Starting phenix.real_space_refine on Mon Jun 16 01:48:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpp_32687/06_2025/7wpp_32687_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpp_32687/06_2025/7wpp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wpp_32687/06_2025/7wpp_32687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpp_32687/06_2025/7wpp_32687.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpp_32687/06_2025/7wpp_32687_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpp_32687/06_2025/7wpp_32687_neut.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.84, per 1000 atoms: 0.65 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: 4.36 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.79 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: 8.04 Time building geometry restraints manager: 5.28 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 1241 or resid 1301 \ through 1304)) selection = (chain 'H' and (resid 767 through 1052 or resid 1054 through 1241 or resid 1301 \ 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 45.970 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.660 ------------------------------------------------------------------------------- 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 : 3.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.003 TRP H 974 HIS 0.010 0.002 HIS E 596 PHE 0.026 0.003 PHE G 535 TYR 0.038 0.003 TYR G 527 ARG 0.011 0.001 ARG H 960 Details of bonding type rmsd link_NAG-ASN : bond 0.06122 ( 10) link_NAG-ASN : angle 5.78050 ( 30) hydrogen bonds : bond 0.28096 ( 446) hydrogen bonds : angle 9.45708 ( 1163) SS BOND : bond 0.00447 ( 116) SS BOND : angle 1.86109 ( 232) covalent geometry : bond 0.00871 (18651) covalent geometry : angle 1.17088 (25309) *********************** 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 : 2.295 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: 1.6649 time to fit residues: 1114.3356 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 : 2.766 ------------------------------------------------------------------------------- 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 199 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 112 optimal weight: 0.3980 chunk 137 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 F1113 GLN F1174 HIS F1221 HIS G 78 ASN G 95 HIS G 277 GLN G 303 GLN G 452 HIS G 596 HIS H1013 GLN H1053 GLN B H1069 GLN H1113 GLN H1221 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.174826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136470 restraints weight = 20746.183| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.81 r_work: 0.3274 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 18777 Z= 0.191 Angle : 0.824 17.740 25571 Z= 0.413 Chirality : 0.054 0.744 2767 Planarity : 0.005 0.050 3360 Dihedral : 6.709 57.525 2773 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.27 % Rotamer: Outliers : 4.36 % Allowed : 13.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.15), residues: 2365 helix: -1.42 (0.25), residues: 317 sheet: -1.78 (0.23), residues: 442 loop : -2.10 (0.14), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 199 HIS 0.005 0.001 HIS H1159 PHE 0.033 0.003 PHE H 999 TYR 0.025 0.002 TYR G 711 ARG 0.006 0.001 ARG G 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 10) link_NAG-ASN : angle 4.88353 ( 30) hydrogen bonds : bond 0.04313 ( 446) hydrogen bonds : angle 5.63130 ( 1163) SS BOND : bond 0.00517 ( 116) SS BOND : angle 1.94061 ( 232) covalent geometry : bond 0.00436 (18651) covalent geometry : angle 0.78978 (25309) *********************** 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 358 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 270 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 VAL cc_start: 0.8437 (t) cc_final: 0.8116 (m) REVERT: E 132 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7647 (mm-30) REVERT: E 154 TYR cc_start: 0.8263 (m-80) cc_final: 0.7724 (m-80) REVERT: E 217 MET cc_start: 0.3020 (mtp) cc_final: 0.2450 (ppp) REVERT: E 252 LYS cc_start: 0.7192 (ptmt) cc_final: 0.6761 (ptmt) REVERT: E 294 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7441 (p) REVERT: E 313 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: E 320 MET cc_start: 0.5276 (tpt) cc_final: 0.4994 (tpt) REVERT: E 419 GLN cc_start: 0.7682 (pp30) cc_final: 0.7203 (mm110) REVERT: E 602 LEU cc_start: 0.8301 (pp) cc_final: 0.8063 (mt) REVERT: E 649 GLU cc_start: 0.6257 (pt0) cc_final: 0.5212 (mm-30) REVERT: E 694 TYR cc_start: 0.5055 (m-10) cc_final: 0.4831 (m-10) REVERT: E 696 ASP cc_start: 0.7239 (t0) cc_final: 0.6995 (t70) REVERT: E 712 ASP cc_start: 0.7338 (t0) cc_final: 0.6923 (OUTLIER) REVERT: F 864 ASP cc_start: 0.8667 (m-30) cc_final: 0.8365 (m-30) REVERT: F 869 THR cc_start: 0.8967 (m) cc_final: 0.8579 (p) REVERT: F 954 GLU cc_start: 0.8346 (tp30) cc_final: 0.8125 (tp30) REVERT: F 1051 MET cc_start: 0.7762 (tpt) cc_final: 0.7357 (tmm) REVERT: F 1057 ASP cc_start: 0.8184 (t0) cc_final: 0.7946 (m-30) REVERT: F 1161 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7207 (pm20) REVERT: G 265 CYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7225 (m) REVERT: G 326 VAL cc_start: 0.8026 (t) cc_final: 0.7761 (p) REVERT: G 343 VAL cc_start: 0.7636 (p) cc_final: 0.7413 (m) REVERT: G 512 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9015 (mp) REVERT: G 578 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7669 (ttp-110) REVERT: G 590 PRO cc_start: 0.7742 (Cg_endo) cc_final: 0.7421 (Cg_exo) REVERT: G 593 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7211 (pm20) REVERT: G 602 LEU cc_start: 0.8072 (pp) cc_final: 0.7764 (mt) REVERT: G 695 MET cc_start: 0.7257 (mmp) cc_final: 0.6947 (mmp) REVERT: G 711 TYR cc_start: 0.8127 (t80) cc_final: 0.7894 (t80) REVERT: G 728 MET cc_start: 0.6908 (tmm) cc_final: 0.6598 (tmm) REVERT: H 795 TYR cc_start: 0.7688 (t80) cc_final: 0.7024 (t80) REVERT: H 842 VAL cc_start: 0.8353 (m) cc_final: 0.8037 (p) REVERT: H 862 VAL cc_start: 0.7982 (OUTLIER) cc_final: 0.7761 (t) REVERT: H 935 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7831 (pp20) REVERT: H 947 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7035 (ptm) REVERT: H 1049 ASN cc_start: 0.6212 (t0) cc_final: 0.5949 (t0) REVERT: H 1061 