Starting phenix.real_space_refine on Sat Jul 4 03:27:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpp_32687/07_2026/7wpp_32687_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpp_32687/07_2026/7wpp_32687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wpp_32687/07_2026/7wpp_32687_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpp_32687/07_2026/7wpp_32687_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wpp_32687/07_2026/7wpp_32687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpp_32687/07_2026/7wpp_32687.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 276 5.16 5 C 11258 2.51 5 N 3129 2.21 5 O 3583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18252 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5427 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5427 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 3629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3692 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 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, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.47, per 1000 atoms: 0.24 Number of scatterers: 18252 At special positions: 0 Unit cell: (160.293, 161.391, 149.314, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 276 16.00 O 3583 8.00 N 3129 7.00 C 11258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=116, symmetry=0 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.02 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 255 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 250 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 257 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 348 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 372 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 384 " distance=2.03 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 524 " distance=2.02 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 440 " distance=2.04 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.02 Simple disulfide: pdb=" SG CYS E 595 " - pdb=" SG CYS E 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 615 " - pdb=" SG CYS E 621 " distance=2.03 Simple disulfide: pdb=" SG CYS E 623 " - pdb=" SG CYS E 648 " distance=2.02 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 687 " distance=2.03 Simple disulfide: pdb=" SG CYS E 661 " - pdb=" SG CYS E 683 " distance=2.03 Simple disulfide: pdb=" SG CYS E 665 " - pdb=" SG CYS E 679 " distance=2.03 Simple disulfide: pdb=" SG CYS E 669 " - pdb=" SG CYS E 707 " distance=2.03 Simple disulfide: pdb=" SG CYS E 689 " - pdb=" SG CYS E 701 " distance=2.04 Simple disulfide: pdb=" SG CYS E 709 " - pdb=" SG CYS E 731 " distance=2.03 Simple disulfide: pdb=" SG CYS E 729 " - pdb=" SG CYS E 738 " distance=2.03 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 804 " distance=2.02 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 799 " distance=2.03 Simple disulfide: pdb=" SG CYS F 792 " - pdb=" SG CYS F 827 " distance=2.03 Simple disulfide: pdb=" SG CYS F 810 " - pdb=" SG CYS F 821 " distance=2.03 Simple disulfide: pdb=" SG CYS F 829 " - pdb=" SG CYS F 851 " distance=2.03 Simple disulfide: pdb=" SG CYS F 846 " - pdb=" SG CYS F 863 " distance=2.03 Simple disulfide: pdb=" SG CYS F 849 " - pdb=" SG CYS F 858 " distance=2.03 Simple disulfide: pdb=" SG CYS F 867 " - pdb=" SG CYS F 996 " distance=2.03 Simple disulfide: pdb=" SG CYS F 889 " - pdb=" SG CYS F1031 " distance=2.03 Simple disulfide: pdb=" SG CYS F 898 " - pdb=" SG CYS F 993 " distance=2.03 Simple disulfide: pdb=" SG CYS F 914 " - pdb=" SG CYS F 921 " distance=2.03 Simple disulfide: pdb=" SG CYS F1046 " - pdb=" SG CYS F1089 " distance=2.03 Simple disulfide: pdb=" SG CYS F1060 " - pdb=" SG CYS F1084 " distance=2.03 Simple disulfide: pdb=" SG CYS F1071 " - pdb=" SG CYS F1111 " distance=2.02 Simple disulfide: pdb=" SG CYS F1091 " - pdb=" SG CYS F1099 " distance=2.04 Simple disulfide: pdb=" SG CYS F1097 " - pdb=" SG CYS H1097 " distance=2.03 