Starting phenix.real_space_refine on Sun Jul 5 08:15:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jv6_22494/07_2026/7jv6_22494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jv6_22494/07_2026/7jv6_22494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7jv6_22494/07_2026/7jv6_22494.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jv6_22494/07_2026/7jv6_22494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jv6_22494/07_2026/7jv6_22494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jv6_22494/07_2026/7jv6_22494.map" model { file = "/net/cci-nas-00/data/ceres_data/7jv6_22494/07_2026/7jv6_22494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jv6_22494/07_2026/7jv6_22494.cif" } resolution = 3.0 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= 0.004 sd= 0.076 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 114 5.16 5 C 16832 2.51 5 N 4476 2.21 5 O 5226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26648 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7476 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 48, 'TRANS': 928} Chain breaks: 11 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 5, 'PHE:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 215 Chain: "L" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'HIS:plan': 2, 'TYR:plan': 6, 'TRP:plan': 2, 'PHE:plan': 3, 'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 149 Chain: "B" Number of atoms: 7476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7476 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 48, 'TRANS': 928} Chain breaks: 11 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 107 Chain: "C" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 5, 'PHE:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 215 Chain: "D" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'HIS:plan': 2, 'TYR:plan': 6, 'TRP:plan': 2, 'PHE:plan': 3, 'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 149 Chain: "E" Number of atoms: 7476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7476 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 48, 'TRANS': 928} Chain breaks: 11 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 107 Chain: "F" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 5, 'PHE:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 215 Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 546 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'HIS:plan': 2, 'TYR:plan': 6, 'TRP:plan': 2, 'PHE:plan': 3, 'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 149 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.32, per 1000 atoms: 0.20 Number of scatterers: 26648 At special positions: 0 Unit cell: (137.55, 145.95, 191.1, 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 114 16.00 O 5226 8.00 N 4476 7.00 C 16832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.33 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.33 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.01 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.02 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.06 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.33 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 343 " " NAG E1307 " - " ASN E 603 " " NAG E1308 " - " ASN E 616 " " NAG E1309 " - " ASN E 657 " " NAG E1310 " - " ASN E 709 " " NAG E1311 " - " ASN E1074 " " NAG E1312 " - " ASN E 165 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN E 717 " " NAG S 1 " - " ASN E 801 " " NAG T 1 " - " ASN E1098 " " NAG U 1 " - " ASN E1134 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 869.7 milliseconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 66 sheets defined 21.8% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 501 through 501 No H-bonds generated for 'chain 'A' and resid 501 through 501' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.827A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.561A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.008A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.195A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.827A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.561A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.879A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.008A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 501 through 501 No H-bonds generated for 'chain 'E' and resid 501 through 501' Processing helix chain 'E' and resid 503 through 505 No H-bonds generated for 'chain 'E' and resid 503 through 505' Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 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 removed outlier: 3.827A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 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 908 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.561A pdb=" N SER E 940 " --> pdb=" O ASP E 936 " (cutoff:3.500A) 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: 3.879A 