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7881 (mpt90) outliers start: 88 outliers final: 33 residues processed: 332 average time/residue: 1.0824 time to fit residues: 411.2055 Evaluate side-chains 235 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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 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 375 SER Chi-restraints excluded: chain E residue 394 SER 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 F residue 771 MET 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 181 THR Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 250 CYS Chi-restraints excluded: chain G residue 265 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 483 GLN Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 512 LEU 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 814 MET Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 914 CYS Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 947 MET 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 197 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 207 optimal weight: 0.1980 chunk 224 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 GLN G 78 ASN G 189 ASN G 368 ASN G 453 ASN H1003 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124869 restraints weight = 30135.677| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.56 r_work: 0.3275 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18777 Z= 0.144 Angle : 0.709 14.881 25571 Z= 0.353 Chirality : 0.050 0.626 2767 Planarity : 0.005 0.046 3360 Dihedral : 6.150 55.708 2773 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.85 % Favored : 93.10 % Rotamer: Outliers : 4.32 % Allowed : 15.40 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.16), residues: 2365 helix: -0.47 (0.26), residues: 331 sheet: -1.20 (0.24), residues: 442 loop : -1.84 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 974 HIS 0.003 0.001 HIS E 421 PHE 0.024 0.002 PHE H 999 TYR 0.020 0.002 TYR H 897 ARG 0.007 0.000 ARG G 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00759 ( 10) link_NAG-ASN : angle 4.45998 ( 30) hydrogen bonds : bond 0.04077 ( 446) hydrogen bonds : angle 5.19153 ( 1163) SS BOND : bond 0.00384 ( 116) SS BOND : angle 1.47505 ( 232) covalent geometry : bond 0.00340 (18651) covalent geometry : angle 0.68166 (25309) *********************** 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 299 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 212 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 GLN cc_start: 0.7848 (mm-40) cc_final: 0.6357 (pm20) REVERT: E 98 VAL cc_start: 0.8372 (t) cc_final: 0.8132 (m) REVERT: E 217 MET cc_start: 0.3191 (mtp) cc_final: 0.2113 (ptt) REVERT: E 228 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6721 (tt) REVERT: E 252 LYS cc_start: 0.7426 (ptmt) cc_final: 0.6945 (ptmm) REVERT: E 302 ARG cc_start: 0.7271 (ttm170) cc_final: 0.6469 (ttt-90) REVERT: E 313 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6999 (mp10) REVERT: E 419 GLN cc_start: 0.7715 (pp30) cc_final: 0.7221 (mm-40) REVERT: E 597 ARG cc_start: 0.7856 (ptp-110) cc_final: 0.7338 (ptm-80) REVERT: E 649 GLU cc_start: 0.6410 (pt0) cc_final: 0.5221 (mm-30) REVERT: E 728 MET cc_start: 0.7679 (tpp) cc_final: 0.7437 (tpt) REVERT: F 864 ASP cc_start: 0.8625 (m-30) cc_final: 0.8269 (m-30) REVERT: F 869 THR cc_start: 0.8859 (m) cc_final: 0.8447 (p) REVERT: F 912 LYS cc_start: 0.8066 (mppt) cc_final: 0.7675 (mptt) REVERT: F 920 LYS cc_start: 0.5810 (OUTLIER) cc_final: 0.5120 (mtmt) REVERT: F 954 GLU cc_start: 0.8415 (tp30) cc_final: 0.8094 (tp30) REVERT: F 968 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7583 (mtmm) REVERT: F 1035 ARG cc_start: 0.7832 (mmp-170) cc_final: 0.7581 (mmp-170) REVERT: F 1057 ASP cc_start: 0.8187 (t0) cc_final: 0.7922 (m-30) REVERT: F 1148 SER cc_start: 0.8406 (m) cc_final: 0.8097 (m) REVERT: G 217 MET cc_start: 0.3134 (mtm) cc_final: 0.2003 (pp-130) REVERT: G 265 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7248 (m) REVERT: G 336 LEU cc_start: 0.7712 (mt) cc_final: 0.7474 (mt) REVERT: G 503 ASP cc_start: 0.3975 (t0) cc_final: 0.3714 (t0) REVERT: G 564 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8524 (tptt) REVERT: G 578 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7475 (ttp-110) REVERT: G 590 PRO cc_start: 0.7729 (Cg_endo) cc_final: 0.7392 (Cg_exo) REVERT: G 593 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7246 (pm20) REVERT: H 795 TYR cc_start: 0.7646 (t80) cc_final: 0.7001 (t80) REVERT: H 802 MET cc_start: 0.5509 (mpt) cc_final: 0.5172 (mpt) REVERT: H 842 VAL cc_start: 0.8270 (m) cc_final: 0.7997 (p) REVERT: H 862 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7784 (t) REVERT: H 947 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6629 (ptm) REVERT: H 1049 ASN cc_start: 0.6162 (t0) cc_final: 0.5821 (t0) REVERT: H 1061 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7832 (mpt90) REVERT: H 1081 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8270 (tp) REVERT: H 1161 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6930 (mp0) outliers start: 87 outliers final: 38 residues processed: 275 average time/residue: 1.1629 time to fit residues: 364.4665 Evaluate side-chains 224 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 2.043 ------------------------------------------------------------------------------- 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 337 LEU 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 821 CYS Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 1050 ILE 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 159 CYS 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 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 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 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 1093 SER Chi-restraints excluded: chain H residue 1161 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 195 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 232 optimal weight: 0.0470 chunk 140 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN E 393 GLN F1188 GLN G 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.170061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124124 restraints weight = 22648.308| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.20 