Starting phenix.real_space_refine on Thu Mar 5 01:27:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpp_32687/03_2026/7wpp_32687_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpp_32687/03_2026/7wpp_32687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wpp_32687/03_2026/7wpp_32687_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpp_32687/03_2026/7wpp_32687_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wpp_32687/03_2026/7wpp_32687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpp_32687/03_2026/7wpp_32687.map" } resolution = 2.85 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= 0.008 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 11258 2.51 5 N 3129 2.21 5 O 3583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 18252 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': 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: "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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.64, per 1000 atoms: 0.25 Number of scatterers: 18252 At special positions: 0 Unit cell: (160.293, 161.391, 149.314, 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 3583 8.00 N 3129 7.00 C 11258 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=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.02 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=2.03 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.02 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 808 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 889 " - pdb=" SG CYS F1031 " distance=2.03 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS F1149 " - pdb=" SG CYS F1169 " distance=2.03 Simple disulfide: pdb=" SG CYS F1153 " - pdb=" SG CYS F1165 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 159 " distance=2.02 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 255 " distance=2.02 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 440 " distance=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS G 623 " - pdb=" SG CYS G 648 " distance=2.02 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=2.03 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=2.03 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=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS H 889 " - pdb=" SG CYS H1031 " distance=2.03 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS H1177 " - pdb=" SG CYS H1190 " distance=2.03 Simple disulfide: pdb=" SG CYS H1199 " - pdb=" SG CYS H1227 " distance=2.03 Simple disulfide: pdb=" SG CYS H1222 " - pdb=" SG CYS H1237 " distance=2.04 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 156 " " NAG E 804 " - " ASN E 99 " " NAG F1301 " - " ASN F1231 " " NAG F1303 " - " ASN F 857 " " NAG F1304 " - " ASN F1147 " " NAG G 803 " - " ASN G 156 " " NAG G 804 " - " ASN G 99 " " NAG H1301 " - " ASN H1231 " " NAG H1303 " - " ASN H1147 " " NAG H1304 " - " ASN H 857 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 937.9 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: 52 helices and 40 sheets defined 17.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'E' and resid 114 through 118 removed outlier: 4.001A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.606A pdb=" N PHE E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 215 through 222 removed outlier: 3.564A pdb=" N LYS E 219 " --> pdb=" O GLY E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 removed outlier: 3.769A pdb=" N SER E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 252 removed outlier: 3.974A pdb=" N LYS E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.532A pdb=" N LEU E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 514 through 517 Processing helix chain 'E' and resid 545 through 551 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 584 removed outlier: 3.809A pdb=" N CYS E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 593 removed outlier: 3.536A pdb=" N PHE E 592 " --> pdb=" O SER E 589 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU E 593 " --> pdb=" O PRO E 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 589 through 593' Processing helix chain 'E' and resid 601 through 613 removed outlier: 3.565A pdb=" N ARG E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 610 " --> pdb=" O ARG E 606 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E 613 " --> pdb=" O ARG E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 637 removed outlier: 4.100A pdb=" N ALA E 627 " --> pdb=" O CYS E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 673 removed outlier: 4.024A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 668 through 673' Processing helix chain 'F' and resid 1017 through 1023 removed outlier: 3.819A pdb=" N ASN F1023 " --> pdb=" O VAL F1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1026 No H-bonds generated for 'chain 'F' and resid 1024 through 1026' Processing helix chain 'F' and resid 1049 through 1061 removed outlier: 3.562A pdb=" N ASP F1057 " --> pdb=" O GLN F1053 " (cutoff:3.500A) Processing helix chain 'F' and resid 1062 through 1067 removed outlier: 6.742A pdb=" N ASP F1066 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL F1067 " --> pdb=" O THR F1064 " (cutoff:3.500A) Processing helix chain 'F' and resid 1068 through 1073 removed outlier: 3.760A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 removed outlier: 3.680A pdb=" N THR F1088 " --> pdb=" O CYS F1084 " (cutoff:3.500A) Processing helix chain 'F' and resid 1100 through 1114 removed outlier: 3.616A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR F1107 " --> pdb=" O THR F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1131 through 1136 removed outlier: 3.659A pdb=" N ARG F1136 " --> pdb=" O GLU F1132 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 4.000A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 183 through 189 removed outlier: 3.607A pdb=" N PHE G 187 " --> pdb=" O ASP G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 192 No H-bonds generated for 'chain 'G' and resid 190 through 192' Processing helix chain 'G' and resid 215 through 222 removed outlier: 3.565A pdb=" N LYS G 219 " --> pdb=" O GLY G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.769A pdb=" N SER G 230 " --> pdb=" O GLN G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 removed outlier: 3.975A pdb=" N LYS G 252 " --> pdb=" O ALA G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.532A pdb=" N LEU G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 514 through 517 Processing helix chain 'G' and resid 545 through 551 Processing helix chain 'G' and resid 568 through 572 Processing helix chain 'G' and resid 573 through 575 No H-bonds generated for 'chain 'G' and resid 573 through 575' Processing helix chain 'G' and resid 576 through 584 removed outlier: 3.810A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 589 through 593 removed outlier: 3.536A pdb=" N PHE G 592 " --> pdb=" O SER G 589 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU G 593 " --> pdb=" O PRO G 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 589 through 593' Processing helix chain 'G' and resid 601 through 613 removed outlier: 3.565A pdb=" N ARG G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS G 613 " --> pdb=" O ARG G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 637 removed outlier: 4.100A pdb=" N ALA G 627 " --> pdb=" O CYS G 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 673 removed outlier: 4.023A pdb=" N LEU G 672 " --> pdb=" O THR G 668 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER G 673 " --> pdb=" O CYS G 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 668 through 673' Processing helix chain 'H' and resid 1017 through 1023 removed outlier: 3.819A pdb=" N ASN H1023 " --> pdb=" O VAL H1019 " (cutoff:3.500A) Processing helix chain 'H' and resid 1024 through 1026 No H-bonds generated for 'chain 'H' and resid 1024 through 1026' Processing helix chain 'H' and resid 1049 through 1061 removed outlier: 3.639A pdb=" N ASP H1057 " --> pdb=" O GLN H1053 " (cutoff:3.500A) Processing helix chain 'H' and resid 1062 through 1067 removed outlier: 6.742A pdb=" N ASP H1066 " --> pdb=" O LEU H1063 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL H1067 " --> pdb=" O THR H1064 " (cutoff:3.500A) Processing helix chain 'H' and resid 1068 through 1073 removed outlier: 3.761A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 removed outlier: 3.681A pdb=" N THR H1088 " --> pdb=" O CYS H1084 " (cutoff:3.500A) Processing helix chain 'H' and resid 1100 through 1114 removed outlier: 3.615A pdb=" N ILE H1104 " --> pdb=" O PHE H1100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR H1107 " --> pdb=" O THR H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1131 through 1136 removed outlier: 3.659A pdb=" N ARG H1136 " --> pdb=" O GLU H1132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 32 through 37 removed outlier: 3.526A pdb=" N LEU E 150 " --> pdb=" O ALA E 33 " (cutoff:3.500A) 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 58 through 62 removed outlier: 6.810A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN E 107 " --> pdb=" O GLN E 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 300 through 305 removed outlier: 5.803A pdb=" N TYR E 301 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER E 330 " --> pdb=" O TYR E 301 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN E 303 " --> pdb=" O GLY E 328 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY E 328 " --> pdb=" O GLN E 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 336 through 337 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 469 through 470 removed outlier: 3.684A pdb=" N GLN E 469 " --> pdb=" O MET E 466 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE E 427 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU E 413 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR E 429 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN E 411 " --> pdb=" O THR E 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 480 through 484 Processing sheet with id=AB2, first strand: chain 'E' and resid 536 through 537 removed outlier: 3.888A pdb=" N LEU E 541 " --> pdb=" O THR E 537 " (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 772 through 773 Processing sheet with id=AB6, first strand: chain 'F' and resid 841 through 844 Processing sheet with id=AB7, first strand: chain 'F' and resid 865 through 866 removed outlier: 5.898A pdb=" N LEU F 970 " --> pdb=" O LEU F 966 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 961 " --> pdb=" O SER F 958 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 875 through 876 Processing sheet with id=AB9, first strand: chain 'F' and resid 890 through 895 removed outlier: 7.178A pdb=" N ILE F 907 " --> pdb=" O LEU F 893 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLN F 895 " --> pdb=" O PHE F 905 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE F 905 " --> pdb=" O GLN F 895 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 926 " --> pdb=" O LEU F 908 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS F 912 " --> pdb=" O LYS F 922 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS F 922 " --> pdb=" O LYS F 912 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 934 " --> pdb=" O ILE F 927 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU F 933 " --> pdb=" O LYS F 944 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 1144 through 1151 removed outlier: 5.110A pdb=" N TYR F1146 " --> pdb=" O HIS F1174 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N HIS F1174 " --> pdb=" O TYR F1146 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER F1148 " --> pdb=" O GLY F1172 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLY F1172 " --> pdb=" O SER F1148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 1182 through 1183 Processing sheet with id=AC3, first strand: chain 'G' and resid 32 through 37 removed outlier: 3.526A pdb=" N LEU G 150 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 42 through 44 Processing sheet with id=AC5, first strand: chain 'G' and resid 58 through 62 removed outlier: 6.810A pdb=" N ILE G 72 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN G 107 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 300 through 305 removed outlier: 5.802A pdb=" N TYR G 301 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER G 330 " --> pdb=" O TYR G 301 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN G 303 " --> pdb=" O GLY G 328 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY G 328 " --> pdb=" O GLN G 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 336 through 337 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 403 through 405 Processing sheet with id=AD2, first strand: chain 'G' and resid 469 through 470 removed outlier: 3.684A pdb=" N GLN G 469 " --> pdb=" O MET G 466 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N THR G 441 " --> pdb=" O VAL G 430 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL G 430 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 443 " --> pdb=" O GLU G 428 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 7.286A 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=AD3, first strand: chain 'G' and resid 480 through 484 Processing sheet with id=AD4, first strand: chain 'G' and resid 536 through 537 removed outlier: 3.887A pdb=" N LEU G 541 " --> pdb=" O THR G 537 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 657 through 659 Processing sheet with id=AD6, first strand: chain 'G' and resid 721 through 723 Processing sheet with id=AD7, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AD8, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AD9, first strand: chain 'H' and resid 865 through 866 removed outlier: 5.898A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR H 961 " --> pdb=" O SER H 958 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 875 through 876 Processing sheet with id=AE2, first strand: chain 'H' and resid 890 through 895 removed outlier: 7.177A pdb=" N ILE H 907 " --> pdb=" O LEU H 893 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN H 895 " --> pdb=" O PHE H 905 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE H 905 " --> pdb=" O GLN H 895 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 926 " --> pdb=" O LEU H 908 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS H 912 " --> pdb=" O LYS H 922 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS H 922 " --> pdb=" O LYS H 912 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 934 " --> pdb=" O ILE H 927 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU H 933 " --> pdb=" O LYS H 944 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 1144 through 1151 removed outlier: 5.111A pdb=" N TYR H1146 " --> pdb=" O HIS H1174 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N HIS H1174 " --> pdb=" O TYR H1146 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER H1148 " --> pdb=" O GLY H1172 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY H1172 " --> pdb=" O SER H1148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 1182 through 1183 446 hydrogen bonds defined for protein. 