Starting phenix.real_space_refine on Fri Mar 6 00:33:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jv6_22494/03_2026/7jv6_22494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jv6_22494/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7jv6_22494/03_2026/7jv6_22494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jv6_22494/03_2026/7jv6_22494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jv6_22494/03_2026/7jv6_22494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jv6_22494/03_2026/7jv6_22494.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "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 dihedrals: 36 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.30, 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.29 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: 6.71 Time building geometry restraints manager: 2.48 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: 16209 17.64 - 35.29: 486 35.29 - 52.93: 72 52.93 - 70.58: 57 70.58 - 88.22: 18 Dihedral angle restraints: 16842 sinusoidal: 6459 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 16839 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 24.790 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 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 : 9.824 88.223 10017 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 covalent geometry : bond 0.01444 (27159) covalent geometry : angle 1.40519 (37091) SS BOND : bond 0.07881 ( 45) SS BOND : angle 4.03933 ( 90) hydrogen bonds : bond 0.16489 ( 1209) hydrogen bonds : angle 8.32793 ( 3447) link_BETA1-4 : bond 0.06888 ( 12) link_BETA1-4 : angle 3.77864 ( 36) link_NAG-ASN : bond 0.06674 ( 48) link_NAG-ASN : angle 2.42293 ( 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 : 0.960 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: 0.5172 time to fit residues: 338.0830 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 : 0.920 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 314 GLN 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 314 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.195416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.174933 restraints weight = 34960.834| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.15 r_work: 0.3807 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27264 Z= 0.162 Angle : 0.635 9.974 37361 Z= 0.339 Chirality : 0.046 0.196 4512 Planarity : 0.004 0.032 4810 Dihedral : 5.107 29.989 5045 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.28 % Allowed : 9.18 % Favored : 88.54 % 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: 0.69 (0.14), residues: 3528 helix: 1.25 (0.20), residues: 675 sheet: 0.34 (0.15), residues: 990 loop : 0.37 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 466 TYR 0.022 0.002 TYR B 495 PHE 0.020 0.002 PHE E 140 TRP 0.010 0.001 TRP A 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00370 (27159) covalent geometry : angle 0.61499 (37091) SS BOND : bond 0.00547 ( 45) SS BOND : angle 1.46827 ( 90) hydrogen bonds : bond 0.04980 ( 1209) hydrogen bonds : angle 6.20295 ( 3447) link_BETA1-4 : bond 0.00591 ( 12) link_BETA1-4 : angle 2.17280 ( 36) link_NAG-ASN : bond 0.00393 ( 48) link_NAG-ASN : angle 2.17029 ( 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 337 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6241 (p0) cc_final: 0.5933 (m-40) REVERT: B 50 SER cc_start: 0.7365 (t) cc_final: 0.6870 (m) REVERT: E 32 PHE cc_start: 0.6361 (m-80) cc_final: 0.6130 (m-10) REVERT: E 81 ASN cc_start: 0.6459 (p0) cc_final: 0.6127 (m-40) REVERT: E 287 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: E 960 ASN cc_start: 0.7668 (m-40) cc_final: 0.7453 (m-40) outliers start: 56 outliers final: 23 residues processed: 317 average time/residue: 0.5084 time to fit residues: 194.4038 Evaluate side-chains 222 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 547 THR Chi-restraints excluded: chain B residue 673 SER 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: 6.9990 chunk 248 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 311 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 244 optimal weight: 0.9980 chunk 284 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 331 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 GLN E 764 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.191535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.166588 restraints weight = 34709.453| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.35 r_work: 0.3574 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27264 Z= 0.199 Angle : 0.608 12.228 37361 Z= 0.320 Chirality : 0.046 0.203 4512 Planarity : 0.004 0.041 4810 Dihedral : 4.656 27.798 5043 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.54 % Allowed : 10.32 % Favored : 86.14 % 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: 0.36 (0.14), residues: 3528 helix: 1.38 (0.20), residues: 678 sheet: 0.02 (0.15), residues: 969 loop : 0.05 