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 982 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.008A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'G' and resid 30 through 34 Processing helix chain 'G' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.007A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.822A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.308A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.596A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.721A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.283A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.863A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE A 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.444A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.917A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.671A pdb=" N ALA A 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.722A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.851A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.635A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.822A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.308A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.596A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.722A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.283A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.444A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.917A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.722A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.850A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AE8, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.635A pdb=" N TRP D 37 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AF2, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.007A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.308A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.596A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.721A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.282A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.119A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.444A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AG2, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.917A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AG6, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.722A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'F' and resid 11 through 12 removed outlier: 5.850A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AH1, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AH2, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.635A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 9 through 12 1284 hydrogen bonds defined for protein. 3447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.85 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 8292 1.34 - 1.48: 7818 1.48 - 1.63: 10911 1.63 - 1.78: 24 1.78 - 1.92: 114 Bond restraints: 27159 Sorted by residual: bond pdb=" CB LEU A1145 " pdb=" CG LEU A1145 " ideal model delta sigma weight residual 1.530 1.604 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" CB LEU E1145 " pdb=" CG LEU E1145 " ideal model delta sigma weight residual 1.530 1.604 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CB LEU B1145 " pdb=" CG LEU B1145 " ideal model delta sigma weight residual 1.530 1.604 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.33e+01 bond pdb=" CB ASN E 422 " pdb=" CG ASN E 422 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.32e+01 ... (remaining 27154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 28982 1.52 - 3.05: 6474 3.05 - 4.57: 1189 4.57 - 6.09: 353 6.09 - 7.61: 93 Bond angle restraints: 37091 Sorted by residual: angle pdb=" C ASP E1139 " pdb=" N PRO E1140 " pdb=" CA PRO E1140 " ideal model delta sigma weight residual 119.56 127.01 -7.45 1.02e+00 9.61e-01 5.33e+01 angle pdb=" C ASP B1139 " pdb=" N PRO B1140 " pdb=" CA PRO B1140 " ideal model delta sigma weight residual 119.56 126.99 -7.43 1.02e+00 9.61e-01 5.30e+01 angle pdb=" C ASP A1139 " pdb=" N PRO A1140 " pdb=" CA PRO A1140 " ideal model delta sigma weight residual 119.56 126.98 -7.42 1.02e+00 9.61e-01 5.29e+01 angle pdb=" C LYS E 811 " pdb=" N PRO E 812 " pdb=" CA PRO E 812 " ideal model delta sigma weight residual 119.56 126.60 -7.04 1.02e+00 9.61e-01 4.77e+01 angle pdb=" C LYS B 811 " pdb=" N PRO B 812 " pdb=" CA PRO B 812 " ideal model delta sigma weight residual 119.56 126.60 -7.04 1.02e+00 9.61e-01 4.77e+01 ... (remaining 37086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 15036 17.64 - 35.29: 399 35.29 - 52.93: 72 52.93 - 70.58: 57 70.58 - 88.22: 18 Dihedral angle restraints: 15582 sinusoidal: 5199 harmonic: 10383 Sorted by residual: dihedral pdb=" CB CYS E1032 " pdb=" SG CYS E1032 " pdb=" SG CYS E1043 " pdb=" CB CYS E1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.84 -77.84 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.83 -77.83 