r_work: 0.3214 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4935 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= 0.165 Angle : 0.716 13.205 25571 Z= 0.358 Chirality : 0.051 0.577 2767 Planarity : 0.005 0.071 3360 Dihedral : 6.225 57.861 2773 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.15 % Favored : 92.81 % Rotamer: Outliers : 4.22 % Allowed : 16.72 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2365 helix: -0.09 (0.28), residues: 331 sheet: -0.90 (0.25), residues: 450 loop : -1.77 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 974 HIS 0.004 0.001 HIS F 874 PHE 0.024 0.002 PHE H 999 TYR 0.023 0.002 TYR H 897 ARG 0.011 0.001 ARG G 643 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 10) link_NAG-ASN : angle 4.14304 ( 30) hydrogen bonds : bond 0.03989 ( 446) hydrogen bonds : angle 5.12243 ( 1163) SS BOND : bond 0.00404 ( 116) SS BOND : angle 1.55146 ( 232) covalent geometry : bond 0.00395 (18651) covalent geometry : angle 0.68991 (25309) *********************** 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 280 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 195 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 VAL cc_start: 0.8635 (t) cc_final: 0.8418 (m) REVERT: E 107 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7533 (mm110) REVERT: E 217 MET cc_start: 0.3198 (mtp) cc_final: 0.2066 (ptt) REVERT: E 228 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6976 (tt) REVERT: E 280 MET cc_start: 0.8164 (ttm) cc_final: 0.7769 (tmm) REVERT: E 313 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: E 346 THR cc_start: 0.7551 (m) cc_final: 0.7129 (p) REVERT: E 419 GLN cc_start: 0.7777 (pp30) cc_final: 0.7292 (mm-40) REVERT: E 543 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: E 694 TYR cc_start: 0.5114 (m-10) cc_final: 0.4749 (m-80) REVERT: E 712 ASP cc_start: 0.7557 (t0) cc_final: 0.7142 (t0) REVERT: E 728 MET cc_start: 0.7829 (tpp) cc_final: 0.7604 (tpt) REVERT: F 793 GLN cc_start: 0.7072 (pp30) cc_final: 0.6628 (tm-30) REVERT: F 869 THR cc_start: 0.8873 (m) cc_final: 0.8519 (p) REVERT: F 911 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8041 (p0) REVERT: F 912 LYS cc_start: 0.8064 (mppt) cc_final: 0.7723 (mptt) REVERT: F 954 GLU cc_start: 0.8444 (tp30) cc_final: 0.8144 (tp30) REVERT: F 1035 ARG cc_start: 0.7946 (mmp-170) cc_final: 0.7703 (mmp-170) REVERT: F 1036 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7700 (mptm) REVERT: F 1057 ASP cc_start: 0.8335 (t0) cc_final: 0.8115 (m-30) REVERT: G 107 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7253 (pp30) REVERT: G 197 GLU cc_start: 0.7746 (mp0) cc_final: 0.7533 (mp0) REVERT: G 280 MET cc_start: 0.8138 (ttm) cc_final: 0.7857 (ttm) REVERT: G 337 LEU cc_start: 0.8583 (tp) cc_final: 0.8364 (tp) REVERT: G 503 ASP cc_start: 0.4444 (t0) cc_final: 0.4045 (t0) REVERT: G 564 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8546 (tptp) REVERT: G 578 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7645 (ttp-110) REVERT: G 590 PRO cc_start: 0.7721 (Cg_endo) cc_final: 0.7353 (Cg_exo) REVERT: G 609 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8359 (mtt-85) REVERT: G 736 MET cc_start: 0.7217 (tpt) cc_final: 0.7015 (tpt) REVERT: H 842 VAL cc_start: 0.8426 (m) cc_final: 0.8184 (p) REVERT: H 862 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8050 (t) REVERT: H 947 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6914 (ptm) REVERT: H 1049 ASN cc_start: 0.6336 (t0) cc_final: 0.5996 (t0) REVERT: H 1061 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7955 (mpt90) REVERT: H 1081 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8518 (tp) REVERT: H 1092 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: H 1161 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7218 (mp0) outliers start: 85 outliers final: 46 residues processed: 254 average time/residue: 1.1834 time to fit residues: 342.2943 Evaluate side-chains 238 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 327 ASP Chi-restraints excluded: chain E residue 337 LEU 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 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 870 ILE Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 935 GLU 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 1156 THR 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 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 659 LEU 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 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 1161 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 192 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 F 952 HIS F1188 GLN G 78 ASN G 313 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.168347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122318 restraints weight = 24461.233| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.23 r_work: 0.3189 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18777 Z= 0.176 Angle : 0.715 12.850 25571 Z= 0.358 Chirality : 0.051 0.599 2767 Planarity : 0.005 0.050 3360 Dihedral : 6.288 58.136 2773 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.77 % Rotamer: Outliers : 4.41 % Allowed : 17.41 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 2365 helix: -0.14 (0.27), residues: 347 sheet: -0.58 (0.25), residues: 440 loop : -1.70 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 222 HIS 0.004 0.001 HIS E 596 PHE 0.020 0.002 PHE H 999 TYR 0.021 0.002 TYR H 897 ARG 0.008 0.001 ARG G 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00782 ( 10) link_NAG-ASN : angle 4.08865 ( 30) hydrogen bonds : bond 0.04054 ( 446) hydrogen bonds : angle 5.05810 ( 1163) SS BOND : bond 0.00397 ( 116) SS BOND : angle 1.53819 ( 232) covalent geometry : bond 0.00423 (18651) covalent geometry : angle 0.68898 (25309) *********************** 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 277 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 188 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 VAL cc_start: 0.8694 (t) cc_final: 0.8462 (m) REVERT: E 107 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7491 (mm110) REVERT: E 217 MET cc_start: 0.3200 (mtp) cc_final: 0.2056 (ptt) REVERT: E 228 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7042 (tt) REVERT: E 252 LYS cc_start: 