1163 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: 3.66 Time building geometry restraints manager: 2.07 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: 6156 1.34 - 1.47: 4334 1.47 - 1.59: 7841 1.59 - 1.71: 0 1.71 - 1.84: 320 Bond restraints: 18651 Sorted by residual: bond pdb=" N LYS G 157 " pdb=" CA LYS G 157 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 9.20e+00 bond pdb=" N CYS H 858 " pdb=" CA CYS H 858 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.88e+00 bond pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.81e+00 bond pdb=" N PHE E 155 " pdb=" CA PHE E 155 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.30e-02 5.92e+03 7.20e+00 bond pdb=" N ASN E 156 " pdb=" CA ASN E 156 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.05e+00 ... (remaining 18646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 24380 2.75 - 5.50: 754 5.50 - 8.24: 133 8.24 - 10.99: 26 10.99 - 13.74: 16 Bond angle restraints: 25309 Sorted by residual: angle pdb=" C THR E 175 " pdb=" N GLN E 176 " pdb=" CA GLN E 176 " ideal model delta sigma weight residual 120.60 132.28 -11.68 1.60e+00 3.91e-01 5.33e+01 angle pdb=" C ALA E 267 " pdb=" N LEU E 268 " pdb=" CA LEU E 268 " ideal model delta sigma weight residual 120.29 130.62 -10.33 1.42e+00 4.96e-01 5.29e+01 angle pdb=" C ALA G 267 " pdb=" N LEU G 268 " pdb=" CA LEU G 268 " ideal model delta sigma weight residual 120.29 130.62 -10.33 1.42e+00 4.96e-01 5.29e+01 angle pdb=" C THR G 175 " pdb=" N GLN G 176 " pdb=" CA GLN G 176 " ideal model delta sigma weight residual 120.60 132.22 -11.62 1.60e+00 3.91e-01 5.28e+01 angle pdb=" C LEU G 228 " pdb=" N LYS G 229 " pdb=" CA LYS G 229 " ideal model delta sigma weight residual 121.81 134.64 -12.83 1.83e+00 2.99e-01 4.91e+01 ... (remaining 25304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10938 17.94 - 35.88: 563 35.88 - 53.82: 127 53.82 - 71.75: 41 71.75 - 89.69: 16 Dihedral angle restraints: 11685 sinusoidal: 4861 harmonic: 6824 Sorted by residual: dihedral pdb=" CB CYS E 312 " pdb=" SG CYS E 312 " pdb=" SG CYS E 348 " pdb=" CB CYS E 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.03 -80.03 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS G 312 " pdb=" SG CYS G 312 " pdb=" SG CYS G 348 " pdb=" CB CYS G 348 " ideal model delta sinusoidal sigma weight residual 93.00 172.99 -79.99 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS F 810 " pdb=" SG CYS F 810 " pdb=" SG CYS F 821 " pdb=" CB CYS F 821 " ideal model delta sinusoidal sigma weight residual 93.00 172.08 -79.08 1 1.00e+01 1.00e-02 7.78e+01 ... (remaining 11682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 2711 0.304 - 0.608: 20 0.608 - 0.911: 27 0.911 - 1.215: 0 1.215 - 1.519: 9 Chirality restraints: 2767 Sorted by residual: chirality pdb=" CB THR G 181 " pdb=" CA THR G 181 " pdb=" OG1 THR G 181 " pdb=" CG2 THR G 181 " both_signs ideal model delta sigma weight residual False 2.55 1.03 1.52 2.00e-01 2.50e+01 5.77e+01 chirality pdb=" CB THR E 181 " pdb=" CA THR E 181 " pdb=" OG1 THR E 181 " pdb=" CG2 THR E 181 " both_signs ideal model delta sigma weight residual False 2.55 1.04 1.52 2.00e-01 2.50e+01 5.74e+01 chirality pdb=" CB THR E 175 " pdb=" CA THR E 175 " pdb=" OG1 THR E 175 " pdb=" CG2 THR E 175 " both_signs ideal model delta sigma weight residual False 2.55 1.07 1.49 2.00e-01 2.50e+01 5.52e+01 ... (remaining 2764 not shown) Planarity restraints: 3370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 804 " 0.333 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG E 804 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG E 804 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG E 804 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG E 804 " 0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H1303 " 0.323 2.00e-02 2.50e+03 2.77e-01 9.62e+02 pdb=" C7 NAG H1303 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG H1303 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG H1303 " -0.490 2.00e-02 2.50e+03 pdb=" O7 NAG H1303 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 803 " -0.301 2.00e-02 2.50e+03 2.52e-01 7.97e+02 pdb=" C7 NAG E 803 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG E 803 " -0.193 2.00e-02 2.50e+03 pdb=" N2 NAG E 803 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG E 803 " -0.017 2.00e-02 2.50e+03 ... (remaining 3367 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 221 2.61 - 3.18: 16044 3.18 - 3.76: 26595 3.76 - 4.33: 37449 4.33 - 4.90: 61322 Nonbonded interactions: 141631 Sorted by model distance: nonbonded pdb=" OG SER F1009 " pdb=" OD1 ASN F1011 " model vdw 2.041 3.040 nonbonded pdb=" OG SER H1009 " pdb=" OD1 ASN H1011 " model vdw 2.041 3.040 nonbonded pdb=" O GLU E 270 " pdb=" OG1 THR E 274 " model vdw 2.057 3.040 nonbonded pdb=" O GLU G 270 " pdb=" OG1 THR G 274 " model vdw 2.058 3.040 nonbonded pdb=" O SER F1093 " pdb=" OG SER H1093 " model vdw 2.068 3.040 ... (remaining 141626 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 1304)) selection = (chain 'H' and (resid 767 through 1052 or resid 1054 through 1304)) } 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.480 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.190 18777 Z= 0.363 Angle : 1.195 17.710 25571 Z= 0.635 Chirality : 0.139 1.519 2767 Planarity : 0.012 0.288 3360 Dihedral : 10.808 89.693 6967 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.98 % Favored : 89.89 % Rotamer: Outliers : 0.74 % Allowed : 2.31 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.14), residues: 2365 helix: -3.60 (0.18), residues: 325 sheet: -2.90 (0.21), residues: 426 loop : -2.84 (0.13), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 960 TYR 0.038 0.003 TYR G 527 PHE 0.026 0.003 PHE G 535 TRP 0.027 0.003 TRP H 974 HIS 0.010 0.002 HIS E 596 Details of bonding type rmsd covalent geometry : bond 0.00871 (18651) covalent geometry : angle 1.17088 (25309) SS BOND : bond 0.00447 ( 116) SS BOND : angle 1.86109 ( 232) hydrogen bonds : bond 0.28096 ( 446) hydrogen bonds : angle 9.45708 ( 1163) link_NAG-ASN : bond 0.06122 ( 10) link_NAG-ASN : angle 5.78050 ( 30) *********************** 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 603 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 589 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 TYR cc_start: 0.7943 (m-80) cc_final: 0.7401 (m-80) REVERT: E 217 MET cc_start: 0.2897 (mtp) cc_final: 0.1206 (ptt) REVERT: F 897 TYR cc_start: 0.7804 (m-10) cc_final: 0.7529 (m-80) REVERT: F 1028 SER cc_start: 0.8280 (p) cc_final: 0.7798 (t) REVERT: G 217 MET cc_start: 0.1917 (mtp) cc_final: 0.1432 (ptt) REVERT: G 233 VAL cc_start: 0.7387 (p) cc_final: 0.7053 (t) REVERT: G 343 VAL cc_start: 0.7235 (p) cc_final: 0.6498 (m) REVERT: H 793 GLN cc_start: 0.6705 (pp30) cc_final: 0.6504 (tm-30) REVERT: H 795 TYR cc_start: 0.7587 (t80) cc_final: 0.7264 (t80) REVERT: H 842 VAL cc_start: 0.8520 (m) cc_final: 0.8300 (p) outliers start: 14 outliers final: 1 residues processed: 593 average time/residue: 0.6214 time to fit residues: 410.9279 Evaluate side-chains 255 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 181 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 HIS E 189 ASN E 368 ASN E 374 ASN F 817 HIS F 942 ASN F 952 HIS F1013 GLN F1174 HIS F1221 HIS G 78 ASN G 95 HIS G 277 GLN G 452 HIS G 596 HIS ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1013 GLN H1069 GLN H1113 GLN H1221 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.177031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132061 restraints weight = 23221.583| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.15 r_work: 0.3327 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18777 Z= 0.164 Angle : 0.798 18.344 25571 Z= 0.397 Chirality : 0.052 0.694 2767 Planarity : 0.005 0.050 3360 Dihedral : 6.579 59.995 2773 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 4.17 % Allowed : 13.73 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.15), residues: 2365 helix: -1.56 (0.25), residues: 321 sheet: -1.79 (0.23), residues: 438 loop : -2.15 (0.14), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 373 TYR 0.026 0.002 TYR G 