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 357 TYR 0.023 0.002 TYR E 365 PHE 0.025 0.002 PHE A 140 TRP 0.014 0.001 TRP B 886 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00469 (27159) covalent geometry : angle 0.58629 (37091) SS BOND : bond 0.00501 ( 45) SS BOND : angle 1.90911 ( 90) hydrogen bonds : bond 0.04595 ( 1209) hydrogen bonds : angle 5.77713 ( 3447) link_BETA1-4 : bond 0.00533 ( 12) link_BETA1-4 : angle 1.71193 ( 36) link_NAG-ASN : bond 0.00466 ( 48) link_NAG-ASN : angle 2.09230 ( 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 315 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 228 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6664 (p0) cc_final: 0.6033 (m-40) REVERT: A 100 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6637 (tt) REVERT: A 357 ARG cc_start: 0.7583 (ttt90) cc_final: 0.7348 (ttt90) REVERT: A 418 ILE cc_start: 0.8363 (mp) cc_final: 0.7999 (mt) REVERT: E 32 PHE cc_start: 0.6634 (m-80) cc_final: 0.6291 (m-10) REVERT: E 81 ASN cc_start: 0.6935 (p0) cc_final: 0.5962 (m-40) REVERT: E 287 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: E 334 ASN cc_start: 0.7506 (m-40) cc_final: 0.7240 (p0) REVERT: E 592 PHE cc_start: 0.7121 (p90) cc_final: 0.6908 (p90) REVERT: E 960 ASN cc_start: 0.8181 (m-40) cc_final: 0.7959 (m-40) REVERT: E 1086 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8316 (mtpt) outliers start: 87 outliers final: 37 residues processed: 295 average time/residue: 0.5087 time to fit residues: 182.1858 Evaluate side-chains 220 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 900 MET Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1030 SER 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 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL 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 E residue 287 ASP Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 531 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 150 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 333 optimal weight: 30.0000 chunk 312 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 231 optimal weight: 0.0020 chunk 265 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 675 GLN A 907 ASN A 957 GLN B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 901 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.191979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154820 restraints weight = 34342.469| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.72 r_work: 0.3603 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27264 Z= 0.145 Angle : 0.558 12.159 37361 Z= 0.291 Chirality : 0.044 0.204 4512 Planarity : 0.004 0.037 4810 Dihedral : 4.394 24.618 5043 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.97 % Allowed : 11.42 % Favored : 85.62 % 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: 1.48 (0.20), residues: 681 sheet: -0.08 (0.15), residues: 996 loop : -0.00 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.019 0.002 TYR E 365 PHE 0.017 0.001 PHE E 238 TRP 0.006 0.001 TRP B 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00337 (27159) covalent geometry : angle 0.53836 (37091) SS BOND : bond 0.00416 ( 45) SS BOND : angle 1.63822 ( 90) hydrogen bonds : bond 0.03991 ( 1209) hydrogen bonds : angle 5.54768 ( 3447) link_BETA1-4 : bond 0.00420 ( 12) link_BETA1-4 : angle 1.46012 ( 36) link_NAG-ASN : bond 0.00340 ( 48) link_NAG-ASN : angle 1.95956 ( 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 278 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 205 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6366 (p0) cc_final: 0.5824 (m-40) REVERT: A 100 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6932 (tt) REVERT: A 319 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7133 (mtp-110) REVERT: A 357 ARG cc_start: 0.7266 (ttt90) cc_final: 0.6951 (tmt-80) REVERT: B 287 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: B 614 ASP cc_start: 0.7273 (t0) cc_final: 0.6957 (t0) REVERT: E 32 PHE cc_start: 0.6612 (m-80) cc_final: 0.6389 (m-10) REVERT: E 81 ASN cc_start: 0.6646 (p0) cc_final: 0.5952 (m-40) REVERT: E 287 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: E 418 ILE cc_start: 0.7987 (mp) cc_final: 0.7726 (mt) REVERT: E 583 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6382 (pt0) outliers start: 73 outliers final: 38 residues processed: 265 average time/residue: 0.5381 time to fit residues: 171.4224 Evaluate side-chains 214 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 878 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE 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 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 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 391 CYS 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 583 GLU 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 1084 ASP 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: 0.8980 chunk 268 optimal weight: 7.9990 chunk 169 optimal