0.7533 (ptmt) cc_final: 0.7046 (ptmm) REVERT: E 302 ARG cc_start: 0.7970 (ttm170) cc_final: 0.6686 (ttt-90) REVERT: E 313 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: E 341 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7149 (pt) REVERT: E 346 THR cc_start: 0.7595 (m) cc_final: 0.7313 (p) REVERT: E 347 GLU cc_start: 0.7845 (tp30) cc_final: 0.7599 (tp30) REVERT: E 419 GLN cc_start: 0.7866 (pp30) cc_final: 0.7340 (mm110) REVERT: E 483 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8646 (pt0) REVERT: E 543 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: E 620 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6887 (tp30) REVERT: E 712 ASP cc_start: 0.7782 (t0) cc_final: 0.7467 (t0) REVERT: E 728 MET cc_start: 0.7830 (tpp) cc_final: 0.7606 (tpt) REVERT: F 793 GLN cc_start: 0.7003 (pp30) cc_final: 0.6546 (tm-30) REVERT: F 869 THR cc_start: 0.9025 (m) cc_final: 0.8707 (p) REVERT: F 911 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.7979 (p0) REVERT: F 912 LYS cc_start: 0.8073 (mppt) cc_final: 0.7759 (mptt) REVERT: F 920 LYS cc_start: 0.5810 (OUTLIER) cc_final: 0.5202 (mtmt) REVERT: F 954 GLU cc_start: 0.8499 (tp30) cc_final: 0.8155 (tp30) REVERT: F 1030 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7198 (pt0) REVERT: F 1035 ARG cc_start: 0.7973 (mmp-170) cc_final: 0.7717 (mmp-170) REVERT: F 1036 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7687 (tppt) REVERT: F 1057 ASP cc_start: 0.8282 (t0) cc_final: 0.8042 (m-30) REVERT: F 1078 GLU cc_start: 0.8028 (tp30) cc_final: 0.7767 (tp30) REVERT: G 67 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8011 (ptmt) REVERT: G 107 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7250 (pp30) REVERT: G 280 MET cc_start: 0.8169 (ttm) cc_final: 0.7897 (ttm) REVERT: G 337 LEU cc_start: 0.8596 (tp) cc_final: 0.8389 (tp) REVERT: G 387 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8217 (mt-10) REVERT: G 416 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8323 (ttm170) REVERT: G 578 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7633 (ttp-170) REVERT: G 700 ASP cc_start: 0.6402 (t0) cc_final: 0.6137 (p0) REVERT: G 736 MET cc_start: 0.7310 (tpt) cc_final: 0.7068 (tpt) REVERT: H 842 VAL cc_start: 0.8474 (m) cc_final: 0.8179 (p) REVERT: H 862 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8148 (t) REVERT: H 947 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6909 (ptm) REVERT: H 1049 ASN cc_start: 0.6385 (t0) cc_final: 0.6026 (t160) REVERT: H 1061 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7884 (mpt90) REVERT: H 1081 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8516 (tp) REVERT: H 1092 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: H 1161 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7213 (mp0) outliers start: 89 outliers final: 48 residues processed: 255 average time/residue: 1.2382 time to fit residues: 359.2766 Evaluate side-chains 240 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 327 ASP 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 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 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 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 1036 LYS 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 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 326 VAL Chi-restraints excluded: chain G residue 329 CYS 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 479 ASP Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 520 THR 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 659 LEU 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 1124 THR Chi-restraints excluded: chain H residue 1161 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 169 optimal weight: 8.9990 chunk 68 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 226 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 952 HIS G 78 ASN G 313 GLN 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 = 0.167384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122019 restraints weight = 24717.490| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.16 r_work: 0.3183 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18777 Z= 0.185 Angle : 0.722 12.307 25571 Z= 0.362 Chirality : 0.051 0.651 2767 Planarity : 0.005 0.048 3360 Dihedral : 6.343 58.855 2773 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.40 % Favored : 92.55 % Rotamer: Outliers : 5.10 % Allowed : 17.02 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2365 helix: -0.11 (0.27), residues: 347 sheet: -0.46 (0.26), residues: 438 loop : -1.66 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 222 HIS 0.004 0.001 HIS F 874 PHE 0.020 0.002 PHE H 999 TYR 0.019 0.002 TYR H 897 ARG 0.006 0.001 ARG G 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00814 ( 10) link_NAG-ASN : angle 3.93282 ( 30) hydrogen bonds : bond 0.04089 ( 446) hydrogen bonds : angle 5.00728 ( 1163) SS BOND : bond 0.00424 ( 116) SS BOND : angle 1.54294 ( 232) covalent geometry : bond 0.00447 (18651) covalent geometry : angle 0.69724 (25309) *********************** 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 284 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 181 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7541 (mm110) REVERT: E 217 MET cc_start: 0.3428 (mtp) cc_final: 0.2081 (pmt) REVERT: E 228 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7176 (tt) REVERT: E 252 LYS cc_start: 0.7625 (ptmt) cc_final: 0.7159 (ptmm) REVERT: E 280 MET cc_start: 0.8051 (ttm) cc_final: 0.7782 (tmm) REVERT: E 302 ARG cc_start: 0.7991 (ttm170) cc_final: 0.6761 (ttt-90) REVERT: E 313 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: E 341 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6978 (pt) REVERT: E 347 GLU cc_start: 0.7808 (tp30) cc_final: 0.7546 (tp30) REVERT: E 419 GLN cc_start: 0.7852 (pp30) cc_final: 0.7417 (mm-40) REVERT: E 483 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8618 (pt0) REVERT: E 543 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: E 620 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6985 (tp30) REVERT: E 712 ASP cc_start: 0.7721 (t0) cc_final: 0.7408 (t0) REVERT: E 728 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7700 (tpt) REVERT: F 793 GLN cc_start: 0.7169 (pp30) cc_final: 0.6824 (tm-30) REVERT: F 869 THR cc_start: 0.9099 (m) cc_final: 0.8803 (p) REVERT: F 911 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8039 (p0) REVERT: F 920 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5388 (mtpt) REVERT: F 952 HIS cc_start: 0.6544 (m170) cc_final: 0.6304 (m-70) REVERT: F 954 GLU cc_start: 0.8558 (tp30) cc_final: 0.8209 (tp30) REVERT: F 1030 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: F 1035 ARG cc_start: 0.7945 (mmp-170) cc_final: 0.7697 (mmp-170) REVERT: F 1036 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7691 (tppt) REVERT: F 1057 ASP cc_start: 0.8318 (t0) cc_final: 0.8096 (m-30) REVERT: G 75 ASP cc_start: 0.8593 (m-30) cc_final: 0.8385 (m-30) REVERT: G 107 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7175 (pp30) REVERT: G 326 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7520 (p) REVERT: G 382 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6591 (pt0) REVERT: G 387 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8178 (mt-10) REVERT: G 416 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8313 (ttm170) REVERT: G 578 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7647 (ttp-110) REVERT: G 609 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8380 (mtt-85) REVERT: G 683 CYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5899 (p) REVERT: G 736 MET cc_start: 0.7386 (tpt) cc_final: 0.7141 (tpt) REVERT: H 842 VAL cc_start: 0.8493 (m) cc_final: 0.8218 (p) REVERT: H 862 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (t) REVERT: H 947 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7074 (ptm) REVERT: H 1049 ASN cc_start: 0.6409 (t0) cc_final: 0.6056 (t160) REVERT: H 1061 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7910 (mpt90) REVERT: H 1092 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: H 1161 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7130 (mp0) outliers start: 103 outliers final: 56 residues processed: 253 average time/residue: 1.1498 time to fit residues: 330.9896 Evaluate side-chains 249 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 172 time to evaluate : 2.106 ------------------------------------------------------------------------------- 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 466 MET 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 728 MET 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 1036 LYS 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 99 ASN 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 326 VAL Chi-restraints excluded: chain G residue 329 CYS 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 520 THR 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 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 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 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1124 THR Chi-restraints excluded: chain H residue 1161 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 27 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN G 78 ASN G 313 GLN 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 = 0.167187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121907 restraints weight = 24514.974| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.11 r_work: 0.3189 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18777 Z= 0.184 Angle : 0.726 12.067 25571 Z= 0.364 Chirality : 0.051 0.607 2767 Planarity : 0.005 0.051 3360 Dihedral : 6.299 58.642 2773 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.28 % Favored : 92.68 % Rotamer: Outliers : 5.35 % Allowed : 17.26 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2365 helix: -0.16 (0.27), residues: 349 sheet: -0.14 (0.28), residues: 362 loop : -1.64 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 222 HIS 0.004 0.001 HIS H 874 PHE 0.018 0.002 PHE H 999 TYR 0.017 0.002 TYR H 897 ARG 0.004 0.001 ARG G 643 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 10) link_NAG-ASN : angle 3.92078 ( 30) hydrogen bonds : bond 0.04059 ( 446) hydrogen bonds : angle 5.00894 ( 1163) SS BOND : bond 0.00411 ( 116) SS BOND : angle 1.59877 ( 232) covalent geometry : bond 0.00445 (18651) covalent geometry : angle 0.70075 (25309) *********************** 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 299 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 191 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.9001 (mtp) cc_final: 0.8623 (mtm) REVERT: E 107 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7490 (mm110) REVERT: E 217 MET cc_start: 0.3453 (mtp) cc_final: 0.2098 (pmt) REVERT: E 228 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7174 (tt) REVERT: E 252 LYS cc_start: 0.7621 (ptmt) cc_final: 0.7192 (ptmm) REVERT: E 280 MET cc_start: 0.8059 (ttm) cc_final: 0.7798 (tmm) REVERT: E 294 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7482 (p) REVERT: E 302 ARG cc_start: 0.7995 (ttm170) cc_final: 0.6777 (ttt-90) REVERT: E 313 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: E 341 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6986 (pt) REVERT: E 347 GLU cc_start: 0.7912 (tp30) cc_final: 0.7538 (tp30) REVERT: E 419 GLN cc_start: 0.7901 (pp30) cc_final: 0.7454 (mm-40) REVERT: E 543 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7214 (mt-10) REVERT: E 644 GLU cc_start: 0.6090 (mm-30) cc_final: 0.5876 (mm-30) REVERT: E 712 ASP cc_start: 0.7767 (t0) cc_final: 0.7430 (t0) REVERT: E 728 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7703 (tpt) REVERT: F 793 GLN cc_start: 0.7283 (pp30) cc_final: 0.6906 (tm-30) REVERT: F 869 THR cc_start: 0.9085 (m) cc_final: 0.8797 (p) REVERT: F 872 MET cc_start: 0.8479 (mtt) cc_final: 0.8241 (mtp) REVERT: F 912 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7925 (mptt) REVERT: F 920 LYS cc_start: 0.5821 (OUTLIER) cc_final: 0.5187 (mtmt) REVERT: F 954 GLU cc_start: 0.8540 (tp30) cc_final: 0.8242 (tp30) REVERT: F 1035 ARG cc_start: 0.8060 (mmp-170) cc_final: 0.7772 (mmp-170) REVERT: F 1057 ASP cc_start: 0.8306 (t0) cc_final: 0.8085 (m-30) REVERT: G 67 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7942 (ptmt) REVERT: G 107 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.6999 (pp30) REVERT: G 197 GLU cc_start: 0.7182 (mp0) cc_final: 0.6930 (mp0) REVERT: G 280 MET cc_start: 0.8154 (ttm) cc_final: 0.7902 (ttm) REVERT: G 326 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7583 (p) REVERT: G 382 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6664 (pt0) REVERT: G 416 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8296 (ttm170) REVERT: G 442 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8668 (ttt180) REVERT: G 578 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7600 (ttp-110) REVERT: G 609 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8355 (mtt-85) REVERT: G 683 CYS cc_start: 0.6322 (OUTLIER) cc_final: 0.5891 (p) REVERT: G 736 MET cc_start: 0.7362 (tpt) cc_final: 0.7098 (tpt) REVERT: H 842 VAL cc_start: 0.8448 (m) cc_final: 0.8181 (p) REVERT: H 862 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8133 (t) REVERT: H 947 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6836 (ptm) REVERT: H 1049 ASN cc_start: 0.6449 (t0) cc_final: 0.6057 (t160) REVERT: H 1061 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7849 (mpt90) REVERT: H 1092 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: H 1154 GLN cc_start: 0.6238 (OUTLIER) cc_final: 0.5837 (tp-100) REVERT: H 1161 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7126 (mp0) outliers start: 108 outliers final: 57 residues processed: 266 average time/residue: 1.1916 time to fit residues: 358.9512 Evaluate side-chains 253 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 174 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 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 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 466 MET 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 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 728 MET 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 912 LYS Chi-restraints excluded: chain F residue 920 LYS 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 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 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 326 VAL Chi-restraints excluded: chain G residue 329 CYS 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 442 ARG 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 520 THR 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 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 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 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1124 THR Chi-restraints excluded: chain H residue 1154 GLN Chi-restraints excluded: chain H residue 1161 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 19 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 115 optimal weight: 30.0000 chunk 223 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN F 952 HIS F1215 ASN G 78 ASN G 313 GLN G 680 ASN H1003 GLN H1188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.163637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117222 restraints weight = 28303.434| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.27 r_work: 0.3153 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 18777 Z= 0.303 Angle : 0.888 13.090 25571 Z= 0.447 Chirality : 0.058 0.707 2767 Planarity : 0.006 0.057 3360 Dihedral : 7.028 59.433 2773 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.38 % Favored : 91.54 % Rotamer: Outliers : 5.44 % Allowed : 17.56 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2365 helix: -0.46 (0.27), residues: 349 sheet: -0.35 (0.28), residues: 350 loop : -1.70 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 222 HIS 0.007 0.002 HIS H 874 PHE 0.024 0.003 PHE G 688 TYR 0.024 0.002 TYR H 897 ARG 0.008 0.001 ARG E 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 10) link_NAG-ASN : angle 4.15864 ( 30) hydrogen bonds : bond 0.05043 ( 446) hydrogen bonds : angle 5.28676 ( 1163) SS BOND : bond 0.00631 ( 116) SS BOND : angle 2.31316 ( 232) covalent geometry : bond 0.00735 (18651) covalent geometry : angle 0.85234 (25309) *********************** 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 301 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 191 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7678 (mm-40) REVERT: E 107 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7473 (mm110) REVERT: E 157 LYS cc_start: 0.8698 (mttm) cc_final: 0.8223 (mtmt) REVERT: E 161 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8731 (mp) REVERT: E 217 MET cc_start: 0.3580 (mtp) cc_final: 0.2164 (pmt) REVERT: E 228 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7363 (tt) REVERT: E 252 LYS cc_start: 0.7686 (ptmt) cc_final: 0.7320 (ptmm) REVERT: E 294 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7421 (p) REVERT: E 313 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7339 (mp10) REVERT: E 347 GLU cc_start: 0.7891 (tp30) cc_final: 0.7532 (tp30) REVERT: E 483 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8527 (pt0) REVERT: E 543 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: E 644 GLU cc_start: 0.6135 (mm-30) cc_final: 0.5818 (mm-30) REVERT: E 728 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7521 (tpp) REVERT: F 793 GLN cc_start: 0.7459 (pp30) cc_final: 0.7031 (tm-30) REVERT: F 869 THR cc_start: 0.9141 (m) cc_final: 0.8887 (p) REVERT: F 920 LYS cc_start: 0.5823 (OUTLIER) cc_final: 0.5370 (mtpt) REVERT: F 937 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.6861 (p90) REVERT: F 952 HIS cc_start: 0.6468 (OUTLIER) cc_final: 0.6261 (m-70) REVERT: F 1051 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7515 (tmm) REVERT: F 1057 ASP cc_start: 0.8333 (t0) cc_final: 0.8115 (m-30) REVERT: G 67 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7968 (ptmt) REVERT: G 107 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.6980 (pp30) REVERT: G 170 GLU cc_start: 0.7454 (pm20) cc_final: 0.7091 (pm20) REVERT: G 416 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8405 (ttm170) REVERT: G 442 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8745 (ttt180) REVERT: G 564 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8631 (tptp) REVERT: G 578 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7548 (ttp-110) REVERT: G 605 LEU cc_start: 0.8966 (tp) cc_final: 0.8715 (tp) REVERT: G 609 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8310 (mtt90) REVERT: G 660 GLN cc_start: 0.7058 (tp40) cc_final: 0.6083 (mm110) REVERT: G 683 CYS cc_start: 0.6383 (OUTLIER) cc_final: 