711 PHE 0.025 0.002 PHE H 999 TRP 0.015 0.002 TRP F 974 HIS 0.005 0.001 HIS G 95 Details of bonding type rmsd covalent geometry : bond 0.00384 (18651) covalent geometry : angle 0.75901 (25309) SS BOND : bond 0.00463 ( 116) SS BOND : angle 2.02022 ( 232) hydrogen bonds : bond 0.04456 ( 446) hydrogen bonds : angle 5.67372 ( 1163) link_NAG-ASN : bond 0.00795 ( 10) link_NAG-ASN : angle 5.03398 ( 30) *********************** 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 355 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 271 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 VAL cc_start: 0.8465 (t) cc_final: 0.8159 (m) REVERT: E 132 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7779 (mm-30) REVERT: E 217 MET cc_start: 0.2934 (mtp) cc_final: 0.2016 (ptt) REVERT: E 294 VAL cc_start: 0.7755 (OUTLIER) cc_final: 0.7484 (p) REVERT: E 320 MET cc_start: 0.5085 (OUTLIER) cc_final: 0.4813 (tpt) REVERT: E 419 GLN cc_start: 0.7582 (pp30) cc_final: 0.7255 (mm110) REVERT: E 602 LEU cc_start: 0.8193 (pp) cc_final: 0.7966 (mt) REVERT: E 649 GLU cc_start: 0.6263 (pt0) cc_final: 0.5241 (mm-30) REVERT: E 694 TYR cc_start: 0.5037 (m-10) cc_final: 0.4818 (m-10) REVERT: E 696 ASP cc_start: 0.7210 (t0) cc_final: 0.6990 (t70) REVERT: E 712 ASP cc_start: 0.7087 (t0) cc_final: 0.6702 (OUTLIER) REVERT: F 864 ASP cc_start: 0.8507 (m-30) cc_final: 0.8200 (m-30) REVERT: F 1049 ASN cc_start: 0.6126 (t0) cc_final: 0.5919 (t0) REVERT: F 1051 MET cc_start: 0.7694 (tpt) cc_final: 0.7259 (tmm) REVERT: F 1161 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: G 201 GLU cc_start: 0.7296 (mp0) cc_final: 0.6660 (mm-30) REVERT: G 313 GLN cc_start: 0.6740 (mp10) cc_final: 0.6462 (mp-120) REVERT: G 326 VAL cc_start: 0.8060 (t) cc_final: 0.7777 (p) REVERT: G 343 VAL cc_start: 0.7660 (p) cc_final: 0.7444 (m) REVERT: G 479 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: G 578 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7533 (ttp-110) REVERT: G 602 LEU cc_start: 0.8025 (pp) cc_final: 0.7579 (mt) REVERT: G 695 MET cc_start: 0.7230 (mmp) cc_final: 0.6907 (mmp) REVERT: G 728 MET cc_start: 0.7003 (tmm) cc_final: 0.6722 (tmm) REVERT: H 795 TYR cc_start: 0.7742 (t80) cc_final: 0.7116 (t80) REVERT: H 842 VAL cc_start: 0.8415 (m) cc_final: 0.8097 (p) REVERT: H 862 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7642 (t) REVERT: H 947 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6778 (ptm) REVERT: H 1049 ASN cc_start: 0.6229 (t0) cc_final: 0.5989 (t0) REVERT: H 1061 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7890 (mpt90) outliers start: 84 outliers final: 33 residues processed: 329 average time/residue: 0.5274 time to fit residues: 197.7021 Evaluate side-chains 237 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1088 THR Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 250 CYS Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 479 ASP Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 19 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 190 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1113 GLN G 78 ASN G 189 ASN G 303 GLN G 453 ASN G 563 GLN H1003 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129185 restraints weight = 23399.927| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.10 r_work: 0.3285 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18777 Z= 0.133 Angle : 0.688 14.263 25571 Z= 0.342 Chirality : 0.049 0.575 2767 Planarity : 0.005 0.048 3360 Dihedral : 5.950 54.460 2773 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 3.97 % Allowed : 15.99 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2365 helix: -0.57 (0.26), residues: 331 sheet: -1.19 (0.24), residues: 438 loop : -1.85 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 373 TYR 0.022 0.001 TYR G 711 PHE 0.021 0.002 PHE H 999 TRP 0.013 0.001 TRP H 974 HIS 0.003 0.001 HIS E 421 Details of bonding type rmsd covalent geometry : bond 0.00308 (18651) covalent geometry : angle 0.66033 (25309) SS BOND : bond 0.00400 ( 116) SS BOND : angle 1.45563 ( 232) hydrogen bonds : bond 0.03883 ( 446) hydrogen bonds : angle 5.14552 ( 1163) link_NAG-ASN : bond 0.00723 ( 10) link_NAG-ASN : angle 4.33848 ( 30) *********************** 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 298 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 218 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 VAL cc_start: 0.8443 (t) cc_final: 0.8158 (m) REVERT: E 217 MET cc_start: 0.3052 (mtp) cc_final: 0.2509 (ppp) REVERT: E 252 LYS cc_start: 0.7371 (ptmt) cc_final: 0.6923 (ptmm) REVERT: E 302 ARG cc_start: 0.7677 (ttm170) cc_final: 0.6555 (ttt-90) REVERT: E 313 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: E 419 GLN cc_start: 0.7679 (pp30) cc_final: 0.7291 (mm-40) REVERT: E 597 ARG cc_start: 0.7843 (ptp-110) cc_final: 0.7377 (ptm-80) REVERT: E 694 TYR cc_start: 0.5252 (m-10) cc_final: 0.4899 (m-80) REVERT: E 712 ASP cc_start: 0.7387 (t0) cc_final: 0.6981 (OUTLIER) REVERT: E 728 MET cc_start: 0.7896 (tpp) cc_final: 0.7668 (tpt) REVERT: F 864 ASP cc_start: 0.8523 (m-30) cc_final: 0.8176 (m-30) REVERT: F 912 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7667 (mptt) REVERT: F 920 LYS cc_start: 0.5958 (OUTLIER) cc_final: 0.5247 (mtmt) REVERT: F 968 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7665 (mtmm) REVERT: F 1078 GLU cc_start: 0.7897 (tp30) cc_final: 0.7654 (tp30) REVERT: G 201 GLU cc_start: 0.7395 (mp0) cc_final: 0.6806 (mm-30) REVERT: G 217 MET cc_start: 0.3181 (mtm) cc_final: 0.2041 (pp-130) REVERT: G 343 VAL cc_start: 0.7559 (p) cc_final: 0.7323 (m) REVERT: G 479 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7087 (m-30) REVERT: G 564 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8412 (tppt) REVERT: G 578 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7803 (ttp-110) REVERT: G 602 LEU cc_start: 0.8117 (pp) cc_final: 0.7912 (mt) REVERT: H 795 TYR cc_start: 0.7738 (t80) cc_final: 0.7156 (t80) REVERT: H 802 MET cc_start: 0.5289 (mpt) cc_final: 0.4930 (mpt) REVERT: H 842 VAL cc_start: 0.8425 (m) cc_final: 0.8188 (p) REVERT: H 862 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7816 (t) REVERT: H 930 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: H 947 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6758 (ptm) REVERT: H 1049 ASN cc_start: 0.6249 (t0) cc_final: 0.5929 (t0) REVERT: H 1061 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7996 (mpt90) outliers start: 80 outliers final: 35 residues processed: 275 average time/residue: 0.5393 time to fit residues: 167.7528 Evaluate side-chains 229 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 479 ASP Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 800 MET Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 930 GLU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 105 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 220 optimal weight: 0.0670 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 393 GLN F1188 GLN G 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125358 restraints weight = 20913.164| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.02 r_work: 0.3236 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18777 Z= 0.173 Angle : 0.721 13.276 25571 Z= 0.360 Chirality : 0.051 0.555 2767 Planarity : 0.005 0.047 3360 Dihedral : 6.162 57.176 2773 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.36 % Favored : 92.60 % Rotamer: Outliers : 4.46 % Allowed : 16.77 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.16), residues: 2365 helix: -0.07 (0.28), residues: 329 sheet: -0.87 (0.25), residues: 448 loop : -1.75 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 373 TYR 0.025 0.002 TYR H 897 PHE 0.026 0.002 PHE H 999 TRP 0.011 0.002 TRP H 974 HIS 0.004 0.001 HIS F 874 Details of