weight: 0.4980 chunk 341 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN E 239 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4293 r_free = 0.4293 target = 0.191191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152969 restraints weight = 34325.138| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.78 r_work: 0.3510 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27264 Z= 0.154 Angle : 0.550 10.215 37361 Z= 0.287 Chirality : 0.044 0.214 4512 Planarity : 0.004 0.037 4810 Dihedral : 4.354 22.853 5043 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.84 % Allowed : 12.43 % Favored : 84.72 % 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: 1.44 (0.21), residues: 681 sheet: -0.15 (0.15), residues: 996 loop : -0.09 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.018 0.001 TYR B 495 PHE 0.021 0.001 PHE A 140 TRP 0.007 0.001 TRP B 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00363 (27159) covalent geometry : angle 0.53143 (37091) SS BOND : bond 0.00472 ( 45) SS BOND : angle 1.63632 ( 90) hydrogen bonds : bond 0.03945 ( 1209) hydrogen bonds : angle 5.43595 ( 3447) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 1.36007 ( 36) link_NAG-ASN : bond 0.00327 ( 48) link_NAG-ASN : angle 1.90958 ( 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 255 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 185 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6681 (p0) cc_final: 0.5830 (m-40) REVERT: A 319 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7242 (mtp-110) REVERT: A 357 ARG cc_start: 0.7466 (ttt90) cc_final: 0.7236 (ttt90) REVERT: A 418 ILE cc_start: 0.8250 (mp) cc_final: 0.7946 (mt) REVERT: B 287 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: B 614 ASP cc_start: 0.7546 (t0) cc_final: 0.7219 (t0) REVERT: E 32 PHE cc_start: 0.6716 (m-80) cc_final: 0.6353 (m-10) REVERT: E 81 ASN cc_start: 0.6754 (p0) cc_final: 0.5907 (m-40) REVERT: E 287 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: E 319 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7057 (mtp-110) REVERT: E 418 ILE cc_start: 0.8206 (mp) cc_final: 0.7947 (mt) REVERT: E 583 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6532 (pt0) REVERT: E 1086 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8109 (mtpt) REVERT: E 1113 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7685 (mt0) outliers start: 70 outliers final: 40 residues processed: 244 average time/residue: 0.5573 time to fit residues: 163.4122 Evaluate side-chains 217 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 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 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 702 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET 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 418 ILE 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 969 ASN 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 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 583 GLU 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: 0.6980 chunk 287 optimal weight: 0.6980 chunk 162 optimal weight: 8.9990 chunk 327 optimal weight: 0.0070 chunk 269 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 271 optimal weight: 8.9990 chunk 116 optimal weight: 50.0000 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 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 = 0.4292 r_free = 0.4292 target = 0.191291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155489 restraints weight = 34425.872| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.67 r_work: 0.3633 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 0.070 27264 Z= 0.142 Angle : 0.536 8.841 37361 Z= 0.279 Chirality : 0.044 0.215 4512 Planarity : 0.004 0.037 4810 Dihedral : 4.307 20.984 5043 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 0.19 (0.14), residues: 3528 helix: 1.53 (0.21), residues: 678 sheet: -0.15 (0.15), residues: 969 loop : -0.15 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.016 0.001 TYR B1067 PHE 0.017 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 covalent geometry : bond 0.00334 (27159) covalent geometry : angle 0.51842 (37091) SS BOND : bond 0.00422 ( 45) SS BOND : angle 1.49043 ( 90) hydrogen bonds : bond 0.03799 ( 1209) hydrogen bonds : angle 5.32050 ( 3447) link_BETA1-4 : bond 0.00409 ( 12) link_BETA1-4 : angle 1.27400 ( 36) link_NAG-ASN : bond 0.00301 ( 48) link_NAG-ASN : angle 1.86200 ( 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 : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6647 (p0) cc_final: 0.5905 (m-40) REVERT: A 319 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7096 (mtp-110) REVERT: A 357 ARG cc_start: 0.7243 (ttt90) cc_final: 0.7029 (ttt90) REVERT: A 392 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: A 418 ILE cc_start: 0.8128 (mp) cc_final: 0.7914 (mt) REVERT: A 547 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8062 (p) REVERT: B 614 ASP cc_start: 0.7142 (t0) cc_final: 