170) REVERT: G 574 ASP cc_start: 0.8271 (p0) cc_final: 0.8039 (p0) REVERT: G 586 ASP cc_start: 0.8588 (m-30) cc_final: 0.8285 (m-30) REVERT: G 820 ASP cc_start: 0.8246 (t70) cc_final: 0.7879 (m-30) REVERT: G 1084 ASP cc_start: 0.7791 (p0) cc_final: 0.7519 (p0) REVERT: G 1092 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7780 (mt-10) outliers start: 82 outliers final: 45 residues processed: 362 average time/residue: 0.5608 time to fit residues: 253.7143 Evaluate side-chains 352 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 566 TRP Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 565 PHE Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 755 GLN Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 353 TRP Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1038 LYS Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain F residue 1123 SER Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1142 GLN Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain G residue 319 ARG Chi-restraints excluded: chain G residue 565 PHE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 724 THR Chi-restraints excluded: chain G residue 747 THR Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain G residue 994 ASP Chi-restraints excluded: chain G residue 1081 ILE Chi-restraints excluded: chain G residue 1117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 281 optimal weight: 0.8980 chunk 110 optimal weight: 40.0000 chunk 176 optimal weight: 0.5980 chunk 231 optimal weight: 0.6980 chunk 428 optimal weight: 0.0020 chunk 315 optimal weight: 0.3980 chunk 381 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 284 optimal weight: 0.0980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN E 607 GLN E1002 GLN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 360 ASN G 280 ASN G 675 GLN G1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.246185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.178189 restraints weight = 43742.161| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.48 r_work: 0.3451 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36190 Z= 0.117 Angle : 0.593 13.532 49333 Z= 0.292 Chirality : 0.043 0.280 5620 Planarity : 0.004 0.057 6238 Dihedral : 4.580 59.346 5972 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.05 % Favored : 97.81 % Rotamer: Outliers : 1.44 % Allowed : 12.99 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 aren not related in a simple way. whole: 0.70 (0.13), residues: 4284 helix: 1.69 (0.13), residues: 1487 sheet: 0.36 (0.20), residues: 609 loop : -0.32 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 190 TYR 0.027 0.001 TYR E 612 PHE 0.042 0.001 PHE C 314 TRP 0.057 0.002 TRP A 461 HIS 0.015 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00258 (36080) covalent geometry : angle 0.57492 (49056) SS BOND : bond 0.00361 ( 44) SS BOND : angle 1.14108 ( 88) hydrogen bonds : bond 0.04122 ( 1614) hydrogen bonds : angle 5.27176 ( 4629) Misc. bond : bond 0.00497 ( 2) link_BETA1-4 : bond 0.00485 ( 22) link_BETA1-4 : angle 2.20725 ( 66) link_NAG-ASN : bond 0.00420 ( 39) link_NAG-ASN : angle 2.44733 ( 117) link_NAG-THR : bond 0.00372 ( 3) link_NAG-THR : angle 1.96948 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7425 (mt) cc_final: 0.6599 (tm) REVERT: A 100 LEU cc_start: 0.3256 (pp) cc_final: 0.2912 (pp) REVERT: A 111 ASP cc_start: 0.5745 (t0) cc_final: 0.5303 (p0) REVERT: A 142 LEU cc_start: 0.0253 (tp) cc_final: -0.0066 (mp) REVERT: A 183 TYR cc_start: 0.2499 (t80) cc_final: 0.2138 (t80) REVERT: A 196 TYR cc_start: 0.3827 (OUTLIER) cc_final: 0.3333 (m-10) REVERT: A 219 ARG cc_start: 0.6212 (ppt170) cc_final: 0.5667 (mpp80) REVERT: A 225 ASP cc_start: 0.4647 (t0) cc_final: 0.4215 (t0) REVERT: A 557 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.5884 (mpm) REVERT: A 572 ASN cc_start: 0.6667 (m-40) cc_final: 0.5467 (t0) REVERT: A 579 MET cc_start: 0.4676 (OUTLIER) cc_final: 0.3476 (ppp) REVERT: C 144 LEU cc_start: 0.4278 (tp) cc_final: 0.3913 (pt) REVERT: C 157 ASP cc_start: 0.3907 (m-30) cc_final: 0.3196 (t0) REVERT: C 198 ASP cc_start: 0.3963 (m-30) cc_final: 0.3501 (p0) REVERT: C 270 MET cc_start: 0.0203 (OUTLIER) cc_final: -0.0748 (ttp) REVERT: C 306 ARG cc_start: 0.5730 (tpt-90) cc_final: 0.5488 (ttm-80) REVERT: C 360 MET cc_start: 0.3773 (ttt) cc_final: 0.3138 (tmm) REVERT: C 373 HIS cc_start: 0.4455 (m90) cc_final: 0.4125 (m170) REVERT: C 442 GLN cc_start: 0.4412 (tm-30) cc_final: 0.3368 (mm-40) REVERT: C 446 ILE cc_start: 0.5557 (pt) cc_final: 0.5217 (pp) REVERT: C 462 MET cc_start: 0.2503 (mtt) cc_final: 0.1740 (ptt) REVERT: C 480 MET cc_start: 0.2648 (mmm) cc_final: 0.2324 (mtm) REVERT: C 514 ARG cc_start: 0.6398 (ptp-170) cc_final: 0.5476 (ptm160) REVERT: C 566 TRP cc_start: 0.1872 (OUTLIER) cc_final: 0.1452 (p90) REVERT: E 90 VAL cc_start: 0.8196 (t) cc_final: 0.7952 (p) REVERT: E 153 MET cc_start: 0.2116 (mmm) cc_final: 0.0930 (ppp) REVERT: E 364 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.6983 (p0) REVERT: E 755 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: E 820 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: E 1084 ASP cc_start: 0.7455 (p0) cc_final: 0.7109 (p0) REVERT: E 1142 GLN cc_start: 0.7226 (tp40) cc_final: 0.6561 (tm-30) REVERT: F 189 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7566 (tt) REVERT: F 200 TYR cc_start: 0.8122 (m-80) cc_final: 0.7688 (m-80) REVERT: F 281 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8236 (pp20) REVERT: F 347 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6947 (t80) REVERT: F 740 MET cc_start: 0.8480 (ttt) cc_final: 0.8197 (ttt) REVERT: F 936 ASP cc_start: 0.7312 (m-30) cc_final: 0.7086 (m-30) REVERT: F 1038 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8805 (mptt) REVERT: G 269 TYR cc_start: 0.8387 (m-80) cc_final: 0.8168 (m-80) REVERT: G 319 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7525 (ttp-170) REVERT: G 574 ASP cc_start: 0.8253 (p0) cc_final: 0.8016 (p0) REVERT: G 586 ASP cc_start: 0.8588 (m-30) cc_final: 0.8277 (m-30) REVERT: G 949 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7204 (mt0) REVERT: G 1084 ASP cc_start: 0.7723 (p0) cc_final: 0.7484 (p0) REVERT: G 1092 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7755 (mt-10) REVERT: G 1119 ASN cc_start: 0.8235 (m-40) cc_final: 0.8030 (m-40) outliers start: 55 outliers final: 24 residues processed: 354 average time/residue: 0.5281 time to fit residues: 232.9560 Evaluate side-chains 333 residues out of total 3813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 566 TRP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 755 GLN Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 353 TRP Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1038 LYS Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain F residue 1123 SER Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain G residue 319 ARG Chi-restraints excluded: chain G residue 565 PHE Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 747 THR Chi-restraints excluded: chain G residue 1117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 176 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 391 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 377 optimal weight: 0.4980 chunk 71 optimal weight: 7.9990 chunk 390 optimal weight: 0.1980 chunk 209 optimal weight: 0.7980 chunk 378 optimal weight: 0.7980 chunk 291 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN E 703 ASN E1002 GLN F 207 HIS ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 360 ASN F1005 GLN F1119 ASN G 52 GLN G 87 ASN G 675 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.245673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.177253 restraints weight = 43674.560| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.55 r_work: 0.3434 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36190 Z= 0.130 Angle : 0.595 12.608 49333 Z= 0.294 Chirality : 0.044 0.288 5620 Planarity : 0.004 0.067 6238 Dihedral : 4.524 52.952 5972 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % Rotamer: Outliers : 1.31 % Allowed : 13.25 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 aren not related in a simple way. whole: 0.66 (0.13), residues: 4284 helix: 1.66 (0.13), residues: 1487 sheet: 0.30 (0.20), residues: 623 loop : -0.34 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 582 TYR 0.029 0.001 TYR E 612 PHE 0.039 0.001 PHE G 400 TRP 0.062 0.001 TRP A 461 HIS 0.010 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00296 (36080) covalent geometry : angle 0.57786 (49056) SS BOND : bond 0.00370 ( 44) SS BOND : angle 1.13564 ( 88) hydrogen bonds : bond 0.04199 ( 1614) hydrogen bonds : angle 5.28974 ( 4629) Misc. bond : bond 0.00481 ( 2) link_BETA1-4 : bond 0.00503 ( 22) link_BETA1-4 : angle 2.15449 ( 66) link_NAG-ASN : bond 0.00404 ( 39) link_NAG-ASN : angle 2.32068 ( 117) link_NAG-THR : bond 0.00356 ( 3) link_NAG-THR : angle 1.92690 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17358.25 seconds wall clock time: 295 minutes 16.50 seconds (17716.50 seconds total)