bonding type rmsd covalent geometry : bond 0.00413 (18651) covalent geometry : angle 0.69569 (25309) SS BOND : bond 0.00441 ( 116) SS BOND : angle 1.55158 ( 232) hydrogen bonds : bond 0.04074 ( 446) hydrogen bonds : angle 5.12243 ( 1163) link_NAG-ASN : bond 0.00739 ( 10) link_NAG-ASN : angle 4.08492 ( 30) *********************** 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 286 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 196 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 VAL cc_start: 0.8617 (t) cc_final: 0.8408 (m) REVERT: E 217 MET cc_start: 0.3097 (mtp) cc_final: 0.1990 (ptt) REVERT: E 228 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7067 (tt) REVERT: E 294 VAL cc_start: 0.7682 (m) cc_final: 0.7461 (p) REVERT: E 302 ARG cc_start: 0.7745 (ttm170) cc_final: 0.6745 (ttt-90) REVERT: E 313 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: E 346 THR cc_start: 0.7538 (m) cc_final: 0.7106 (p) REVERT: E 419 GLN cc_start: 0.7773 (pp30) cc_final: 0.7334 (mm-40) REVERT: E 543 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: F 864 ASP cc_start: 0.8591 (m-30) cc_final: 0.8242 (m-30) REVERT: F 911 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8048 (p0) REVERT: F 912 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7856 (mptt) REVERT: F 1078 GLU cc_start: 0.7972 (tp30) cc_final: 0.7727 (tp30) REVERT: G 107 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7252 (pp30) REVERT: G 265 CYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7239 (m) REVERT: G 343 VAL cc_start: 0.7719 (p) cc_final: 0.7488 (m) REVERT: G 503 ASP cc_start: 0.4355 (t0) cc_final: 0.3974 (t0) REVERT: G 564 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8582 (tptt) REVERT: G 578 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7739 (ttp-110) REVERT: G 609 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8392 (mtt90) REVERT: H 795 TYR cc_start: 0.7831 (t80) cc_final: 0.7620 (t80) REVERT: H 802 MET cc_start: 0.5759 (OUTLIER) cc_final: 0.5129 (mpt) REVERT: H 842 VAL cc_start: 0.8431 (m) cc_final: 0.8171 (p) REVERT: H 862 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8002 (t) REVERT: H 947 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6788 (ptm) REVERT: H 1049 ASN cc_start: 0.6354 (t0) cc_final: 0.6014 (t160) REVERT: H 1061 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7959 (mpt90) REVERT: H 1092 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6374 (mp0) outliers start: 90 outliers final: 46 residues processed: 258 average time/residue: 0.5563 time to fit residues: 162.8549 Evaluate side-chains 235 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 935 GLU Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 479 ASP Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 802 MET Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 927 ILE Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 135 optimal weight: 0.0870 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN E 322 GLN F1188 GLN G 78 ASN G 368 ASN H 952 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120657 restraints weight = 30096.589| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.55 r_work: 0.3215 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18777 Z= 0.178 Angle : 0.712 13.201 25571 Z= 0.357 Chirality : 0.051 0.584 2767 Planarity : 0.005 0.048 3360 Dihedral : 6.267 58.966 2773 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.23 % Favored : 92.72 % Rotamer: Outliers : 4.86 % Allowed : 17.36 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.16), residues: 2365 helix: 0.01 (0.28), residues: 341 sheet: -0.70 (0.26), residues: 426 loop : -1.70 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 373 TYR 0.024 0.002 TYR G 711 PHE 0.022 0.002 PHE H 999 TRP 0.013 0.002 TRP G 222 HIS 0.005 0.001 HIS E 596 Details of bonding type rmsd covalent geometry : bond 0.00428 (18651) covalent geometry : angle 0.68727 (25309) SS BOND : bond 0.00404 ( 116) SS BOND : angle 1.50158 ( 232) hydrogen bonds : bond 0.04052 ( 446) hydrogen bonds : angle 5.05183 ( 1163) link_NAG-ASN : bond 0.00579 ( 10) link_NAG-ASN : angle 4.04563 ( 30) *********************** 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 294 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 196 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7417 (mm110) REVERT: E 154 TYR cc_start: 0.8567 (m-80) cc_final: 0.8241 (m-80) REVERT: E 217 MET cc_start: 0.3217 (mtp) cc_final: 0.2109 (ptt) REVERT: E 228 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6975 (tt) REVERT: E 252 LYS cc_start: 0.7538 (ptmt) cc_final: 0.7010 (ptmm) REVERT: E 302 ARG cc_start: 0.7670 (ttm170) cc_final: 0.6604 (ttt-90) REVERT: E 313 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: E 341 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6989 (pt) REVERT: E 346 THR cc_start: 0.7511 (m) cc_final: 0.7269 (p) REVERT: E 347 GLU cc_start: 0.7685 (tp30) cc_final: 0.7465 (tp30) REVERT: E 356 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7523 (mmt-90) REVERT: E 419 GLN cc_start: 0.7901 (pp30) cc_final: 0.7346 (mm110) REVERT: E 543 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: E 620 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6867 (tp30) REVERT: E 712 ASP cc_start: 0.7686 (t0) cc_final: 0.7374 (t0) REVERT: F 793 GLN cc_start: 0.6804 (pp30) cc_final: 0.6391 (tm-30) REVERT: F 912 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7861 (mptt) REVERT: F 920 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5101 (mtmt) REVERT: F 1036 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7523 (mptm) REVERT: F 1078 GLU cc_start: 0.7898 (tp30) cc_final: 0.7640 (tp30) REVERT: G 67 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7952 (ptmt) REVERT: G 107 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7140 (pp30) REVERT: G 108 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7364 (mtp-110) REVERT: G 503 ASP cc_start: 0.4456 (t0) cc_final: 0.4091 (t0) REVERT: G 578 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7443 (ttp-110) REVERT: G 605 LEU cc_start: 0.8890 (tp) cc_final: 0.8674 (tp) REVERT: G 609 ARG cc_start: 0.8681 (mtp85) cc_final: 0.8209 (mtt-85) REVERT: G 700 ASP cc_start: 0.6296 (t0) cc_final: 0.5997 (p0) REVERT: G 736 MET cc_start: 0.6916 (tpt) cc_final: 0.6652 (tpt) REVERT: H 795 TYR cc_start: 0.7635 (t80) cc_final: 0.7386 (t80) REVERT: H 842 VAL cc_start: 0.8330 (m) cc_final: 0.8075 (p) REVERT: H 862 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7996 (t) REVERT: H 947 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6760 (ptm) REVERT: H 1049 ASN cc_start: 0.6307 (t0) cc_final: 0.5941 (t160) REVERT: H 1061 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7851 (mpt90) REVERT: H 1092 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6250 (mp0) outliers start: 98 outliers final: 55 residues processed: 268 average time/residue: 0.5844 time to fit residues: 177.0536 Evaluate side-chains 248 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 178 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 804 CYS Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1036 LYS Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 479 ASP Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 927 ILE Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 179 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 GLN F 952 HIS G 78 ASN H1003 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119314 restraints weight = 22600.962| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.04 r_work: 0.3167 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 18777 Z= 0.234 Angle : 0.794 12.459 25571 Z= 0.399 Chirality : 0.054 0.649 2767 Planarity : 0.006 0.051 3360 Dihedral : 6.686 59.010 2773 