Starting phenix.real_space_refine on Thu Mar 5 01:22:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wn4_32621/03_2026/7wn4_32621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wn4_32621/03_2026/7wn4_32621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wn4_32621/03_2026/7wn4_32621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wn4_32621/03_2026/7wn4_32621.map" model { file = "/net/cci-nas-00/data/ceres_data/7wn4_32621/03_2026/7wn4_32621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wn4_32621/03_2026/7wn4_32621.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 276 5.16 5 C 11242 2.51 5 N 3127 2.21 5 O 3573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s 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: 18224 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5427 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 675} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5427 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 3629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3692 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.08, per 1000 atoms: 0.28 Number of scatterers: 18224 At special positions: 0 Unit cell: (159.08, 161.02, 146.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 276 16.00 O 3573 8.00 N 3127 7.00 C 11242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=116, symmetry=0 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 200 " distance=2.02 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.04 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 255 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 250 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 257 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 329 " distance=2.02 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 348 " distance=2.02 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 372 " distance=2.02 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 384 " distance=2.03 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 524 " distance=2.02 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 440 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.02 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.03 Simple disulfide: pdb=" SG CYS E 595 " - pdb=" SG CYS E 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 615 " - pdb=" SG CYS E 621 " distance=2.02 Simple disulfide: pdb=" SG CYS E 623 " - pdb=" SG CYS E 648 " distance=2.02 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 687 " distance=2.03 Simple disulfide: pdb=" SG CYS E 661 " - pdb=" SG CYS E 683 " distance=2.03 Simple disulfide: pdb=" SG CYS E 665 " - pdb=" SG CYS E 679 " distance=2.03 Simple disulfide: pdb=" SG CYS E 669 " - pdb=" SG CYS E 707 " distance=2.03 Simple disulfide: pdb=" SG CYS E 689 " - pdb=" SG CYS E 701 " distance=2.03 Simple disulfide: pdb=" SG CYS E 709 " - pdb=" SG CYS E 731 " distance=2.03 Simple disulfide: pdb=" SG CYS E 729 " - pdb=" SG CYS E 738 " distance=2.05 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 808 " distance=2.04 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 804 " distance=2.02 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 799 " distance=2.03 Simple disulfide: pdb=" SG CYS F 792 " - pdb=" SG CYS F 827 " distance=2.03 Simple disulfide: pdb=" SG CYS F 810 " - pdb=" SG CYS F 821 " distance=2.03 Simple disulfide: pdb=" SG CYS F 829 " - pdb=" SG CYS F 851 " distance=2.02 Simple disulfide: pdb=" SG CYS F 846 " - pdb=" SG CYS F 863 " distance=2.03 Simple disulfide: pdb=" SG CYS F 849 " - pdb=" SG CYS F 858 " distance=2.03 Simple disulfide: pdb=" SG CYS F 867 " - pdb=" SG CYS F 996 " distance=2.02 Simple disulfide: pdb=" SG CYS F 889 " - pdb=" SG CYS F1031 " distance=2.02 Simple disulfide: pdb=" SG CYS F 898 " - pdb=" SG CYS F 993 " distance=2.03 Simple disulfide: pdb=" SG CYS F 914 " - pdb=" SG CYS F 921 " distance=2.02 Simple disulfide: pdb=" SG CYS F1046 " - pdb=" SG CYS F1089 " distance=2.03 Simple disulfide: pdb=" SG CYS F1060 " - pdb=" SG CYS F1084 " distance=2.03 Simple disulfide: pdb=" SG CYS F1071 " - pdb=" SG CYS F1111 " distance=2.02 Simple disulfide: pdb=" SG CYS F1091 " - pdb=" SG CYS F1099 " distance=2.03 Simple disulfide: pdb=" SG CYS F1097 " - pdb=" SG CYS H1097 " distance=2.03 Simple disulfide: pdb=" SG CYS F1101 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F1130 " - pdb=" SG CYS F1173 " distance=2.03 Simple disulfide: pdb=" SG CYS F1142 " - pdb=" SG CYS H1142 " distance=2.02 Simple disulfide: pdb=" SG CYS F1149 " - pdb=" SG CYS F1169 " distance=2.03 Simple disulfide: pdb=" SG CYS F1153 " - pdb=" SG CYS F1165 " distance=2.03 Simple disulfide: pdb=" SG CYS F1157 " - pdb=" SG CYS F1196 " distance=2.03 Simple disulfide: pdb=" SG CYS F1177 " - pdb=" SG CYS F1190 " distance=2.03 Simple disulfide: pdb=" SG CYS F1199 " - pdb=" SG CYS F1227 " distance=2.03 Simple disulfide: pdb=" SG CYS F1222 " - pdb=" SG CYS F1237 " distance=2.03 Simple disulfide: pdb=" SG CYS F1225 " - pdb=" SG CYS F1234 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 57 " - pdb=" SG CYS G 200 " distance=2.02 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 255 " distance=2.03 Simple disulfide: pdb=" SG CYS G 225 " - pdb=" SG CYS G 250 " distance=2.03 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 275 " distance=2.03 Simple disulfide: pdb=" SG CYS G 257 " - pdb=" SG CYS G 263 " distance=2.03 Simple disulfide: pdb=" SG CYS G 265 " - pdb=" SG CYS G 291 " distance=2.03 Simple disulfide: pdb=" SG CYS G 295 " - pdb=" SG CYS G 329 " distance=2.03 Simple disulfide: pdb=" SG CYS G 304 " - pdb=" SG CYS G 325 " distance=2.03 Simple disulfide: pdb=" SG CYS G 308 " - pdb=" SG CYS G 321 " distance=2.02 Simple disulfide: pdb=" SG CYS G 312 " - pdb=" SG CYS G 348 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 342 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 372 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 384 " distance=2.03 Simple disulfide: pdb=" SG CYS G 370 " - pdb=" SG CYS G 379 " distance=2.03 Simple disulfide: pdb=" SG CYS G 388 " - pdb=" SG CYS G 524 " distance=2.02 Simple disulfide: pdb=" SG CYS G 410 " - pdb=" SG CYS G 559 " distance=2.03 Simple disulfide: pdb=" SG CYS G 418 " - pdb=" SG CYS G 521 " distance=2.02 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 440 " distance=2.03 Simple disulfide: pdb=" SG CYS G 570 " - pdb=" SG CYS G 613 " distance=2.03 Simple disulfide: pdb=" SG CYS G 584 " - pdb=" SG CYS G 608 " distance=2.03 Simple disulfide: pdb=" SG CYS G 595 " - pdb=" SG CYS G 633 " distance=2.03 Simple disulfide: pdb=" SG CYS G 615 " - pdb=" SG CYS G 621 " distance=2.02 Simple disulfide: pdb=" SG CYS G 623 " - pdb=" SG CYS G 648 " distance=2.03 Simple disulfide: pdb=" SG CYS G 652 " - pdb=" SG CYS G 687 " distance=2.03 Simple disulfide: pdb=" SG CYS G 661 " - pdb=" SG CYS G 683 " distance=2.03 Simple disulfide: pdb=" SG CYS G 665 " - pdb=" SG CYS G 679 " distance=2.03 Simple disulfide: pdb=" SG CYS G 669 " - pdb=" SG CYS G 707 " distance=2.04 Simple disulfide: pdb=" SG CYS G 689 " - pdb=" SG CYS G 701 " distance=2.04 Simple disulfide: pdb=" SG CYS G 709 " - pdb=" SG CYS G 731 " distance=2.03 Simple disulfide: pdb=" SG CYS G 729 " - pdb=" SG CYS G 738 " distance=2.04 Simple disulfide: pdb=" SG CYS H 767 " - pdb=" SG CYS H 808 " distance=2.03 Simple disulfide: pdb=" SG CYS H 776 " - pdb=" SG CYS H 804 " distance=2.03 Simple disulfide: pdb=" SG CYS H 788 " - pdb=" SG CYS H 799 " distance=2.03 Simple disulfide: pdb=" SG CYS H 792 " - pdb=" SG CYS H 827 " distance=2.03 Simple disulfide: pdb=" SG CYS H 810 " - pdb=" SG CYS H 821 " distance=2.03 Simple disulfide: pdb=" SG CYS H 829 " - pdb=" SG CYS H 851 " distance=2.03 Simple disulfide: pdb=" SG CYS H 846 " - pdb=" SG CYS H 863 " distance=2.03 Simple disulfide: pdb=" SG CYS H 849 " - pdb=" SG CYS H 858 " distance=2.03 Simple disulfide: pdb=" SG CYS H 867 " - pdb=" SG CYS H 996 " distance=2.02 Simple disulfide: pdb=" SG CYS H 889 " - pdb=" SG CYS H1031 " distance=2.02 Simple disulfide: pdb=" SG CYS H 898 " - pdb=" SG CYS H 993 " distance=2.03 Simple disulfide: pdb=" SG CYS H 914 " - pdb=" SG CYS H 921 " distance=2.03 Simple disulfide: pdb=" SG CYS H1046 " - pdb=" SG CYS H1089 " distance=2.03 Simple disulfide: pdb=" SG CYS H1060 " - pdb=" SG CYS H1084 " distance=2.03 Simple disulfide: pdb=" SG CYS H1071 " - pdb=" SG CYS H1111 " distance=2.02 Simple disulfide: pdb=" SG CYS H1091 " - pdb=" SG CYS H1099 " distance=2.03 Simple disulfide: pdb=" SG CYS H1101 " - pdb=" SG CYS H1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H1130 " - pdb=" SG CYS H1173 " distance=2.03 Simple disulfide: pdb=" SG CYS H1149 " - pdb=" SG CYS H1169 " distance=2.03 Simple disulfide: pdb=" SG CYS H1153 " - pdb=" SG CYS H1165 " distance=2.03 Simple disulfide: pdb=" SG CYS H1157 " - pdb=" SG CYS H1196 " distance=2.03 Simple disulfide: pdb=" SG CYS H1177 " - pdb=" SG CYS H1190 " distance=2.03 Simple disulfide: pdb=" SG CYS H1199 " - pdb=" SG CYS H1227 " distance=2.02 Simple disulfide: pdb=" SG CYS H1222 " - pdb=" SG CYS H1237 " distance=2.03 Simple disulfide: pdb=" SG CYS H1225 " - pdb=" SG CYS H1234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 803 " - " ASN E 99 " " NAG E 804 " - " ASN E 156 " " NAG F1302 " - " ASN F 857 " " NAG F1303 " - " ASN F1147 " " NAG G 803 " - " ASN G 99 " " NAG G 804 " - " ASN G 156 " " NAG H1302 " - " ASN H 857 " " NAG H1303 " - " ASN H1147 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 951.8 milliseconds 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 40 sheets defined 21.1% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.657A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.584A pdb=" N ARG E 236 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 252 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 284 through 290 removed outlier: 4.414A pdb=" N HIS E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 289 " --> pdb=" O TRP E 285 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 290' Processing helix chain 'E' and resid 513 through 517 Processing helix chain 'E' and resid 531 through 535 removed outlier: 3.596A pdb=" N ASP E 534 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE E 535 " --> pdb=" O GLY E 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 531 through 535' Processing helix chain 'E' and resid 545 through 552 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 573 through 575 No H-bonds generated for 'chain 'E' and resid 573 through 575' Processing helix chain 'E' and resid 576 through 586 removed outlier: 4.079A pdb=" N VAL E 586 " --> pdb=" O GLU E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 598 Proline residue: E 590 - end of helix removed outlier: 4.875A pdb=" N ALA E 594 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS E 596 " --> pdb=" O GLU E 593 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG E 597 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 615 Processing helix chain 'E' and resid 617 through 637 removed outlier: 3.599A pdb=" N CYS E 623 " --> pdb=" O ARG E 619 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 628 " --> pdb=" O GLY E 624 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG E 636 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 674 removed outlier: 4.137A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 789 removed outlier: 3.603A pdb=" N THR F 789 " --> pdb=" O LEU F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 791 through 797 removed outlier: 4.323A pdb=" N ASP F 796 " --> pdb=" O CYS F 792 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU F 797 " --> pdb=" O GLN F 793 " (cutoff:3.500A) Processing helix chain 'F' and resid 1003 through 1008 removed outlier: 3.604A pdb=" N ASP F1006 " --> pdb=" O GLN F1003 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU F1007 " --> pdb=" O ASN F1004 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR F1008 " --> pdb=" O ASN F1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1003 through 1008' Processing helix chain 'F' and resid 1017 through 1025 Processing helix chain 'F' and resid 1049 through 1061 Processing helix chain 'F' and resid 1062 through 1065 Processing