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.83 -77.83 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 15579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3470 0.093 - 0.186: 758 0.186 - 0.278: 191 0.278 - 0.371: 66 0.371 - 0.464: 27 Chirality restraints: 4512 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.55e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.39e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.28e+01 ... (remaining 4509 not shown) Planarity restraints: 4858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 331 " -0.051 2.00e-02 2.50e+03 5.12e-02 3.28e+01 pdb=" CG ASN E 331 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN E 331 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN E 331 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.050 2.00e-02 2.50e+03 5.09e-02 3.24e+01 pdb=" CG ASN B 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.050 2.00e-02 2.50e+03 5.07e-02 3.21e+01 pdb=" CG ASN A 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.061 2.00e-02 2.50e+03 ... (remaining 4855 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 10827 2.90 - 3.40: 24007 3.40 - 3.90: 44277 3.90 - 4.40: 49947 4.40 - 4.90: 82746 Nonbonded interactions: 211804 Sorted by model distance: nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.402 3.120 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.402 3.120 nonbonded pdb=" NZ LYS E1028 " pdb=" O PHE E1042 " model vdw 2.402 3.120 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.409 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.409 3.120 ... (remaining 211799 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' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'D' and (resid 2 through 81 or (resid 82 through 89 and (name N or name C \ A or name C or name O or name CB )) or resid 90 through 110)) selection = (chain 'G' and (resid 2 through 34 or (resid 35 through 41 and (name N or name C \ A or name C or name O or name CB )) or resid 42 through 81 or (resid 82 through \ 89 and (name N or name CA or name C or name O or name CB )) or resid 90 through \ 110)) selection = (chain 'L' and (resid 2 through 34 or (resid 35 through 41 and (name N or name C \ A or name C or name O or name CB )) or resid 42 through 110)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.170 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 : 0.015 0.302 27264 Z= 0.816 Angle : 1.427 13.368 37361 Z= 0.954 Chirality : 0.095 0.464 4512 Planarity : 0.005 0.026 4810 Dihedral : 10.085 88.223 8757 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.13), residues: 3528 helix: 0.02 (0.18), residues: 705 sheet: 0.69 (0.16), residues: 942 loop : 0.64 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.036 0.004 TYR E 495 PHE 0.022 0.003 PHE E 515 TRP 0.016 0.005 TRP A 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01444 / 0.79 (27159) covalent geometry : angle 1.40519 / 0.95 (37091) SS BOND : bond 0.07881 / 5.58 ( 45) SS BOND : angle 4.03933 / 2.78 ( 90) hydrogen bonds : bond 0.16489 / 10.71 ( 1209) hydrogen bonds : angle 8.32793 / 5.77 ( 3447) link_BETA1-4 : bond 0.06888 / 4.11 ( 12) link_BETA1-4 : angle 3.77864 / 2.36 ( 36) link_NAG-ASN : bond 0.06674 / 4.16 ( 48) link_NAG-ASN : angle 2.42293 / 1.59 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 0.774 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 81 ASN cc_start: 0.6255 (p0) cc_final: 0.5903 (m-40) REVERT: A 561 PRO cc_start: 0.5802 (Cg_exo) cc_final: 0.5563 (Cg_endo) REVERT: A 572 THR cc_start: 0.6665 (p) cc_final: 0.6438 (p) REVERT: B 81 ASN cc_start: 0.6247 (p0) cc_final: 0.5919 (m-40) REVERT: B 1050 MET cc_start: 0.8419 (ptt) cc_final: 0.8187 (ptm) REVERT: E 32 PHE cc_start: 0.6123 (m-80) cc_final: 0.5915 (m-80) REVERT: E 81 ASN cc_start: 0.6177 (p0) cc_final: 0.5786 (m-40) REVERT: E 395 VAL cc_start: 0.8037 (t) cc_final: 0.7834 (t) REVERT: E 572 THR cc_start: 0.6567 (p) cc_final: 0.6338 (p) REVERT: E 960 ASN cc_start: 0.7718 (m-40) cc_final: 0.7468 (m-40) outliers start: 0 outliers final: 1 residues processed: 545 average time/residue: 0.4537 time to fit residues: 298.6573 Evaluate side-chains 256 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 770 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 764 ASN A 804 GLN A 907 ASN A 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 784 GLN B 935 GLN B 957 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 ASN E 764 ASN E 784 GLN E 935 GLN E 957 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.195459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.173764 restraints weight = 34936.478| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 1.19 r_work: 0.3789 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27264 Z= 0.165 Angle : 0.640 10.006 37361 Z= 0.341 Chirality : 0.046 0.191 4512 Planarity : 0.004 0.033 4810 Dihedral : 4.593 25.000 3785 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.19 % Allowed : 9.35 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3528 helix: 1.32 (0.20), residues: 675 sheet: 0.34 (0.15), residues: 993 loop : 0.39 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 466 TYR 0.024 0.002 TYR B 495 PHE 0.020 0.002 PHE B 855 TRP 0.010 0.001 TRP A 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (27159) covalent geometry : angle 0.62023 / 0.34 (37091) SS BOND : bond 0.00589 / 0.41 ( 45) SS BOND : angle 1.45040 / 0.97 ( 90) hydrogen bonds : bond 0.05062 / 3.29 ( 1209) hydrogen bonds : angle 6.23986 / 4.35 ( 3447) link_BETA1-4 : bond 0.00441 / 0.27 ( 12) link_BETA1-4 : angle 2.08128 / 1.28 ( 36) link_NAG-ASN : bond 0.00373 / 0.25 ( 48) link_NAG-ASN : angle 2.16088 / 1.