0.6851 (t0) REVERT: E 32 PHE cc_start: 0.6655 (m-80) cc_final: 0.6353 (m-10) REVERT: E 81 ASN cc_start: 0.6696 (p0) cc_final: 0.5902 (m-40) REVERT: E 319 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6985 (mtp-110) REVERT: E 357 ARG cc_start: 0.7212 (ttt90) cc_final: 0.6829 (ttt90) REVERT: E 1086 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8143 (mtpt) REVERT: E 1113 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7588 (mt0) outliers start: 71 outliers final: 40 residues processed: 245 average time/residue: 0.5960 time to fit residues: 173.8006 Evaluate side-chains 213 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER 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 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 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 1037 SER 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 461 LEU 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 1084 ASP Chi-restraints excluded: chain E residue 1086 LYS Chi-restraints excluded: chain E residue 1113 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 292 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 334 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN 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 = 0.4273 r_free = 0.4273 target = 0.190445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.169926 restraints weight = 34129.672| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.07 r_work: 0.3657 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27264 Z= 0.160 Angle : 0.546 8.607 37361 Z= 0.284 Chirality : 0.045 0.232 4512 Planarity : 0.004 0.039 4810 Dihedral : 4.439 26.326 5043 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.09 % Allowed : 12.96 % 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: 1.54 (0.21), residues: 675 sheet: -0.11 (0.16), residues: 885 loop : -0.29 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 567 TYR 0.016 0.001 TYR B1067 PHE 0.016 0.002 PHE E 238 TRP 0.007 0.001 TRP B 886 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00382 (27159) covalent geometry : angle 0.52849 (37091) SS BOND : bond 0.00422 ( 45) SS BOND : angle 1.48820 ( 90) hydrogen bonds : bond 0.03863 ( 1209) hydrogen bonds : angle 5.30444 ( 3447) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.23545 ( 36) link_NAG-ASN : bond 0.00304 ( 48) link_NAG-ASN : angle 1.89573 ( 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 266 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 190 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6876 (p0) cc_final: 0.5840 (m-40) REVERT: A 319 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7189 (mtp-110) REVERT: A 392 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: A 418 ILE cc_start: 0.8330 (mp) cc_final: 0.8072 (mt) REVERT: A 547 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8097 (p) REVERT: B 287 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: B 614 ASP cc_start: 0.7316 (t0) cc_final: 0.6993 (t0) REVERT: E 32 PHE cc_start: 0.6806 (m-80) cc_final: 0.6465 (m-10) REVERT: E 81 ASN cc_start: 0.6944 (p0) cc_final: 0.5904 (m-40) REVERT: E 319 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6990 (mtp-110) REVERT: E 357 ARG cc_start: 0.7477 (ttt90) cc_final: 0.7049 (ttt90) REVERT: E 1086 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8355 (mtpt) REVERT: E 1113 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7679 (mt0) outliers start: 76 outliers final: 47 residues processed: 253 average time/residue: 0.5492 time to fit residues: 166.6964 Evaluate side-chains 220 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 390 LEU 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 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 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 B residue 50 SER 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 461 LEU Chi-restraints excluded: chain B residue 531 THR 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 1037 SER 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 461 LEU 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 1084 ASP 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: 0.0870 chunk 275 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 337 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 195 optimal weight: 0.0980 chunk 245 optimal weight: 3.9990 chunk 348 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4295 r_free = 0.4295 target = 0.191594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.156280 restraints weight = 34289.192| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.61 r_work: 0.3653 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27264 Z= 0.128 Angle : 0.523 7.575 37361 Z= 0.272 Chirality : 0.044 0.217 4512 Planarity : 0.003 0.038 4810 Dihedral : 4.317 30.239 5043 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.97 % Allowed : 13.53 % Favored : 83.50 % 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: 0.15 (0.14), residues: 3528 helix: 1.69 (0.21), residues: 657 sheet: -0.12 (0.15), residues: 918 loop : -0.27 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.017 0.001 TYR B1067 PHE 0.016 0.001 PHE E 238 TRP 0.004 0.001 TRP B 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00298 (27159) covalent geometry : angle 0.50793 (37091) SS BOND : bond 0.00401 ( 45) SS BOND : angle 1.28062 ( 90) hydrogen bonds : bond 0.03610 ( 1209) hydrogen bonds : angle 5.19983 ( 3447) link_BETA1-4 : bond 0.00409 ( 12) link_BETA1-4 : angle 1.16798 ( 36) link_NAG-ASN : bond 0.00282 ( 48) link_NAG-ASN : angle 1.79664 ( 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 256 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 183 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6674 (p0) cc_final: 0.5795 (m-40) REVERT: A 319 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7094 (mtp-110) REVERT: A 392 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: A 547 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.8049 (p) REVERT: E 32 PHE cc_start: 0.6649 (m-80) cc_final: 0.6411 (m-10) REVERT: E 81 ASN cc_start: 0.6724 (p0) cc_final: 0.5777 (m-40) REVERT: E 319 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7130 (mtp-110) REVERT: E 357 ARG cc_start: 0.7149 (ttt90) cc_final: 0.6790 (ttt90) REVERT: E 1086 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8121 (mtpt) outliers start: 73 outliers final: 43 residues processed: 242 average time/residue: 0.5472 time to fit residues: 158.9607 Evaluate side-chains 213 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 547 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 875 SER 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 52 GLN 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 547 THR 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 1037 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 349 SER 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 461 LEU 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 1081 ILE Chi-restraints excluded: chain E residue 1084 ASP 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: 0.0870 chunk 312 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 272 optimal weight: 6.9990 chunk 149 optimal weight: 0.0870 chunk 146 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN E 188 ASN E 239 GLN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** 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 = 0.4265 r_free = 0.4265 target = 0.191111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174546 restraints weight = 34710.165| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 0.88 r_work: 0.3854 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work: 0.3732 rms_B_bonded: 3.12 restraints_weight: 0.1250 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 27264 Z= 0.197 Angle : 0.578 8.223 37361 Z= 0.300 Chirality : 0.046 0.250 4512 Planarity : 0.004 0.038 4810 Dihedral : 4.677 36.727 5043 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.89 % Allowed : 14.22 % Favored : 82.89 % 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: 0.04 (0.14), residues: 3528 helix: 1.44 (0.21), residues: 672 sheet: -0.12 (0.16), residues: 918 loop : -0.34 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.017 0.002 TYR E 269 PHE 0.016 0.002 PHE E 238 TRP 0.010 0.001 TRP B 886 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00473 (27159) covalent geometry : angle 0.56096 (37091) SS BOND : bond 0.00424 ( 45) SS BOND : angle 1.44761 ( 90) hydrogen bonds : bond 0.04065 ( 1209) hydrogen bonds : angle 5.33971 ( 3447) link_BETA1-4 : bond 0.00356 ( 12) link_BETA1-4 : angle 1.23562 ( 36) link_NAG-ASN : bond 0.00356 ( 48) link_NAG-ASN : angle 1.98730 ( 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 244 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 173 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6659 (p0) cc_final: 0.5789 (m-40) REVERT: A 319 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6909 (mtp-110) REVERT: A 1092 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: B 201 PHE cc_start: 0.7453 (t80) cc_final: 0.7107 (t80) REVERT: B 287 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7195 (m-30) REVERT: B 1139 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6858 (p0) REVERT: E 81 ASN cc_start: 0.6770 (p0) cc_final: 0.5809 (m-40) REVERT: E 319 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6897 (mtp-110) REVERT: E 357 ARG cc_start: 0.6984 (ttt90) cc_final: 0.6666 (ttt90) REVERT: E 1086 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8161 (mtpt) outliers start: 71 outliers final: 43 residues processed: 230 average time/residue: 0.4981 time to fit residues: 139.2854 Evaluate side-chains 216 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 461 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 875 SER 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 1092 GLU Chi-restraints excluded: chain B residue 50 SER 