0.6080 (p) REVERT: G 695 MET cc_start: 0.7288 (mmp) cc_final: 0.6783 (mmt) REVERT: H 771 MET cc_start: 0.5097 (OUTLIER) cc_final: 0.3493 (ttm) REVERT: H 844 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8868 (mp) REVERT: H 947 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6936 (ptm) REVERT: H 1049 ASN cc_start: 0.6402 (t0) cc_final: 0.5996 (t160) REVERT: H 1061 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7805 (mpt90) REVERT: H 1092 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: H 1161 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7043 (mp0) outliers start: 110 outliers final: 60 residues processed: 269 average time/residue: 1.2291 time to fit residues: 375.3646 Evaluate side-chains 258 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 173 time to evaluate : 2.193 ------------------------------------------------------------------------------- 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 101 THR 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 294 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 329 CYS 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 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 663 THR Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 728 MET 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 870 ILE Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain F residue 952 HIS Chi-restraints excluded: chain F residue 982 VAL 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 67 LYS Chi-restraints excluded: chain G residue 99 ASN 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 329 CYS 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 442 ARG 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 520 THR 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 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 898 CYS 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 935 GLU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG 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 1161 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 192 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 183 optimal weight: 40.0000 chunk 13 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 233 optimal weight: 0.0040 chunk 165 optimal weight: 0.7980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN E 226 GLN E 660 GLN G 78 ASN G 313 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.169951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123267 restraints weight = 25682.528| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.10 r_work: 0.3229 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18777 Z= 0.116 Angle : 0.655 11.383 25571 Z= 0.329 Chirality : 0.047 0.541 2767 Planarity : 0.005 0.049 3360 Dihedral : 5.921 55.380 2773 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.48 % Allowed : 19.67 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2365 helix: -0.16 (0.27), residues: 363 sheet: -0.23 (0.27), residues: 384 loop : -1.51 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 222 HIS 0.020 0.001 HIS F 952 PHE 0.021 0.001 PHE E 735 TYR 0.016 0.001 TYR E 113 ARG 0.005 0.000 ARG E 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 10) link_NAG-ASN : angle 3.83406 ( 30) hydrogen bonds : bond 0.03342 ( 446) hydrogen bonds : angle 4.86152 ( 1163) SS BOND : bond 0.00305 ( 116) SS BOND : angle 1.26286 ( 232) covalent geometry : bond 0.00262 (18651) covalent geometry : angle 0.63340 (25309) *********************** 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 259 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 189 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8758 (mtp) cc_final: 0.8499 (mtm) REVERT: E 107 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7420 (mm110) REVERT: E 217 MET cc_start: 0.3504 (mtp) cc_final: 0.1887 (ptm) REVERT: E 228 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7013 (tt) REVERT: E 280 MET cc_start: 0.7980 (ttm) cc_final: 0.7689 (tmm) REVERT: E 302 ARG cc_start: 0.7860 (ttm170) cc_final: 0.6736 (ttt-90) REVERT: E 341 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7125 (pp) REVERT: E 347 GLU cc_start: 0.7905 (tp30) cc_final: 0.7546 (tp30) REVERT: E 543 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: E 644 GLU cc_start: 0.6156 (mm-30) cc_final: 0.5797 (mm-30) REVERT: E 684 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7698 (tt) REVERT: E 712 ASP cc_start: 0.7702 (t0) cc_final: 0.7439 (t0) REVERT: F 793 GLN cc_start: 0.7180 (pp30) cc_final: 0.6813 (tm-30) REVERT: F 869 THR cc_start: 0.9011 (m) cc_final: 0.8721 (p) REVERT: F 872 MET cc_start: 0.8398 (mtt) cc_final: 0.8145 (mtp) REVERT: F 920 LYS cc_start: 0.5745 (OUTLIER) cc_final: 0.5163 (mtmt) REVERT: F 1051 MET cc_start: 0.7996 (mmm) cc_final: 0.7477 (tmm) REVERT: F 1057 ASP cc_start: 0.8203 (t0) cc_final: 0.7962 (m-30) REVERT: F 1185 GLU cc_start: 0.6771 (mp0) cc_final: 0.6556 (mp0) REVERT: G 107 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7057 (pp30) REVERT: G 280 MET cc_start: 0.8069 (ttm) cc_final: 0.7829 (ttm) REVERT: G 382 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6744 (pt0) REVERT: G 609 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8378 (mtt-85) REVERT: G 649 GLU cc_start: 0.7283 (pt0) cc_final: 0.7083 (pt0) REVERT: H 771 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.3429 (mtm) REVERT: H 862 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8108 (t) REVERT: H 947 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6921 (ptm) REVERT: H 1049 ASN cc_start: 0.6373 (t0) cc_final: 0.5983 (t160) REVERT: H 1061 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7921 (mpt90) REVERT: H 1081 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8526 (tp) REVERT: H 1161 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6895 (mp0) outliers start: 70 outliers final: 31 residues processed: 236 average time/residue: 1.1190 time to fit residues: 301.7612 Evaluate side-chains 215 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 314 SER Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 466 MET 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 F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 920 LYS 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 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 