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6431 (p0) cc_final: 0.6014 (m-40) REVERT: A 875 SER cc_start: 0.8523 (t) cc_final: 0.8217 (m) REVERT: B 50 SER cc_start: 0.7530 (t) cc_final: 0.7030 (m) REVERT: B 81 ASN cc_start: 0.6518 (p0) cc_final: 0.6273 (m-40) REVERT: B 646 ARG cc_start: 0.7008 (mmm-85) cc_final: 0.6798 (mmm-85) REVERT: E 32 PHE cc_start: 0.6447 (m-80) cc_final: 0.6136 (m-10) REVERT: E 81 ASN cc_start: 0.6688 (p0) cc_final: 0.6134 (m-40) REVERT: E 287 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: E 960 ASN cc_start: 0.7912 (m-40) cc_final: 0.7701 (m-40) outliers start: 54 outliers final: 24 residues processed: 315 average time/residue: 0.4344 time to fit residues: 166.4353 Evaluate side-chains 232 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 702 GLU Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 231 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 311 optimal weight: 0.5980 chunk 157 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 284 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 331 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 764 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 957 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 GLN E 764 ASN E 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.193059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.166007 restraints weight = 34860.128| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.42 r_work: 0.3574 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27264 Z= 0.155 Angle : 0.572 11.864 37361 Z= 0.301 Chirality : 0.044 0.180 4512 Planarity : 0.004 0.037 4810 Dihedral : 4.356 22.542 3783 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.80 % Allowed : 10.81 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3528 helix: 1.52 (0.20), residues: 678 sheet: 0.16 (0.15), residues: 963 loop : 0.15 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.020 0.002 TYR A 365 PHE 0.021 0.002 PHE A 140 TRP 0.009 0.001 TRP B 886 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (27159) covalent geometry : angle 0.55293 / 0.30 (37091) SS BOND : bond 0.00599 / 0.42 ( 45) SS BOND : angle 1.72671 / 0.98 ( 90) hydrogen bonds : bond 0.04319 / 2.84 ( 1209) hydrogen bonds : angle 5.71771 / 3.99 ( 3447) link_BETA1-4 : bond 0.00628 / 0.42 ( 12) link_BETA1-4 : angle 1.50660 / 0.96 ( 36) link_NAG-ASN : bond 0.00380 / 0.26 ( 48) link_NAG-ASN : angle 1.96254 / 1.31 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 229 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6642 (p0) cc_final: 0.5999 (m-40) REVERT: A 418 ILE cc_start: 0.8331 (mp) cc_final: 0.7960 (mt) REVERT: A 495 TYR cc_start: 0.6218 (m-80) cc_final: 0.5936 (m-80) REVERT: B 48 LEU cc_start: 0.7598 (mp) cc_final: 0.7368 (tp) REVERT: B 81 ASN cc_start: 0.6847 (p0) cc_final: 0.6060 (m-40) REVERT: B 1139 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6511 (p0) REVERT: E 32 PHE cc_start: 0.6641 (m-80) cc_final: 0.6267 (m-10) REVERT: E 81 ASN cc_start: 0.6853 (p0) cc_final: 0.6071 (m-40) REVERT: E 287 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: E 334 ASN cc_start: 0.7305 (m-40) cc_final: 0.7019 (p0) REVERT: E 390 LEU cc_start: 0.8392 (mt) cc_final: 0.8180 (mt) REVERT: E 960 ASN cc_start: 0.8194 (m-40) cc_final: 0.7984 (m-40) REVERT: E 1139 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6742 (p0) outliers start: 69 outliers final: 38 residues processed: 281 average time/residue: 0.4158 time to fit residues: 143.4440 Evaluate side-chains 227 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 957 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain E residue 1139 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 150 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 333 optimal weight: 30.0000 chunk 312 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 231 optimal weight: 0.0050 chunk 265 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.192682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154659 restraints weight = 34323.032| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.78 r_work: 0.3525 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 27264 Z= 0.146 Angle : 0.553 11.418 37361 Z= 0.289 Chirality : 0.044 0.177 4512 Planarity : 0.004 0.037 4810 Dihedral : 4.236 21.395 3783 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.97 % Allowed : 11.13 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3528 helix: 1.50 (0.20), residues: 681 sheet: -0.03 (0.15), residues: 996 loop : 0.07 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.023 0.002 TYR A 396 PHE 0.018 0.002 PHE B 194 TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (27159) covalent geometry : angle 0.53509 / 0.29 (37091) SS BOND : bond 0.00451 / 0.32 ( 45) SS BOND : angle 1.57720 / 0.90 ( 90) hydrogen bonds : bond 0.04025 / 2.65 ( 1209) hydrogen bonds : angle 5.53962 / 3.87 ( 3447) link_BETA1-4 : bond 0.00439 / 0.27 ( 12) link_BETA1-4 : angle 1.31543 / 0.84 ( 36) link_NAG-ASN : bond 0.00331 / 0.23 ( 48) link_NAG-ASN : angle 1.86221 / 1.24 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 206 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6463 (p0) cc_final: 0.5886 (m-40) REVERT: A 418 ILE cc_start: 0.8259 (mp) cc_final: 0.7949 (mt) REVERT: A 869 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8526 (mtt) REVERT: A 1139 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6645 (p0) REVERT: B 50 SER cc_start: 0.7851 (t) cc_final: 0.7337 (m) REVERT: B 81 ASN cc_start: 0.6770 (p0) cc_final: 0.6051 (m-40) REVERT: B 287 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: E 32 PHE cc_start: 0.6555 (m-80) cc_final: 0.6267 (m-10) REVERT: E 81 ASN cc_start: 0.6972 (p0) cc_final: 0.6065 (m-40) REVERT: E 287 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: E 418 ILE cc_start: 0.8140 (mp) cc_final: 0.7829 (mt) REVERT: E 1086 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8076 (mtpt) outliers start: 73 outliers final: 36 residues processed: 265 average time/residue: 0.4348 time to fit residues: 140.9926 Evaluate side-chains 222 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Chi-restraints excluded: chain E residue 1123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 6 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 268 optimal weight: 8.9990 chunk 169 optimal weight: 0.6980 chunk 341 optimal weight: 50.0000 chunk 55 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 167 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 907 ASN A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 901 GLN E 271 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.190883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.167197 restraints weight = 34232.512| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.26 r_work: 0.3583 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27264 Z= 0.175 Angle : 0.564 9.519 37361 Z= 0.294 Chirality : 0.045 0.206 4512 Planarity : 0.004 0.039 4810 Dihedral : 4.278 21.028 3783 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.33 % Allowed : 11.54 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3528 helix: 1.45 (0.21), residues: 678 sheet: -0.16 (0.15), residues: 996 loop : -0.12 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 357 TYR 0.024 0.002 TYR B 453 PHE 0.028 0.002 PHE A 140 TRP 0.011 0.001 TRP B 886 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (27159) covalent geometry : angle 0.54712 / 0.29 (37091) SS BOND : bond 0.00457 / 0.32 ( 45) SS BOND : angle 1.56704 / 0.91 ( 90) hydrogen bonds : bond 0.04043 / 2.67 ( 1209) hydrogen bonds : angle 5.45572 / 3.81 ( 3447) link_BETA1-4 : bond 0.00345 / 0.20 ( 12) link_BETA1-4 : angle 1.22850 / 0.79 ( 36) link_NAG-ASN : bond 0.00333 / 0.23 ( 48) link_NAG-ASN : angle 1.85959 / 1.25 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 190 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6621 (p0) cc_final: 0.5852 (m-40) REVERT: A 319 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7240 (mtp-110) REVERT: A 357 ARG cc_start: 0.7764 (ttt90) cc_final: 0.7468 (ttt90) REVERT: A 418 ILE cc_start: 0.8445 (mp) cc_final: 0.8155 (mt) REVERT: B 81 ASN cc_start: 0.6912 (p0) cc_final: 0.6017 (m-40) REVERT: B 287 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: B 334 ASN cc_start: 0.7381 (m-40) cc_final: 0.7094 (t0) REVERT: B 614 ASP cc_start: 0.7334 (t0) cc_final: 0.6986 (t0) REVERT: B 1139 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6573 (p0) REVERT: E 32 PHE cc_start: 0.6738 (m-80) cc_final: 0.6320 (m-10) REVERT: E 81 ASN cc_start: 0.6921 (p0) cc_final: 0.5958 (m-40) REVERT: E 287 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: E 319 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7003 (mtp-110) REVERT: E 418 ILE cc_start: 0.8302 (mp) cc_final: 0.8027 (mt) REVERT: E 1086 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8341 (mtpt) REVERT: E 1113 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7747 (mt0) outliers start: 82 outliers final: 47 residues processed: 260 average time/residue: 0.4564 time to fit residues: 144.2014 Evaluate side-chains 222 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1086 LYS Chi-restraints excluded: chain E residue 1113 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 