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.04 % Favored : 91.92 % Rotamer: Outliers : 5.54 % Allowed : 17.21 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2365 helix: -0.21 (0.28), residues: 337 sheet: -0.62 (0.27), residues: 402 loop : -1.64 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 373 TYR 0.025 0.002 TYR H 897 PHE 0.026 0.003 PHE H 999 TRP 0.014 0.002 TRP G 553 HIS 0.005 0.001 HIS F 874 Details of bonding type rmsd covalent geometry : bond 0.00567 (18651) covalent geometry : angle 0.76621 (25309) SS BOND : bond 0.00509 ( 116) SS BOND : angle 1.81207 ( 232) hydrogen bonds : bond 0.04525 ( 446) hydrogen bonds : angle 5.13262 ( 1163) link_NAG-ASN : bond 0.00758 ( 10) link_NAG-ASN : angle 4.02782 ( 30) *********************** 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 305 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 193 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7565 (mm-40) REVERT: E 107 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7565 (mm110) REVERT: E 154 TYR cc_start: 0.8607 (m-80) cc_final: 0.8150 (m-80) REVERT: E 157 LYS cc_start: 0.8752 (mttm) cc_final: 0.8419 (mtmt) REVERT: E 217 MET cc_start: 0.3611 (mtp) cc_final: 0.2264 (pmt) REVERT: E 228 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7340 (tt) REVERT: E 252 LYS cc_start: 0.7686 (ptmt) cc_final: 0.7239 (ptmm) REVERT: E 294 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7276 (p) REVERT: E 313 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: E 347 GLU cc_start: 0.7869 (tp30) cc_final: 0.7608 (tp30) REVERT: E 363 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8163 (mt) REVERT: E 419 GLN cc_start: 0.7920 (pp30) cc_final: 0.7380 (mm-40) REVERT: E 483 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8601 (pt0) REVERT: E 543 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: E 712 ASP cc_start: 0.7873 (t0) cc_final: 0.7451 (t0) REVERT: F 793 GLN cc_start: 0.7307 (pp30) cc_final: 0.6876 (tm-30) REVERT: F 920 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5439 (mtpt) REVERT: F 937 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.6789 (p90) REVERT: F 1030 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6834 (pt0) REVERT: G 107 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7155 (pp30) REVERT: G 116 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8615 (mmtp) REVERT: G 326 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7600 (p) REVERT: G 382 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6650 (pt0) REVERT: G 416 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8421 (ttm170) REVERT: G 503 ASP cc_start: 0.4746 (t0) cc_final: 0.4399 (t70) REVERT: G 578 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7665 (ttp-110) REVERT: G 605 LEU cc_start: 0.8955 (tp) cc_final: 0.8741 (tp) REVERT: G 609 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8338 (mtt90) REVERT: G 660 GLN cc_start: 0.7020 (tp40) cc_final: 0.6283 (tp-100) REVERT: G 700 ASP cc_start: 0.6492 (t0) cc_final: 0.6233 (p0) REVERT: H 795 TYR cc_start: 0.7805 (t80) cc_final: 0.7599 (t80) REVERT: H 842 VAL cc_start: 0.8505 (m) cc_final: 0.8234 (p) REVERT: H 844 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8893 (mp) REVERT: H 862 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8101 (t) REVERT: H 947 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.7014 (ptm) REVERT: H 1049 ASN cc_start: 0.6514 (t0) cc_final: 0.6159 (t160) REVERT: H 1061 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7807 (mpt90) REVERT: H 1092 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6303 (mp0) outliers start: 112 outliers final: 62 residues processed: 273 average time/residue: 0.5466 time to fit residues: 168.8409 Evaluate side-chains 253 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 171 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 483 GLN Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 786 LEU Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1030 GLN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 416 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 844 ILE Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 927 ILE Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1124 THR Chi-restraints excluded: chain H residue 1156 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 123 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN F 952 HIS G 78 ASN ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1003 GLN H1188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121621 restraints weight = 24690.043| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.16 r_work: 0.3200 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18777 Z= 0.156 Angle : 0.699 11.613 25571 Z= 0.349 Chirality : 0.050 0.690 2767 Planarity : 0.005 0.050 3360 Dihedral : 6.218 57.893 2773 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.60 % Favored : 93.36 % Rotamer: Outliers : 4.41 % Allowed : 18.83 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.16), residues: 2365 helix: -0.23 (0.27), residues: 361 sheet: -0.40 (0.28), residues: 360 loop : -1.60 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 373 TYR 0.023 0.002 TYR G 711 PHE 0.016 0.002 PHE H 999 TRP 0.018 0.002 TRP G 222 HIS 0.004 0.001 HIS F 817 Details of bonding type rmsd covalent geometry : bond 0.00373 (18651) covalent geometry : angle 0.67330 (25309) SS BOND : bond 0.00408 ( 116) SS BOND : angle 1.52885 ( 232) hydrogen bonds : bond 0.03789 ( 446) hydrogen bonds : angle 4.96698 ( 1163) link_NAG-ASN : bond 0.00604 ( 10) link_NAG-ASN : angle 3.94108 ( 30) *********************** 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 266 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 177 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7540 (mm110) REVERT: E 154 TYR cc_start: 0.8638 (m-80) cc_final: 0.8247 (m-80) REVERT: E 217 MET cc_start: 0.3456 (mtp) cc_final: 0.2092 (pmt) REVERT: E 228 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7215 (tt) REVERT: E 252 LYS cc_start: 0.7635 (ptmt) cc_final: 0.7186 (ptmm) REVERT: E 313 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: E 341 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7003 (pt) REVERT: E 347 GLU cc_start: 0.7849 (tp30) cc_final: 0.7484 (tp30) REVERT: E 419 GLN cc_start: 0.7866 (pp30) cc_final: 0.7450 (mm-40) REVERT: E 543 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: E 712 ASP cc_start: 0.7786 (t0) cc_final: 0.7463 (t0) REVERT: F 793 GLN cc_start: 0.7140 (pp30) cc_final: 0.6792 (tm-30) REVERT: F 920 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5253 (mtmt) REVERT: F 1030 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7041 (pt0) REVERT: G 67 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7958 (ptmt) REVERT: G 107 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7153 (pp30) REVERT: G 382 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6715 (pt0) REVERT: G 503 ASP cc_start: 0.4404 (t0) cc_final: 0.3861 (t0) REVERT: G 578 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7628 (ttp-110) REVERT: G 609 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8382 (mtt-85) REVERT: G 660 GLN cc_start: 0.7119 (tp40) cc_final: 0.6051 (mm110) REVERT: H 795 TYR cc_start: 0.7795 (t80) cc_final: 0.7572 (t80) REVERT: H 842 VAL cc_start: 0.8452 (m) cc_final: 0.8207 (p) REVERT: H 862 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8129 (t) REVERT: H 947 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6857 (ptm) REVERT: H 1049 ASN cc_start: 0.6391 (t0) cc_final: 0.6019 (t160) REVERT: H 1061 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7986 (mpt90) REVERT: H 1092 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6188 (mp0) outliers start: 89 outliers final: 54 residues processed: 239 average time/residue: 