helix chain 'F' and resid 1068 through 1075 removed outlier: 3.606A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU F1074 " --> pdb=" O ASP F1070 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 Processing helix chain 'F' and resid 1097 through 1114 removed outlier: 4.382A pdb=" N THR F1103 " --> pdb=" O CYS F1099 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR F1107 " --> pdb=" O THR F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1131 through 1136 removed outlier: 3.841A pdb=" N ARG F1136 " --> pdb=" O GLU F1132 " (cutoff:3.500A) Processing helix chain 'F' and resid 1218 through 1222 Processing helix chain 'G' and resid 114 through 118 removed outlier: 4.327A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 209 through 213 removed outlier: 3.791A pdb=" N ILE G 212 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 231 removed outlier: 4.168A pdb=" N GLY G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS G 229 " --> pdb=" O CYS G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 removed outlier: 4.348A pdb=" N ARG G 236 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 237 " --> pdb=" O PHE G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 255 removed outlier: 3.996A pdb=" N CYS G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 263 removed outlier: 3.665A pdb=" N CYS G 263 " --> pdb=" O GLY G 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 260 through 263' Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.639A pdb=" N LEU G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.863A pdb=" N CYS G 348 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 469 removed outlier: 3.559A pdb=" N GLN G 469 " --> pdb=" O MET G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 517 Processing helix chain 'G' and resid 545 through 552 Processing helix chain 'G' and resid 568 through 572 removed outlier: 3.720A pdb=" N ALA G 571 " --> pdb=" O ASP G 568 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU G 572 " --> pdb=" O PRO G 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 568 through 572' Processing helix chain 'G' and resid 576 through 584 removed outlier: 3.877A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 596 Proline residue: G 590 - end of helix removed outlier: 4.911A pdb=" N ALA G 594 " --> pdb=" O THR G 591 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS G 596 " --> pdb=" O GLU G 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 615 Processing helix chain 'G' and resid 617 through 635 removed outlier: 3.825A pdb=" N ALA G 627 " --> pdb=" O CYS G 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 707 No H-bonds generated for 'chain 'G' and resid 705 through 707' Processing helix chain 'H' and resid 785 through 789 Processing helix chain 'H' and resid 1003 through 1008 removed outlier: 3.795A pdb=" N ASP H1006 " --> pdb=" O GLN H1003 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU H1007 " --> pdb=" O ASN H1004 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR H1008 " --> pdb=" O ASN H1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1003 through 1008' Processing helix chain 'H' and resid 1017 through 1024 Processing helix chain 'H' and resid 1049 through 1061 Processing helix chain 'H' and resid 1062 through 1065 Processing helix chain 'H' and resid 1068 through 1073 removed outlier: 3.776A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 Processing helix chain 'H' and resid 1097 through 1114 removed outlier: 4.771A pdb=" N THR H1103 " --> pdb=" O CYS H1099 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR H1107 " --> pdb=" O THR H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1130 through 1134 removed outlier: 3.990A pdb=" N ARG H1133 " --> pdb=" O CYS H1130 " (cutoff:3.500A) Processing helix chain 'H' and resid 1192 through 1196 Processing helix chain 'H' and resid 1218 through 1222 Processing sheet with id=AA1, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'E' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.782A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE E 94 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 300 through 305 removed outlier: 4.173A pdb=" N CYS E 304 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL E 326 " --> pdb=" O CYS E 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 337 through 338 Processing sheet with id=AA6, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AA8, first strand: chain 'E' and resid 403 through 405 Processing sheet with id=AA9, first strand: chain 'E' and resid 455 through 458 removed outlier: 5.084A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE E 425 " --> pdb=" O LEU E 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 465 through 466 removed outlier: 3.515A pdb=" N GLN E 469 " --> pdb=" O MET E 466 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 475 through 476 removed outlier: 3.514A pdb=" N GLN E 483 " --> pdb=" O ARG E 491 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 657 through 659 Processing sheet with id=AB4, first strand: chain 'E' and resid 721 through 723 Processing sheet with id=AB5, first strand: chain 'F' and resid 841 through 844 Processing sheet with id=AB6, first strand: chain 'F' and resid 865 through 866 removed outlier: 4.727A pdb=" N TRP F 974 " --> pdb=" O ILE F 962 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 874 through 876 Processing sheet with id=AB8, first strand: chain 'F' and resid 890 through 891 Processing sheet with id=AB9, first strand: chain 'F' and resid 928 through 929 removed outlier: 3.612A pdb=" N VAL F 929 " --> pdb=" O GLY F 932 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 936 through 937 Processing sheet with id=AC2, first strand: chain 'F' and resid 1144 through 1146 removed outlier: 3.663A pdb=" N ARG F1145 " --> pdb=" O HIS F1174 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 1150 through 1151 Processing sheet with id=AC4, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AC5, first strand: chain 'G' and resid 42 through 44 Processing sheet with id=AC6, first strand: chain 