78 optimal weight: 2.9990 chunk 306 optimal weight: 0.3980 chunk 287 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 327 optimal weight: 0.7980 chunk 269 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 119 optimal weight: 0.8980 chunk 271 optimal weight: 8.9990 chunk 116 optimal weight: 50.0000 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 957 GLN B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN E 239 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.191952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.156282 restraints weight = 34379.717| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.63 r_work: 0.3645 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27264 Z= 0.130 Angle : 0.524 7.257 37361 Z= 0.274 Chirality : 0.044 0.197 4512 Planarity : 0.004 0.038 4810 Dihedral : 4.087 20.043 3783 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.89 % Allowed : 12.88 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3528 helix: 1.56 (0.21), residues: 675 sheet: -0.11 (0.15), residues: 936 loop : -0.16 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 567 TYR 0.016 0.001 TYR B1067 PHE 0.026 0.001 PHE A 140 TRP 0.006 0.001 TRP B 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (27159) covalent geometry : angle 0.50986 / 0.27 (37091) SS BOND : bond 0.00498 / 0.35 ( 45) SS BOND : angle 1.35925 / 0.84 ( 90) hydrogen bonds : bond 0.03708 / 2.45 ( 1209) hydrogen bonds : angle 5.27985 / 3.69 ( 3447) link_BETA1-4 : bond 0.00361 / 0.21 ( 12) link_BETA1-4 : angle 1.10621 / 0.72 ( 36) link_NAG-ASN : bond 0.00287 / 0.20 ( 48) link_NAG-ASN : angle 1.70184 / 1.13 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 187 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6576 (p0) cc_final: 0.5859 (m-40) REVERT: A 319 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7046 (mtp-110) REVERT: A 392 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: A 547 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8052 (p) REVERT: A 869 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8494 (mtt) REVERT: B 81 ASN cc_start: 0.6598 (p0) cc_final: 0.5885 (m-40) REVERT: B 287 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: B 614 ASP cc_start: 0.7175 (t0) cc_final: 0.6878 (t0) REVERT: B 1139 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6621 (p0) REVERT: E 32 PHE cc_start: 0.6614 (m-80) cc_final: 0.6336 (m-10) REVERT: E 81 ASN cc_start: 0.6727 (p0) cc_final: 0.5933 (m-40) REVERT: E 319 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6933 (mtp-110) REVERT: E 357 ARG cc_start: 0.7226 (ttt90) cc_final: 0.6962 (ttt90) REVERT: E 1086 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8156 (mtpt) outliers start: 71 outliers final: 39 residues processed: 244 average time/residue: 0.4660 time to fit residues: 136.8341 Evaluate side-chains 218 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 334 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 255 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.190573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.169613 restraints weight = 34064.329| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.10 r_work: 0.3648 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27264 Z= 0.165 Angle : 0.544 7.932 37361 Z= 0.283 Chirality : 0.045 0.213 4512 Planarity : 0.004 0.039 4810 Dihedral : 4.137 19.822 3783 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.17 % Allowed : 12.88 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3528 helix: 1.61 (0.21), residues: 657 sheet: -0.17 (0.15), residues: 936 loop : -0.26 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 567 TYR 0.018 0.001 TYR B 365 PHE 0.023 0.002 PHE A 140 TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (27159) covalent geometry : angle 0.52942 / 0.28 (37091) SS BOND : bond 0.00492 / 0.35 ( 45) SS BOND : angle 1.37210 / 0.83 ( 90) hydrogen bonds : bond 0.03868 / 2.57 ( 1209) hydrogen bonds : angle 5.29387 / 3.70 ( 3447) link_BETA1-4 : bond 0.00333 / 0.20 ( 12) link_BETA1-4 : angle 1.13099 / 0.73 ( 36) link_NAG-ASN : bond 0.00297 / 0.21 ( 48) link_NAG-ASN : angle 1.75609 / 1.16 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 187 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6817 (p0) cc_final: 0.5863 (m-40) REVERT: A 319 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7224 (mtp-110) REVERT: A 392 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: A 418 ILE cc_start: 0.8334 (mp) cc_final: 0.8022 (mt) REVERT: A 547 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8093 (p) REVERT: A 740 MET cc_start: 0.7729 (mmm) cc_final: 0.7525 (mmt) REVERT: A 869 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8545 (mtt) REVERT: B 81 ASN cc_start: 0.6882 (p0) cc_final: 0.5939 (m-40) REVERT: B 237 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.5893 (ptt-90) REVERT: B 287 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: B 614 ASP cc_start: 0.7457 (t0) cc_final: 0.7127 (t0) REVERT: B 1139 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6458 (p0) REVERT: E 32 PHE cc_start: 0.6776 (m-80) cc_final: 0.6437 (m-10) REVERT: E 81 ASN cc_start: 0.6957 (p0) cc_final: 0.5951 (m-40) REVERT: E 195 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7571 (ptmm) REVERT: E 319 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7009 (mtp-110) REVERT: E 357 ARG cc_start: 0.7426 (ttt90) cc_final: 0.7036 (ttt90) REVERT: E 1086 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8406 (mtpt) REVERT: E 1113 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7744 (mt0) outliers start: 78 outliers final: 42 residues processed: 245 average time/residue: 0.4934 time to fit residues: 145.3540 Evaluate side-chains 223 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Chi-restraints excluded: chain E residue 1113 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 275 optimal weight: 0.0040 chunk 133 optimal weight: 2.9990 chunk 337 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 chunk 348 optimal weight: 0.0050 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.192514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157453 restraints weight = 34290.831| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.62 r_work: 0.3680 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27264 Z= 0.112 Angle : 0.509 7.819 37361 Z= 0.265 Chirality : 0.044 0.193 4512 Planarity : 0.003 0.044 4810 Dihedral : 3.955 18.723 3783 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.72 % Allowed : 13.69 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3528 helix: 1.77 (0.21), residues: 657 sheet: -0.11 (0.15), residues: 936 loop : -0.22 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 567 TYR 0.017 0.001 TYR B1067 PHE 0.023 0.001 PHE A 140 TRP 0.004 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (27159) covalent geometry : angle 0.49652 / 0.26 (37091) SS BOND : bond 0.00402 / 0.28 ( 45) SS BOND : angle 1.19151 / 0.75 ( 90) hydrogen bonds : bond 0.03469 / 2.29 ( 1209) hydrogen bonds : angle 5.14302 / 3.59 ( 3447) link_BETA1-4 : bond 0.00391 / 0.23 ( 12) link_BETA1-4 : angle 1.04288 / 0.68 ( 36) link_NAG-ASN : bond 0.00267 / 0.19 ( 48) link_NAG-ASN : angle 1.59533 / 1.06 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6662 (p0) cc_final: 0.5713 (m-40) REVERT: A 319 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7040 (mtp-110) REVERT: A 392 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: A 418 ILE cc_start: 0.7907 (mp) cc_final: 0.7685 (mt) REVERT: A 869 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8484 (mtt) REVERT: B 81 ASN cc_start: 0.6677 (p0) cc_final: 0.5735 (m-40) REVERT: B 1139 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6616 (p0) REVERT: E 32 PHE cc_start: 0.6583 (m-80) cc_final: 0.6330 (m-10) REVERT: E 81 ASN cc_start: 0.6655 (p0) cc_final: 0.5800 (m-40) REVERT: E 319 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7107 (mtp-110) REVERT: E 357 ARG cc_start: 0.7147 (ttt90) cc_final: 0.6844 (ttt90) REVERT: E 1086 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8140 (mtpt) outliers start: 67 outliers final: 33 residues processed: 239 average time/residue: 0.4675 time to fit residues: 134.7450 Evaluate side-chains 214 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 205 optimal weight: 0.0980 chunk 312 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 272 optimal weight: 0.0980 chunk 149 optimal weight: 0.0370 chunk 146 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.193055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157660 restraints weight = 34294.914| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.64 r_work: 0.3675 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27264 Z= 0.104 Angle : 0.500 7.305 37361 Z= 0.261 Chirality : 0.043 0.183 4512 Planarity : 0.003 0.046 4810 Dihedral : 3.842 18.006 3783 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.95 % Allowed : 15.03 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3528 helix: 1.84 (0.21), residues: 660 sheet: -0.06 (0.16), residues: 903 loop : -0.20 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.018 0.001 TYR A 365 PHE 0.025 0.001 PHE A 140 TRP 0.004 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (27159) covalent geometry : angle 0.48810 / 0.26 (37091) SS BOND : bond 0.00354 / 0.25 ( 45) SS BOND : angle 1.13520 / 0.71 ( 90) hydrogen bonds : bond 0.03353 / 2.21 ( 1209) hydrogen bonds : angle 5.05049 / 3.53 ( 3447) link_BETA1-4 : bond 0.00448 / 0.27 ( 12) link_BETA1-4 : angle 1.04961 / 0.68 ( 36) link_NAG-ASN : bond 0.00255 / 0.18 ( 48) link_NAG-ASN : angle 1.51808 / 1.01 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6651 (p0) cc_final: 0.5716 (m-40) REVERT: A 319 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7059 (mtp-110) REVERT: A 392 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: A 418 ILE cc_start: 0.7919 (mp) cc_final: 0.7685 (mt) REVERT: A 869 