0.5628 time to fit residues: 152.8405 Evaluate side-chains 233 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1030 GLN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 480 LEU Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 188 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN F 952 HIS G 78 ASN ** H 794 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 = 0.3939 r_free = 0.3939 target = 0.167253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120460 restraints weight = 29971.685| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.31 r_work: 0.3169 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18777 Z= 0.172 Angle : 0.721 11.549 25571 Z= 0.360 Chirality : 0.051 0.650 2767 Planarity : 0.005 0.050 3360 Dihedral : 6.198 59.476 2773 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.32 % Favored : 92.64 % Rotamer: Outliers : 4.76 % Allowed : 18.73 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.16), residues: 2365 helix: -0.08 (0.27), residues: 349 sheet: -0.17 (0.30), residues: 330 loop : -1.59 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 373 TYR 0.027 0.002 TYR G 711 PHE 0.018 0.002 PHE H 999 TRP 0.019 0.002 TRP G 222 HIS 0.004 0.001 HIS F 817 Details of bonding type rmsd covalent geometry : bond 0.00412 (18651) covalent geometry : angle 0.69607 (25309) SS BOND : bond 0.00418 ( 116) SS BOND : angle 1.59688 ( 232) hydrogen bonds : bond 0.03964 ( 446) hydrogen bonds : angle 4.99569 ( 1163) link_NAG-ASN : bond 0.00778 ( 10) link_NAG-ASN : angle 3.89316 ( 30) *********************** 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 272 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 176 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8885 (mtp) cc_final: 0.8531 (mtm) REVERT: E 107 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7493 (mm110) REVERT: E 154 TYR cc_start: 0.8684 (m-80) cc_final: 0.8046 (m-80) REVERT: E 217 MET cc_start: 0.3480 (mtp) cc_final: 0.2107 (pmt) REVERT: E 228 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7224 (tt) REVERT: E 252 LYS cc_start: 0.7632 (ptmt) cc_final: 0.7203 (ptmm) REVERT: E 280 MET cc_start: 0.8038 (ttm) cc_final: 0.7633 (tmm) REVERT: E 313 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: E 341 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7068 (pp) REVERT: E 347 GLU cc_start: 0.7929 (tp30) cc_final: 0.7544 (tp30) REVERT: E 419 GLN cc_start: 0.7911 (pp30) cc_final: 0.7421 (mm-40) REVERT: E 543 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: E 644 GLU cc_start: 0.6112 (mm-30) cc_final: 0.5870 (mm-30) REVERT: E 712 ASP cc_start: 0.7796 (t0) cc_final: 0.7458 (t0) REVERT: F 793 GLN cc_start: 0.7202 (pp30) cc_final: 0.6820 (tm-30) REVERT: F 920 LYS cc_start: 0.5847 (OUTLIER) cc_final: 0.5199 (mtmt) REVERT: F 1030 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: F 1051 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7591 (tmm) REVERT: F 1187 LEU cc_start: 0.5713 (mt) cc_final: 0.5484 (mp) REVERT: G 107 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7003 (pp30) REVERT: G 382 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6673 (pt0) REVERT: G 503 ASP cc_start: 0.4508 (t0) cc_final: 0.4032 (t0) REVERT: G 578 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7563 (ttp-110) REVERT: G 609 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8369 (mtt-85) REVERT: G 660 GLN cc_start: 0.7088 (tp40) cc_final: 0.6085 (mm110) REVERT: H 771 MET cc_start: 0.4890 (OUTLIER) cc_final: 0.3375 (mtm) REVERT: H 795 TYR cc_start: 0.7797 (t80) cc_final: 0.7578 (t80) REVERT: H 842 VAL cc_start: 0.8461 (m) cc_final: 0.8235 (p) REVERT: H 844 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8904 (mp) REVERT: H 862 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8171 (t) REVERT: H 947 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6908 (ptm) REVERT: H 952 HIS cc_start: 0.6776 (m-70) cc_final: 0.6333 (m170) REVERT: H 1061 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7893 (mpt90) REVERT: H 1092 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6181 (mp0) outliers start: 96 outliers final: 60 residues processed: 240 average time/residue: 0.5540 time to fit residues: 151.2984 Evaluate side-chains 245 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1030 GLN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1051 MET Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 771 MET Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 844 ILE Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1124 THR Chi-restraints excluded: chain H residue 1156 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 225 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 952 HIS F1215 ASN G 78 ASN ** H 794 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 = 0.3942 r_free = 0.3942 target = 0.167464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121243 restraints weight = 28310.918| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.32 r_work: 0.3167 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18777 Z= 0.170 Angle : 0.714 11.435 25571 Z= 0.356 Chirality : 0.051 0.640 2767 Planarity : 0.005 0.052 3360 Dihedral : 6.131 59.891 2773 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer: Outliers : 4.71 % Allowed : 18.98 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.16), residues: 2365 helix: -0.23 (0.27), residues: 363 sheet: -0.12 (0.30), residues: 330 loop : -1.55 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 373 TYR 0.027 0.002 TYR G 711 PHE 0.018 0.002 PHE H 999 TRP 0.022 0.002 TRP G 222 HIS 0.004 0.001 HIS H 874 Details of bonding type rmsd covalent geometry : bond 0.00409 (18651) covalent geometry : angle 0.68905 (25309) SS BOND : bond 0.00400 ( 116) SS BOND : angle 1.56111 ( 232) hydrogen bonds : bond 0.03938 ( 446) hydrogen bonds : angle 4.97824 ( 1163) link_NAG-ASN : bond 0.00786 ( 10) link_NAG-ASN : angle 3.88096 ( 30) *********************** 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 264 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 169 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7484 (mm110) REVERT: E 154 TYR cc_start: 0.8681 (m-80) cc_final: 0.8050 (m-80) REVERT: E 157 LYS cc_start: 0.8738 (mttm) cc_final: 0.8346 (mtmt) REVERT: E 161 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8760 (mp) REVERT: E 217 MET cc_start: 0.3502 (mtp) cc_final: 0.1892 (ptm) REVERT: E 228 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7218 (tt) REVERT: E 252 LYS cc_start: 0.7731 (ptmt) cc_final: 0.7297 (ptmm) REVERT: E 280 MET cc_start: 0.7993 (ttm) cc_final: 0.7595 (tmm) REVERT: E 313 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7379 (mp10) REVERT: E 341 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7131 (pp) REVERT: E 347 GLU cc_start: 0.8052 (tp30) cc_final: 0.7609 (tp30) REVERT: E 543 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: E 712 ASP cc_start: 0.7750 (t0) cc_final: 0.7400 (t0) REVERT: F 793 GLN cc_start: 0.7240 (pp30) cc_final: 0.6858 (tm-30) REVERT: F 920 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5191 (mtmt) REVERT: F 1030 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: F 1051 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7510 (tmm) REVERT: F 1185 GLU cc_start: 0.6817 (mp0) cc_final: 0.6588 (mp0) REVERT: F 1187 LEU cc_start: 0.5770 (mt) cc_final: 0.5542 (mp) REVERT: G 65 CYS cc_start: 0.5323 (OUTLIER) cc_final: 0.5086 (t) REVERT: G 67 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7958 (ptmm) REVERT: G 107 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7026 (pp30) REVERT: G 116 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8431 (mmtm) REVERT: G 326 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7511 (p) REVERT: G 382 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6708 (pt0) REVERT: G 503 ASP cc_start: 0.4741 (t0) cc_final: 0.4208 (t0) REVERT: G 564 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8660 (tptp) REVERT: G 578 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7555 (ttp-110) REVERT: G 605 LEU cc_start: 0.8935 (tp) cc_final: 0.8712 (tp) REVERT: G 609 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8380 (mtt-85) REVERT: G 660 GLN cc_start: 0.7084 (tp40) cc_final: 0.6135 (mm110) REVERT: H 771 MET cc_start: 0.4892 (OUTLIER) cc_final: 0.3382 (mtm) REVERT: H 842 VAL cc_start: 0.8467 (m) cc_final: 0.8231 (p) REVERT: H 844 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8898 (mp) REVERT: H 862 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8160 (t) REVERT: H 947 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6856 (ptm) REVERT: H 952 HIS cc_start: 0.6809 (m-70) cc_final: 0.6375 (m170) REVERT: H 1061 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7928 (mpt90) REVERT: H 1092 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: H 1154 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5805 (tp-100) outliers start: 95 outliers final: 60 residues processed: 236 average time/residue: 0.5597 time to fit residues: 150.1601 Evaluate side-chains 249 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 166 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 854 ARG Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1030 GLN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1051 MET Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 65 CYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 480 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 564 LYS Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 771 MET Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 844 ILE Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1154 GLN Chi-restraints excluded: chain H residue 1156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 1 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 171 optimal weight: 0.0370 chunk 112 optimal weight: 0.0870 chunk 193 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN F 952 HIS G 78 ASN ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1049 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 = 0.3969 r_free = 0.3969 target = 0.169955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125672 restraints weight = 22837.495| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.06 r_work: 0.3227 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18777 Z= 0.121 Angle : 0.650 11.075 25571 Z= 0.322 Chirality : 0.048 0.576 2767 Planarity : 0.005 0.055 3360 Dihedral : 5.708 59.284 2773 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.97 % Allowed : 19.81 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2365 helix: -0.04 (0.27), residues: 363 sheet: 0.09 (0.30), residues: 332 loop : -1.47 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 373 TYR 0.027 0.001 TYR G 711 PHE 0.015 0.002 PHE H 999 TRP 0.019 0.001 TRP G 222 HIS 0.003 0.001 HIS F 817 Details of bonding type rmsd covalent geometry : bond 0.00280 (18651) covalent geometry : angle 0.62947 (25309) SS BOND : bond 0.00303 ( 116) SS BOND : angle 1.25720 ( 232) hydrogen bonds : bond 0.03433 ( 446) hydrogen bonds : angle 4.80813 ( 1163) link_NAG-ASN : bond 0.00811 ( 10) link_NAG-ASN : angle 3.76506 ( 30) ********************** 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 261 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 181 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8676 (mtp) cc_final: 0.8407 (mtm) REVERT: E 78 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.7083 (p0) REVERT: E 107 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7485 (mm110) REVERT: E 154 TYR cc_start: 0.8469 (m-80) cc_final: 0.8182 (m-80) REVERT: E 217 MET cc_start: 0.3190 (mtp) cc_final: 0.2032 (ptt) REVERT: E 228 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6731 (tt) REVERT: E 252 LYS cc_start: 0.7679 (ptmt) cc_final: 0.7254 (ptmm) REVERT: E 280 MET cc_start: 0.7919 (ttm) cc_final: 0.7560 (tmm) REVERT: E 302 ARG cc_start: 0.7483 (ttp-110) cc_final: 0.6560 (ttt-90) REVERT: E 341 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7079 (pp) REVERT: E 419 GLN cc_start: 0.7858 (pp30) cc_final: 0.7428 (mm-40) REVERT: E 712 ASP cc_start: 0.7525 (t0) cc_final: 0.7095 (t0) REVERT: F 793 GLN cc_start: 0.7025 (pp30) cc_final: 0.6666 (tm-30) REVERT: F 1051 MET cc_start: 0.7995 (mmm) cc_final: 0.7431 (tmm) REVERT: F 1185 GLU cc_start: 0.6671 (mp0) cc_final: 0.6446 (mp0) REVERT: F 1187 LEU cc_start: 0.5721 (mt) cc_final: 0.5488 (mp) REVERT: G 107 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7069 (pp30) REVERT: G 116 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8419 (mmtm) REVERT: G 503 ASP cc_start: 0.4361 (t0) cc_final: 0.3843 (t0) REVERT: G 564 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8607 (tptp) REVERT: G 609 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8373 (mtt-85) REVERT: G 660 GLN cc_start: 0.7074 (tp40) cc_final: 0.6099 (tp40) REVERT: H 771 MET cc_start: 0.4850 (OUTLIER) cc_final: 0.3334 (mtm) REVERT: H 862 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8212 (t) REVERT: H 947 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6685 (ptm) REVERT: H 952 HIS cc_start: 0.6707 (m-70) cc_final: 0.6350 (m170) REVERT: H 1061 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7991 (mpt90) REVERT: H 1070 ASP cc_start: 0.7835 (m-30) cc_final: 0.7579 (m-30) REVERT: H 1092 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5510 (pm20) REVERT: H 1154 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.5554 (tp-100) outliers start: 80 outliers final: 43 residues processed: 235 average time/residue: 0.5656 time to fit residues: 149.8815 Evaluate side-chains 227 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 480 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 564 LYS Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 771 MET Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1154 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 27 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 186 optimal weight: 0.6980 chunk 198 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 192 optimal weight: 0.0980 chunk 210 optimal weight: 6.9990 chunk 67 optimal weight: 0.0170 chunk 176 optimal weight: 6.9990 overall best weight: 1.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN F 952 HIS G 78 ASN ** H 794 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 = 0.3962 r_free = 0.3962 target = 0.169333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122565 restraints weight = 29951.404| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.18 r_work: 0.3212 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18777 Z= 0.132 Angle : 0.674 16.436 25571 Z= 0.331 Chirality : 0.048 0.581 2767 Planarity : 0.005 0.052 3360 Dihedral : 5.730 59.697 2773 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.33 % Allowed : 20.40 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.17), residues: 2365 helix: -0.02 (0.27), residues: 363 sheet: 0.15 (0.29), residues: 342 loop : -1.45 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 373 TYR 0.025 0.001 TYR G 711 PHE 0.015 0.002 PHE H 999 TRP 0.018 0.001 TRP G 222 HIS 0.004 0.001 HIS H 874 Details of bonding type rmsd covalent geometry : bond 0.00312 (18651) covalent geometry : angle 0.65203 (25309) SS BOND : bond 0.00318 ( 116) SS BOND : angle 1.35192 ( 232) hydrogen bonds : bond 0.03574 ( 446) hydrogen bonds : angle 4.81529 ( 1163) link_NAG-ASN : bond 0.00790 ( 10) link_NAG-ASN : angle 3.74211 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9401.32 seconds wall clock time: 159 minutes 52.08 seconds (9592.08 seconds total)