'G' and resid 59 through 62 removed outlier: 5.651A pdb=" N LEU G 60 " --> pdb=" O GLY G 74 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY G 74 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 62 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER G 83 " --> pdb=" O ASP G 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 300 through 305 removed outlier: 4.438A pdb=" N CYS G 304 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL G 326 " --> pdb=" O CYS G 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 350 through 351 Processing sheet with id=AC9, first strand: chain 'G' and resid 362 through 364 Processing sheet with id=AD1, first strand: chain 'G' and resid 386 through 389 Processing sheet with id=AD2, first strand: chain 'G' and resid 395 through 398 Processing sheet with id=AD3, first strand: chain 'G' and resid 454 through 458 removed outlier: 6.881A pdb=" N GLU G 428 " --> pdb=" O ARG G 442 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL G 444 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL G 426 " --> pdb=" O VAL G 444 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL G 446 " --> pdb=" O SER G 424 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER G 424 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 415 " --> pdb=" O ILE G 425 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR G 429 " --> pdb=" O GLN G 411 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN G 411 " --> pdb=" O THR G 429 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 657 through 658 Processing sheet with id=AD5, first strand: chain 'G' and resid 693 through 695 Processing sheet with id=AD6, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AD7, first strand: chain 'H' and resid 815 through 817 Processing sheet with id=AD8, first strand: chain 'H' and resid 829 through 830 Processing sheet with id=AD9, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AE1, first strand: chain 'H' and resid 865 through 866 removed outlier: 4.614A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 874 through 876 Processing sheet with id=AE3, first strand: chain 'H' and resid 890 through 891 Processing sheet with id=AE4, first strand: chain 'H' and resid 1144 through 1151 removed outlier: 4.101A pdb=" N CYS H1149 " --> pdb=" O VAL H1170 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL H1170 " --> pdb=" O CYS H1149 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1151 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: 3.54 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6170 1.34 - 1.47: 4292 1.47 - 1.59: 7840 1.59 - 1.72: 1 1.72 - 1.84: 320 Bond restraints: 18623 Sorted by residual: bond pdb=" CA ASP F 975 " pdb=" C ASP F 975 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.66e-02 3.63e+03 1.46e+01 bond pdb=" CA ASP H 975 " pdb=" C ASP H 975 " ideal model delta sigma weight residual 1.525 1.473 0.052 1.38e-02 5.25e+03 1.41e+01 bond pdb=" N VAL H 850 " pdb=" CA VAL H 850 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.85e+00 bond pdb=" N VAL E 102 " pdb=" CA VAL E 102 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.20e-02 6.94e+03 8.61e+00 bond pdb=" N CYS H 851 " pdb=" CA CYS H 851 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.15e-02 7.56e+03 7.97e+00 ... (remaining 18618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 23781 1.89 - 3.78: 1289 3.78 - 5.67: 164 5.67 - 7.56: 33 7.56 - 9.45: 4 Bond angle restraints: 25271 Sorted by residual: angle pdb=" C TRP H 974 " pdb=" N ASP H 975 " pdb=" CA ASP H 975 " ideal model delta sigma weight residual 122.83 113.38 9.45 1.54e+00 4.22e-01 3.77e+01 angle pdb=" N VAL H1230 " pdb=" CA VAL H1230 " pdb=" C VAL H1230 " ideal model delta sigma weight residual 113.71 109.22 4.49 9.50e-01 1.11e+00 2.23e+01 angle pdb=" CA PRO H1038 " pdb=" N PRO H1038 " pdb=" CD PRO H1038 " ideal model delta sigma weight residual 112.00 105.61 6.39 1.40e+00 5.10e-01 2.08e+01 angle pdb=" N LYS E 157 " pdb=" CA LYS E 157 " pdb=" C LYS E 157 " ideal model delta sigma weight residual 113.55 107.82 5.73 1.26e+00 6.30e-01 2.07e+01 angle pdb=" C TRP F 974 " pdb=" N ASP F 975 " pdb=" CA ASP F 975 " ideal model delta sigma weight residual 122.65 115.35 7.30 1.66e+00 3.63e-01 1.93e+01 ... (remaining 25266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10352 17.94 - 35.88: 1008 35.88 - 53.81: 206 53.81 - 71.75: 46 71.75 - 89.69: 31 Dihedral angle restraints: 11643 sinusoidal: 4819 harmonic: 6824 Sorted by residual: dihedral pdb=" CA MET E 111 " pdb=" C MET E 111 " pdb=" N PRO E 112 " pdb=" CA PRO E 112 " ideal model delta harmonic sigma weight residual 180.00 121.65 58.35 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CB CYS E 65 " pdb=" SG CYS E 65 " pdb=" SG CYS E 159 " pdb=" CB CYS E 159 " ideal model delta sinusoidal sigma weight residual -86.00 2.79 -88.79 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS H1130 " pdb=" SG CYS H1130 " pdb=" SG CYS H1173 " pdb=" CB CYS H1173 " ideal model delta sinusoidal sigma weight residual -86.00 -173.61 87.61 1 1.00e+01 1.00e-02 9.20e+01 ... (remaining 11640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2728 0.146 - 0.292: 26 0.292 - 0.438: 1 0.438 - 0.584: 1 0.584 - 0.730: 1 Chirality restraints: 2757 Sorted by residual: chirality pdb=" C1 NAG G 804 " pdb=" ND2 ASN G 156 " pdb=" C2 NAG G 804 " pdb=" O5 NAG G 804 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG F1302 " pdb=" ND2 ASN F 857 " pdb=" C2 NAG F1302 " pdb=" O5 NAG F1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.87 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" C1 NAG G 803 " pdb=" ND2 ASN G 99 " pdb=" C2 NAG G 803 " pdb=" O5 NAG G 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2754 not shown) Planarity restraints: 3366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H1037 " 0.075 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO H1038 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO H1038 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO H1038 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 804 " 0.045 2.00e-02 