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8463 (mtt) REVERT: A 1144 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6950 (mt-10) REVERT: B 81 ASN cc_start: 0.6744 (p0) cc_final: 0.5707 (m-40) REVERT: B 1139 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6685 (p0) REVERT: E 32 PHE cc_start: 0.6583 (m-80) cc_final: 0.6326 (m-10) REVERT: E 81 ASN cc_start: 0.6651 (p0) cc_final: 0.5734 (m-40) REVERT: E 357 ARG cc_start: 0.7142 (ttt90) cc_final: 0.6828 (ttt90) REVERT: E 1086 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8123 (mtpt) outliers start: 48 outliers final: 27 residues processed: 226 average time/residue: 0.4475 time to fit residues: 123.0122 Evaluate side-chains 203 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 35 optimal weight: 0.7980 chunk 296 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 131 optimal weight: 0.0970 chunk 244 optimal weight: 1.9990 chunk 108 optimal weight: 40.0000 chunk 327 optimal weight: 0.1980 chunk 211 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.192975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.158894 restraints weight = 34334.917| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.61 r_work: 0.3681 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27264 Z= 0.111 Angle : 0.503 7.193 37361 Z= 0.262 Chirality : 0.044 0.190 4512 Planarity : 0.003 0.047 4810 Dihedral : 3.815 17.499 3783 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.83 % Allowed : 14.91 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3528 helix: 1.86 (0.21), residues: 660 sheet: -0.06 (0.16), residues: 927 loop : -0.17 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.017 0.001 TYR B1067 PHE 0.023 0.001 PHE A 140 TRP 0.005 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (27159) covalent geometry : angle 0.49133 / 0.26 (37091) SS BOND : bond 0.00351 / 0.24 ( 45) SS BOND : angle 1.15236 / 0.73 ( 90) hydrogen bonds : bond 0.03365 / 2.23 ( 1209) hydrogen bonds : angle 5.00882 / 3.50 ( 3447) link_BETA1-4 : bond 0.00389 / 0.23 ( 12) link_BETA1-4 : angle 1.02714 / 0.67 ( 36) link_NAG-ASN : bond 0.00250 / 0.18 ( 48) link_NAG-ASN : angle 1.51035 / 1.00 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6585 (p0) cc_final: 0.5590 (m-40) REVERT: A 319 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7023 (mtp-110) REVERT: A 392 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: A 418 ILE cc_start: 0.7945 (mp) cc_final: 0.7714 (mt) REVERT: A 869 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8442 (mtt) REVERT: A 1144 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6936 (mt-10) REVERT: B 81 ASN cc_start: 0.6744 (p0) cc_final: 0.5594 (m-40) REVERT: B 201 PHE cc_start: 0.7427 (t80) cc_final: 0.7040 (t80) REVERT: B 1139 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6776 (p0) REVERT: E 81 ASN cc_start: 0.6671 (p0) cc_final: 0.5708 (m-40) REVERT: E 319 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7091 (mtp-110) REVERT: E 357 ARG cc_start: 0.7102 (ttt90) cc_final: 0.6803 (ttt90) REVERT: E 1086 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8118 (mtpt) outliers start: 45 outliers final: 27 residues processed: 215 average time/residue: 0.4808 time to fit residues: 125.1800 Evaluate side-chains 208 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1086 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 191 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 329 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 103 optimal weight: 50.0000 chunk 104 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 145 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 239 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN E 239 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.191453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160006 restraints weight = 34098.626| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.57 r_work: 0.3558 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27264 Z= 0.143 Angle : 0.526 7.066 37361 Z= 0.274 Chirality : 0.044 0.201 4512 Planarity : 0.004 0.049 4810 Dihedral : 3.936 17.409 3783 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.95 % Allowed : 15.03 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3528 helix: 1.81 (0.21), residues: 657 sheet: -0.10 (0.15), residues: 912 loop : -0.24 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.017 0.001 TYR E 365 PHE 0.024 0.001 PHE A 140 TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (27159) covalent geometry : angle 0.51338 / 0.27 (37091) SS BOND : bond 0.00368 / 0.26 ( 45) SS BOND : angle 1.17376 / 0.74 ( 90) hydrogen bonds : bond 0.03624 / 2.40 ( 1209) hydrogen bonds : angle 5.08720 / 3.55 ( 3447) link_BETA1-4 : bond 0.00380 / 0.23 ( 12) link_BETA1-4 : angle 1.06308 / 0.69 ( 36) link_NAG-ASN : bond 0.00272 / 0.19 ( 48) link_NAG-ASN : angle 1.62426 / 1.07 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6468.45 seconds wall clock time: 123 minutes 14.21 seconds (7394.21 seconds total)