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 376 THR 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 533 LEU Chi-restraints excluded: chain B residue 547 THR 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 1037 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 461 LEU 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 1081 ILE Chi-restraints excluded: chain E residue 1084 ASP 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: 9.9990 chunk 296 optimal weight: 0.9980 chunk 141 optimal weight: 0.0670 chunk 157 optimal weight: 0.0570 chunk 201 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 327 optimal weight: 0.7980 chunk 211 optimal weight: 0.4980 chunk 248 optimal weight: 0.9980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 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** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.191753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157553 restraints weight = 34284.535| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.62 r_work: 0.3653 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27264 Z= 0.112 Angle : 0.522 7.463 37361 Z= 0.272 Chirality : 0.044 0.292 4512 Planarity : 0.003 0.037 4810 Dihedral : 4.382 36.491 5043 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.15 % Allowed : 15.03 % Favored : 82.81 % 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: 1.62 (0.21), residues: 672 sheet: -0.11 (0.15), residues: 927 loop : -0.31 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.017 0.001 TYR B1067 PHE 0.016 0.001 PHE E 238 TRP 0.003 0.000 TRP B 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00254 (27159) covalent geometry : angle 0.50656 (37091) SS BOND : bond 0.00378 ( 45) SS BOND : angle 1.24890 ( 90) hydrogen bonds : bond 0.03496 ( 1209) hydrogen bonds : angle 5.17011 ( 3447) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 1.12960 ( 36) link_NAG-ASN : bond 0.00283 ( 48) link_NAG-ASN : angle 1.79162 ( 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 229 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6679 (p0) cc_final: 0.5541 (m-40) REVERT: A 319 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7071 (mtp-110) REVERT: A 392 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: A 1092 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: E 81 ASN cc_start: 0.6798 (p0) cc_final: 0.5685 (m-40) REVERT: E 319 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7119 (mtp-110) REVERT: E 357 ARG cc_start: 0.7123 (ttt90) cc_final: 0.6768 (ttt90) REVERT: E 592 PHE cc_start: 0.7425 (p90) cc_final: 0.7149 (p90) outliers start: 53 outliers final: 37 residues processed: 218 average time/residue: 0.5191 time to fit residues: 137.0116 Evaluate side-chains 207 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 533 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 875 SER 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 A residue 1092 GLU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 376 THR 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 758 SER 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 1037 SER 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 461 LEU 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 1081 ILE Chi-restraints excluded: chain E residue 1084 ASP 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: 0.5980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 103 optimal weight: 50.0000 chunk 104 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 145 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 314 GLN ** A 422 ASN ** 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** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.190853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.171509 restraints weight = 34129.705| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 0.97 r_work: 0.3674 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4230 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= 0.138 Angle : 0.532 7.329 37361 Z= 0.277 Chirality : 0.044 0.245 4512 Planarity : 0.004 0.038 4810 Dihedral : 4.356 36.752 5043 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.99 % Allowed : 15.32 % Favored : 82.69 % 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: 0.10 (0.14), residues: 3528 helix: 1.60 (0.21), residues: 672 sheet: -0.13 (0.15), residues: 924 loop : -0.31 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE E 238 TRP 0.005 0.001 TRP B 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00326 (27159) covalent geometry : angle 0.51715 (37091) SS BOND : bond 0.00384 ( 45) SS BOND : angle 1.22314 ( 90) hydrogen bonds : bond 0.03596 ( 1209) hydrogen bonds : angle 5.15914 ( 3447) link_BETA1-4 : bond 0.00390 ( 12) link_BETA1-4 : angle 1.13268 ( 36) link_NAG-ASN : bond 0.00286 ( 48) link_NAG-ASN : angle 1.79712 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7375.70 seconds wall clock time: 126 minutes 34.29 seconds (7594.29 seconds total)