2.50e+03 3.67e-02 1.69e+01 pdb=" C7 NAG G 804 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG G 804 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG G 804 " -0.059 2.00e-02 2.50e+03 pdb=" O7 NAG G 804 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H1303 " 0.044 2.00e-02 2.50e+03 3.65e-02 1.67e+01 pdb=" C7 NAG H1303 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG H1303 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG H1303 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG H1303 " -0.008 2.00e-02 2.50e+03 ... (remaining 3363 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 622 2.69 - 3.24: 18203 3.24 - 3.79: 27201 3.79 - 4.35: 35952 4.35 - 4.90: 60491 Nonbonded interactions: 142469 Sorted by model distance: nonbonded pdb=" OH TYR F 883 " pdb=" O LEU F 995 " model vdw 2.137 3.040 nonbonded pdb=" NE2 GLN G 431 " pdb=" O ASP G 435 " model vdw 2.164 3.120 nonbonded pdb=" OG SER H1129 " pdb=" OE1 GLU H1131 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR E 311 " pdb=" OE1 GLN E 313 " model vdw 2.183 3.040 nonbonded pdb=" O THR E 668 " pdb=" OG SER E 671 " model vdw 2.190 3.040 ... (remaining 142464 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 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and (resid 767 through 1052 or resid 1054 through 1303)) selection = (chain 'H' and (resid 767 through 1052 or resid 1054 through 1303)) } 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=0.50 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: 0.550 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: 0.420 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.030 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.007 0.102 18747 Z= 0.350 Angle : 0.995 17.026 25527 Z= 0.579 Chirality : 0.054 0.730 2757 Planarity : 0.006 0.110 3358 Dihedral : 14.185 89.689 6925 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.54 % Favored : 86.29 % Rotamer: Outliers : 0.15 % Allowed : 0.44 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.09 % 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: -3.02 (0.16), residues: 2365 helix: -0.74 (0.28), residues: 335 sheet: -2.69 (0.27), residues: 364 loop : -2.26 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 597 TYR 0.026 0.002 TYR E 711 PHE 0.019 0.002 PHE F1021 TRP 0.026 0.002 TRP E 502 HIS 0.008 0.001 HIS G 726 Details of bonding type rmsd covalent geometry : bond 0.00747 (18623) covalent geometry : angle 0.95579 (25271) SS BOND : bond 0.00510 ( 116) SS BOND : angle 1.88810 ( 232) hydrogen bonds : bond 0.19019 ( 466) hydrogen bonds : angle 7.84761 ( 1151) link_NAG-ASN : bond 0.01097 ( 8) link_NAG-ASN : angle 7.51701 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 593 GLU cc_start: 0.8162 (tp30) cc_final: 0.7927 (mm-30) REVERT: F 1049 ASN cc_start: 0.7047 (t0) cc_final: 0.6780 (t0) REVERT: G 111 MET cc_start: 0.9140 (ttt) cc_final: 0.8809 (ttt) REVERT: G 280 MET cc_start: 0.8270 (tmm) cc_final: 0.7677 (tmm) REVERT: G 737 HIS cc_start: 0.6647 (m90) cc_final: 0.6416 (m90) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.1426 time to fit residues: 48.6886 Evaluate side-chains 173 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 ASN F1226 HIS G 104 GLN ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN G 381 ASN H1069 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100326 restraints weight = 30368.776| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.76 r_work: 0.2997 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18747 Z= 0.167 Angle : 0.724 10.653 25527 Z= 0.369 Chirality : 0.047 0.174 2757 Planarity : 0.005 0.080 3358 Dihedral : 5.834 53.381 2730 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.48 % Favored : 90.40 % Rotamer: Outliers : 0.93 % Allowed : 8.29 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.67 (0.16), residues: 2365 helix: -0.39 (0.27), residues: 345 sheet: -2.57 (0.26), residues: 388 loop : -1.99 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 597 TYR 0.030 0.001 TYR E 711 PHE 0.021 0.001 PHE E 579 TRP 0.010 0.001 TRP G 222 HIS 0.018 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00394 (18623) covalent geometry : angle 0.70029 (25271) SS BOND : bond 0.00390 ( 116) SS BOND : angle 1.45134 ( 232) hydrogen bonds : bond 0.04790 ( 466) hydrogen bonds : angle 5.87942 ( 1151) link_NAG-ASN : bond 0.00454 ( 8) link_NAG-ASN : angle 4.63189 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 93 ASP cc_start: 0.9069 (p0) cc_final: 0.8709 (p0) REVERT: E 249 LEU cc_start: 0.8184 (pp) cc_final: 0.7791 (mt) REVERT: E 476 LEU cc_start: 0.8452 (tt) cc_final: 0.8104 (mp) REVERT: E 593 GLU cc_start: 0.8809 (tp30) cc_final: 0.8591 (mm-30) REVERT: E 696 ASP cc_start: 0.8071 (t0) cc_final: 0.7831 (t70) REVERT: E 728 MET cc_start: 0.6962 (tmm) cc_final: 0.6700 (tmm) REVERT: E 740 MET cc_start: 0.7010 (mmm) cc_final: 0.6737 (tpt) REVERT: G 111 MET cc_start: 0.9593 (ttt) cc_final: 0.9285 (ttt) REVERT: G 280 MET cc_start: 0.8810 (tmm) cc_final: 0.7750 (tmm) REVERT: H 897 TYR cc_start: 0.8833 (m-80) cc_final: 0.8576 (m-10) outliers start: 18 outliers final: 11 residues processed: 207 average time/residue: 0.1445 time to fit residues: 45.4076 Evaluate side-chains 182 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 719 GLU Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 1075 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 146 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 HIS F1215 ASN F1226 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 313 GLN G 381 ASN ** H1011 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 = 0.3634 r_free = 0.3634 target = 0.130679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.095032 restraints weight = 27486.143| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.38 r_work: 0.3000 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 18747 Z= 0.209 Angle : 0.707 8.730 25527 Z= 0.360 Chirality : 0.047 0.205 2757 Planarity : 0.006 0.117 3358 Dihedral : 5.747 58.851 2730 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.70 % Favored : 89.21 % Rotamer: Outliers : 1.81 % Allowed : 11.03 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.57 (0.17), residues: 2365 helix: -0.22 (0.27), residues: 341 sheet: -2.53 (0.26), residues: 388 loop : -1.92 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 597 TYR 0.024 0.001 TYR E 711 PHE 0.015 0.001 PHE F1021 TRP 0.007 0.001 TRP G 502 HIS 0.015 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00508 (18623) covalent geometry : angle 0.68488 (25271) SS BOND : bond 0.00432 ( 116) SS BOND : angle 1.46164 ( 232) hydrogen bonds : bond 0.04657 ( 466) hydrogen bonds : angle 5.58031 ( 1151) link_NAG-ASN : bond 0.00827 ( 8) link_NAG-ASN : angle 4.12936 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 252 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8302 (ptmm) REVERT: E 593 GLU cc_start: 0.8840 (tp30) cc_final: 0.8638 (mm-30) REVERT: E 696 ASP cc_start: 0.7975 (t0) cc_final: 0.7739 (t70) REVERT: E 711 TYR cc_start: 0.8443 (t80) cc_final: 0.8236 (t80) REVERT: E 740 MET cc_start: 0.6967 (mmm) cc_final: 0.6757 (tpt) REVERT: F 952 HIS cc_start: 0.7424 (m-70) cc_final: 0.7195 (m-70) REVERT: G 111 MET cc_start: 0.9553 (ttt) cc_final: 0.9236 (ttt) REVERT: G 280 MET cc_start: 0.8765 (tmm) cc_final: 0.8456 (tmm) REVERT: G 333 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7385 (tp30) REVERT: G 365 ARG cc_start: 0.7070 (tpp-160) cc_final: 0.6587 (mmt180) REVERT: G 737 HIS cc_start: 0.6632 (m90) cc_final: 0.6413 (m90) REVERT: H 897 TYR cc_start: 0.8863 (m-80) cc_final: 0.8635 (m-10) outliers start: 36 outliers final: 22 residues processed: 208 average time/residue: 0.1349 time to fit residues: 43.4688 Evaluate side-chains 195 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 719 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 772 VAL Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 161 optimal weight: 0.0170 chunk 29 optimal weight: 10.0000 chunk 201 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 219 optimal weight: 0.0040 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 225 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.7834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 ASN ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101221 restraints weight = 33252.393| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.09 r_work: 0.2993 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 18747 Z= 0.134 Angle : 0.643 8.577 25527 Z= 0.327 Chirality : 0.044 0.175 2757 Planarity : 0.005 0.103 3358 Dihedral : 5.439 59.026 2730 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.01 % Favored : 90.95 % Rotamer: Outliers : 1.96 % Allowed : 13.34 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.46 (0.17), residues: 2365 helix: -0.28 (0.27), residues: 367 sheet: -2.29 (0.26), residues: 374 loop : -1.89 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 597 TYR 0.013 0.001 TYR F 988 PHE 0.016 0.001 PHE H1100 TRP 0.032 0.001 TRP G 502 HIS 0.017 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00319 (18623) covalent geometry : angle 0.62653 (25271) SS BOND : bond 0.00329 ( 116) SS BOND : angle 1.24872 ( 232) hydrogen bonds : bond 0.03956 ( 466) hydrogen bonds : angle 5.36676 ( 1151) link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 3.28558 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8149 (pp) cc_final: 0.7629 (mt) REVERT: E 252 LYS cc_start: 0.8560 (ptpt) cc_final: 0.8281 (ptmm) REVERT: E 581 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7622 (mm-30) REVERT: G 111 MET cc_start: 0.9429 (ttt) cc_final: 0.9078 (ttt) REVERT: G 152 ASP cc_start: 0.8822 (t70) cc_final: 0.8614 (t0) REVERT: G 280 MET cc_start: 0.8672 (tmm) cc_final: 0.8405 (tmm) REVERT: G 333 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: G 365 ARG cc_start: 0.6922 (tpp-160) cc_final: 0.6582 (mmt180) REVERT: H 897 TYR cc_start: 0.8728 (m-80) cc_final: 0.8523 (m-10) outliers start: 39 outliers final: 23 residues processed: 236 average time/residue: 0.1355 time to fit residues: 49.5974 Evaluate side-chains 207 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 719 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 187 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS E 556 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 ASN ** G 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.133117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098988 restraints weight = 39188.763| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.72 r_work: 0.3009 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18747 Z= 0.141 Angle : 0.656 8.798 25527 Z= 0.333 Chirality : 0.045 0.175 2757 Planarity : 0.005 0.100 3358 Dihedral : 5.368 57.810 2730 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.52 % Favored : 90.44 % Rotamer: Outliers : 2.21 % Allowed : 14.22 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.40 (0.17), residues: 2365 helix: -0.34 (0.26), residues: 379 sheet: -2.22 (0.27), residues: 368 loop : -1.84 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 597 TYR 0.018 0.001 TYR H 897 PHE 0.015 0.001 PHE H1100 TRP 0.043 0.001 TRP G 502 HIS 0.022 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00340 (18623) covalent geometry : angle 0.63765 (25271) SS BOND : bond 0.00343 ( 116) SS BOND : angle 1.44451 ( 232) hydrogen bonds : bond 0.03869 ( 466) hydrogen bonds : angle 5.27762 ( 1151) link_NAG-ASN : bond 0.00358 ( 8) link_NAG-ASN : angle 3.09230 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 LEU cc_start: 0.8951 (mt) cc_final: 0.8737 (mt) REVERT: E 249 LEU cc_start: 0.8230 (pp) cc_final: 0.7815 (mt) REVERT: E 252 LYS cc_start: 0.8563 (ptpt) cc_final: 0.8265 (ptmm) REVERT: E 347 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8289 (mt-10) REVERT: E 581 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7869 (mm-30) REVERT: G 111 MET cc_start: 0.9501 (ttt) cc_final: 0.9206 (ttt) REVERT: G 280 MET cc_start: 0.8791 (tmm) cc_final: 0.8419 (tmm) REVERT: G 333 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: G 365 ARG cc_start: 0.7037 (tpp-160) cc_final: 0.6642 (mmt180) outliers start: 44 outliers final: 26 residues