329 CYS 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 520 THR Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 622 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 862 VAL 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 Chi-restraints excluded: chain H residue 1161 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 228 optimal weight: 0.0570 chunk 9 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 112 optimal weight: 0.0010 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.8110 ------------------------------------------------------------------------------- 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 F1013 GLN G 78 ASN G 313 GLN H1003 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.167005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121235 restraints weight = 24500.496| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.05 r_work: 0.3189 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5995 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= 0.172 Angle : 0.732 15.741 25571 Z= 0.363 Chirality : 0.050 0.580 2767 Planarity : 0.005 0.051 3360 Dihedral : 6.122 58.593 2773 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.19 % Allowed : 20.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2365 helix: -0.17 (0.27), residues: 361 sheet: -0.12 (0.28), residues: 378 loop : -1.50 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 222 HIS 0.005 0.001 HIS H 874 PHE 0.020 0.002 PHE E 735 TYR 0.016 0.002 TYR H 897 ARG 0.006 0.001 ARG G 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 10) link_NAG-ASN : angle 3.81130 ( 30) hydrogen bonds : bond 0.03958 ( 446) hydrogen bonds : angle 4.90937 ( 1163) SS BOND : bond 0.00414 ( 116) SS BOND : angle 1.59188 ( 232) covalent geometry : bond 0.00414 (18651) covalent geometry : angle 0.70729 (25309) ********************** 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 242 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8936 (mtp) cc_final: 0.8617 (mtm) REVERT: E 107 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7460 (mm110) REVERT: E 217 MET cc_start: 0.3499 (mtp) cc_final: 0.2130 (pmt) REVERT: E 228 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7179 (tt) REVERT: E 252 LYS cc_start: 0.7827 (ptmt) cc_final: 0.7440 (ptmm) REVERT: E 280 MET cc_start: 0.8040 (ttm) cc_final: 0.7681 (tmm) REVERT: E 302 ARG cc_start: 0.7848 (ttm170) cc_final: 0.6626 (ttt-90) REVERT: E 341 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7126 (pp) REVERT: E 347 GLU cc_start: 0.8026 (tp30) cc_final: 0.7553 (tp30) REVERT: E 543 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: E 644 GLU cc_start: 0.6166 (mm-30) cc_final: 0.5931 (mm-30) REVERT: F 793 GLN cc_start: 0.7299 (pp30) cc_final: 0.6884 (tm-30) REVERT: F 869 THR cc_start: 0.9089 (m) cc_final: 0.8802 (p) REVERT: F 920 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5168 (mtmt) REVERT: F 1057 ASP cc_start: 0.8295 (t0) cc_final: 0.8080 (m-30) REVERT: G 67 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8070 (ptmt) REVERT: G 107 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7041 (pp30) REVERT: G 170 GLU cc_start: 0.7439 (pm20) cc_final: 0.7136 (pm20) REVERT: G 299 MET cc_start: 0.8464 (mtt) cc_final: 0.8152 (mtt) REVERT: G 382 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6742 (pt0) REVERT: G 609 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8352 (mtt-85) REVERT: G 649 GLU cc_start: 0.7336 (pt0) cc_final: 0.7125 (pt0) REVERT: G 660 GLN cc_start: 0.7094 (tp40) cc_final: 0.6150 (mm110) REVERT: H 862 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8206 (t) REVERT: H 947 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6850 (ptm) REVERT: H 1049 ASN cc_start: 0.6451 (t0) cc_final: 0.6036 (t160) REVERT: H 1061 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7886 (mpt90) REVERT: H 1092 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6279 (mp0) REVERT: H 1161 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6922 (mp0) outliers start: 64 outliers final: 38 residues processed: 220 average time/residue: 1.2619 time to fit residues: 314.0589 Evaluate side-chains 223 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 341 LEU Chi-restraints excluded: chain E residue 346 THR 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 787 GLU Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 1156 THR 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 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 329 CYS 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 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 520 THR Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 622 LEU 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 926 THR 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 1124 THR Chi-restraints excluded: chain H residue 1161 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 204 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 189 optimal weight: 0.0470 chunk 211 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 952 HIS G 78 ASN G 313 GLN H1003 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121060 restraints weight = 22703.834| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.99 r_work: 0.3192 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.495 18777 Z= 0.262 Angle : 0.943 59.199 25571 Z= 0.501 Chirality : 0.054 0.780 2767 Planarity : 0.005 0.079 3360 Dihedral : 6.126 58.617 2773 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.99 % Allowed : 20.45 % Favored : 76.56 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2365 helix: -0.18 (0.27), residues: 361 sheet: -0.11 (0.28), residues: 378 loop : -1.50 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 222 HIS 0.005 0.001 HIS H 874 PHE 0.020 0.002 PHE E 735 TYR 0.014 0.002 TYR F 988 ARG 0.005 0.001 ARG G 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 10) link_NAG-ASN : angle 3.81362 ( 30) hydrogen bonds : bond 0.03979 ( 446) hydrogen bonds : angle 4.90901 ( 1163) SS BOND : bond 0.02736 ( 116) SS BOND : angle 3.44253 ( 232) covalent geometry : bond 0.00600 (18651) covalent geometry : angle 0.87878 (25309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21067.06 seconds wall clock time: 363 minutes 21.12 seconds (21801.12 seconds total)