processed: 231 average time/residue: 0.1330 time to fit residues: 48.2660 Evaluate side-chains 205 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 381 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 975 ASP Chi-restraints excluded: chain H residue 1075 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.097814 restraints weight = 29658.628| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.77 r_work: 0.2947 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 18747 Z= 0.293 Angle : 0.767 15.032 25527 Z= 0.389 Chirality : 0.049 0.281 2757 Planarity : 0.006 0.107 3358 Dihedral : 5.787 59.769 2730 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 2.26 % Allowed : 15.06 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.37 (0.17), residues: 2365 helix: -0.13 (0.27), residues: 349 sheet: -2.27 (0.27), residues: 348 loop : -1.84 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 597 TYR 0.031 0.002 TYR E 711 PHE 0.019 0.002 PHE F1021 TRP 0.049 0.002 TRP G 502 HIS 0.020 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00713 (18623) covalent geometry : angle 0.74269 (25271) SS BOND : bond 0.00557 ( 116) SS BOND : angle 1.83762 ( 232) hydrogen bonds : bond 0.04649 ( 466) hydrogen bonds : angle 5.40581 ( 1151) link_NAG-ASN : bond 0.00445 ( 8) link_NAG-ASN : angle 3.39438 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 TYR cc_start: 0.8306 (m-80) cc_final: 0.7997 (m-80) REVERT: E 252 LYS cc_start: 0.8609 (ptpt) cc_final: 0.8291 (ptmm) REVERT: E 581 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7916 (mm-30) REVERT: G 111 MET cc_start: 0.9568 (ttt) cc_final: 0.9367 (ttt) REVERT: G 199 TRP cc_start: 0.8846 (m100) cc_final: 0.8580 (m100) REVERT: G 280 MET cc_start: 0.8905 (tmm) cc_final: 0.8344 (tmm) REVERT: G 333 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7439 (tp30) outliers start: 45 outliers final: 34 residues processed: 216 average time/residue: 0.1370 time to fit residues: 46.0516 Evaluate side-chains 219 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 957 GLU Chi-restraints excluded: chain H residue 975 ASP Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1187 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 162 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 134 optimal weight: 0.0770 chunk 216 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS F1226 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099190 restraints weight = 36843.979| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.71 r_work: 0.2985 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18747 Z= 0.142 Angle : 0.670 12.971 25527 Z= 0.338 Chirality : 0.045 0.259 2757 Planarity : 0.005 0.095 3358 Dihedral : 5.473 57.403 2730 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.11 % Allowed : 15.89 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.32 (0.17), residues: 2365 helix: -0.12 (0.27), residues: 363 sheet: -2.24 (0.26), residues: 368 loop : -1.80 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 597 TYR 0.037 0.001 TYR E 711 PHE 0.016 0.001 PHE H1100 TRP 0.049 0.001 TRP G 502 HIS 0.024 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00338 (18623) covalent geometry : angle 0.65529 (25271) SS BOND : bond 0.00343 ( 116) SS BOND : angle 1.32898 ( 232) hydrogen bonds : bond 0.03869 ( 466) hydrogen bonds : angle 5.24972 ( 1151) link_NAG-ASN : bond 0.00335 ( 8) link_NAG-ASN : angle 2.92098 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 TYR cc_start: 0.8095 (m-80) cc_final: 0.7798 (m-80) REVERT: E 249 LEU cc_start: 0.8102 (pp) cc_final: 0.7650 (mt) REVERT: E 252 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8308 (ptmm) REVERT: E 254 LEU cc_start: 0.7478 (mt) cc_final: 0.7214 (mt) REVERT: E 347 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8211 (mt-10) REVERT: E 581 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7669 (mm-30) REVERT: G 111 MET cc_start: 0.9445 (ttt) cc_final: 0.9149 (ttt) REVERT: G 280 MET cc_start: 0.8587 (tmm) cc_final: 0.8180 (tmm) REVERT: G 333 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7227 (tp30) REVERT: G 365 ARG cc_start: 0.6785 (tpp-160) cc_final: 0.6515 (mmt180) REVERT: G 740 MET cc_start: 0.5235 (ttp) cc_final: 0.5011 (tmm) outliers start: 42 outliers final: 32 residues processed: 224 average time/residue: 0.1341 time to fit residues: 46.6042 Evaluate side-chains 216 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 957 GLU Chi-restraints excluded: chain H residue 975 ASP Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1173 CYS Chi-restraints excluded: chain H residue 1187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 138 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS F 901 ASN ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098527 restraints weight = 38989.519| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.78 r_work: 0.2990 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18747 Z= 0.160 Angle : 0.674 13.399 25527 Z= 0.340 Chirality : 0.045 0.244 2757 Planarity : 0.005 0.098 3358 Dihedral : 5.396 57.380 2730 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 2.16 % Allowed : 16.14 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.26 (0.17), residues: 2365 helix: -0.09 (0.27), residues: 363 sheet: -2.22 (0.26), residues: 368 loop : -1.75 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 597 TYR 0.015 0.001 TYR F 988 PHE 0.014 0.001 PHE H1100 TRP 0.046 0.001 TRP G 502 HIS 0.008 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00385 (18623) covalent geometry : angle 0.65979 (25271) SS BOND : bond 0.00447 ( 116) SS BOND : angle 1.33366 ( 232) hydrogen bonds : bond 0.03924 ( 466) hydrogen bonds : angle 5.16428 ( 1151) link_NAG-ASN : bond 0.00326 ( 8) link_NAG-ASN : angle 2.87004 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.581 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: E 249 LEU cc_start: 0.8134 (pp) cc_final: 0.7722 (mt) REVERT: E 252 LYS cc_start: 0.8557 (ptpt) cc_final: 0.8307 (ptmm) REVERT: E 254 LEU cc_start: 0.7480 (mt) cc_final: 0.7235 (mt) REVERT: E 287 ASP cc_start: 0.7799 (m-30) cc_final: 0.7408 (m-30) REVERT: E 347 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8211 (mt-10) REVERT: E 469 GLN cc_start: 0.8601 (mt0) cc_final: 0.8398 (tt0) REVERT: E 581 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7806 (mm-30) REVERT: G 111 MET cc_start: 0.9420 (ttt) cc_final: 0.9196 (ttt) REVERT: G 280 MET cc_start: 0.8594 (tmm) cc_final: 0.8134 (tmm) REVERT: G 333 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: G 365 ARG cc_start: 0.6805 (tpp-160) cc_final: 0.6435 (mmt180) outliers start: 43 outliers final: 33 residues processed: 220 average time/residue: 0.1319 time to fit residues: 44.9806 Evaluate side-chains 215 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 975 ASP Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1173 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS F 901 ASN ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095973 restraints weight = 39447.147| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.82 r_work: 0.2951 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 18747 Z= 0.247 Angle : 0.740 13.380 25527 Z= 0.374 Chirality : 0.048 0.239 2757 Planarity : 0.006 0.101 3358 Dihedral : 5.677 59.159 2730 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 2.11 % Allowed : 16.14 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.37 (0.17), residues: 2365 helix: -0.20 (0.27), residues: 363 sheet: -2.24 (0.27), residues: 356 loop : -1.84 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 597 TYR 0.016 0.002 TYR F 988 PHE 0.017 0.002 PHE F1021 TRP 0.050 0.002 TRP G 502 HIS 0.007 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00598 (18623) covalent geometry : angle 0.72200 (25271) SS BOND : bond 0.00489 ( 116) SS BOND : angle 1.58385 ( 232) hydrogen bonds : bond 0.04431 ( 466) hydrogen bonds : angle 5.25624 ( 1151) link_NAG-ASN : bond 0.00396 ( 8) link_NAG-ASN : angle 3.12596 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 252 LYS cc_start: 0.8563 (ptpt) cc_final: 0.8320 (ptmm) REVERT: E 287 ASP cc_start: 0.8011 (m-30) cc_final: 0.7617 (m-30) REVERT: E 469 GLN cc_start: 0.8831 (mt0) cc_final: 0.8532 (tt0) REVERT: E 536 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9018 (mp) REVERT: E 581 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8014 (mm-30) REVERT: G 280 MET cc_start: 0.8866 (tmm) cc_final: 0.8296 (tmm) REVERT: G 333 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7460 (tp30) outliers start: 42 outliers final: 37 residues processed: 215 average time/residue: 0.1259 time to fit residues: 41.9136 Evaluate side-chains 215 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 237 CYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 975 ASP Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1173 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098927 restraints weight = 30048.945| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.75 r_work: 0.2962 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 18747 Z= 0.220 Angle : 0.746 14.678 25527 Z= 0.375 Chirality : 0.047 0.237 2757 Planarity : 0.005 0.102 3358 Dihedral : 5.735 58.692 2730 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 1.96 % Allowed : 16.63 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.37 (0.17), residues: 2365 helix: -0.21 (0.27), residues: 363 sheet: -2.20 (0.27), residues: 348 loop : -1.85 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 597 TYR 0.016 0.001 TYR F 988 PHE 0.015 0.001 PHE F1021 TRP 0.053 0.002 TRP G 502 HIS 0.010 0.001 HIS G 737 Details of bonding type rmsd covalent geometry : bond 0.00534 (18623) covalent geometry : angle 0.72234 (25271) SS BOND : bond 0.00437 ( 116) SS BOND : angle 1.85594 ( 232) hydrogen bonds : bond 0.04262 ( 466) hydrogen bonds : angle 5.24961 ( 1151) link_NAG-ASN : bond 0.00362 ( 8) link_NAG-ASN : angle 3.01434 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 252 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8331 (ptmm) REVERT: E 287 ASP cc_start: 0.8006 (m-30) cc_final: 0.7609 (m-30) REVERT: E 469 GLN cc_start: 0.8814 (mt0) cc_final: 0.8505 (tt0) REVERT: E 536 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9010 (mp) REVERT: E 581 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7986 (mm-30) REVERT: F 957 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8187 (tm-30) REVERT: G 280 MET cc_start: 0.8788 (tmm) cc_final: 0.8259 (tmm) REVERT: G 333 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: G 365 ARG cc_start: 0.6925 (tpp-160) cc_final: 0.6353 (mmt180) REVERT: G 740 MET cc_start: 0.5476 (ttp) cc_final: 0.5159 (tmm) outliers start: 39 outliers final: 36 residues processed: 207 average time/residue: 0.1368 time to fit residues: 44.0945 Evaluate side-chains 216 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 237 CYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 975 ASP Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1173 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100218 restraints weight = 29419.185| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.74 r_work: 0.2986 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 18747 Z= 0.155 Angle : 0.695 13.313 25527 Z= 0.350 Chirality : 0.046 0.242 2757 Planarity : 0.005 0.098 3358 Dihedral : 5.524 57.228 2730 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 2.11 % Allowed : 16.43 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.28 (0.17), residues: 2365 helix: -0.09 (0.27), residues: 363 sheet: -2.21 (0.28), residues: 326 loop : -1.80 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 597 TYR 0.015 0.001 TYR F 988 PHE 0.015 0.001 PHE H1100 TRP 0.048 0.001 TRP G 502 HIS 0.008 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00373 (18623) covalent geometry : angle 0.67761 (25271) SS BOND : bond 0.00363 ( 116) SS BOND : angle 1.52549 ( 232) hydrogen bonds : bond 0.03896 ( 466) hydrogen bonds : angle 5.17351 ( 1151) link_NAG-ASN : bond 0.00309 ( 8) link_NAG-ASN : angle 2.77227 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5158.18 seconds wall clock time: 88 minutes 48.80 seconds (5328.80 seconds total)