Simple disulfide: pdb=" SG CYS F1101 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F1130 " - pdb=" SG CYS F1173 " distance=2.03 Simple disulfide: pdb=" SG CYS F1142 " - pdb=" SG CYS H1142 " distance=2.03 Simple disulfide: pdb=" SG CYS F1149 " - pdb=" SG CYS F1169 " distance=2.03 Simple disulfide: pdb=" SG CYS F1153 " - pdb=" SG CYS F1165 " distance=2.04 Simple disulfide: pdb=" SG CYS F1157 " - pdb=" SG CYS F1196 " distance=2.03 Simple disulfide: pdb=" SG CYS F1177 " - pdb=" SG CYS F1190 " distance=2.03 Simple disulfide: pdb=" SG CYS F1199 " - pdb=" SG CYS F1227 " distance=2.03 Simple disulfide: pdb=" SG CYS F1222 " - pdb=" SG CYS F1237 " distance=2.03 Simple disulfide: pdb=" SG CYS F1225 " - pdb=" SG CYS F1234 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 57 " - pdb=" SG CYS G 200 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 159 " distance=2.02 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 255 " distance=2.02 Simple disulfide: pdb=" SG CYS G 225 " - pdb=" SG CYS G 250 " distance=2.03 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 275 " distance=2.03 Simple disulfide: pdb=" SG CYS G 257 " - pdb=" SG CYS G 263 " distance=2.03 Simple disulfide: pdb=" SG CYS G 265 " - pdb=" SG CYS G 291 " distance=2.03 Simple disulfide: pdb=" SG CYS G 295 " - pdb=" SG CYS G 329 " distance=2.03 Simple disulfide: pdb=" SG CYS G 304 " - pdb=" SG CYS G 325 " distance=2.03 Simple disulfide: pdb=" SG CYS G 308 " - pdb=" SG CYS G 321 " distance=2.03 Simple disulfide: pdb=" SG CYS G 312 " - pdb=" SG CYS G 348 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 342 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 372 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 384 " distance=2.02 Simple disulfide: pdb=" SG CYS G 370 " - pdb=" SG CYS G 379 " distance=2.03 Simple disulfide: pdb=" SG CYS G 388 " - pdb=" SG CYS G 524 " distance=2.02 Simple disulfide: pdb=" SG CYS G 410 " - pdb=" SG CYS G 559 " distance=2.03 Simple disulfide: pdb=" SG CYS G 418 " - pdb=" SG CYS G 521 " distance=2.03 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 440 " distance=2.04 Simple disulfide: pdb=" SG CYS G 570 " - pdb=" SG CYS G 613 " distance=2.03 Simple disulfide: pdb=" SG CYS G 584 " - pdb=" SG CYS G 608 " distance=2.02 Simple disulfide: pdb=" SG CYS G 595 " - pdb=" SG CYS G 633 " distance=2.03 Simple disulfide: pdb=" SG CYS G 615 " - pdb=" SG CYS G 621 " distance=2.03 Simple disulfide: pdb=" SG CYS G 623 " - pdb=" SG CYS G 648 " distance=2.02 Simple disulfide: pdb=" SG CYS G 652 " - pdb=" SG CYS G 687 " distance=2.03 Simple disulfide: pdb=" SG CYS G 661 " - pdb=" SG CYS G 683 " distance=2.03 Simple disulfide: pdb=" SG CYS G 665 " - pdb=" SG CYS G 679 " distance=2.03 Simple disulfide: pdb=" SG CYS G 669 " - pdb=" SG CYS G 707 " distance=2.03 Simple disulfide: pdb=" SG CYS G 689 " - pdb=" SG CYS G 701 " distance=2.04 Simple disulfide: pdb=" SG CYS G 709 " - pdb=" SG CYS G 731 " distance=2.03 Simple disulfide: pdb=" SG CYS G 729 " - pdb=" SG CYS G 738 " distance=2.03 Simple disulfide: pdb=" SG CYS H 767 " - pdb=" SG CYS H 808 " distance=2.03 Simple disulfide: pdb=" SG CYS H 776 " - pdb=" SG CYS H 804 " distance=2.02 Simple disulfide: pdb=" SG CYS H 788 " - pdb=" SG CYS H 799 " distance=2.03 Simple disulfide: pdb=" SG CYS H 792 " - pdb=" SG CYS H 827 " distance=2.03 Simple disulfide: pdb=" SG CYS H 810 " - pdb=" SG CYS H 821 " distance=2.04 Simple disulfide: pdb=" SG CYS H 829 " - pdb=" SG CYS H 851 " distance=2.03 Simple disulfide: pdb=" SG CYS H 846 " - pdb=" SG CYS H 863 " distance=2.03 Simple disulfide: pdb=" SG CYS H 849 " - pdb=" SG CYS H 858 " distance=2.03 Simple disulfide: pdb=" SG CYS H 867 " - pdb=" SG CYS H 996 " distance=2.03 Simple disulfide: pdb=" SG CYS H 889 " - pdb=" SG CYS H1031 " distance=2.03 Simple disulfide: pdb=" SG CYS H 898 " - pdb=" SG CYS H 993 " distance=2.03 Simple disulfide: pdb=" SG CYS H 914 " - pdb=" SG CYS H 921 " distance=2.03 Simple disulfide: pdb=" SG CYS H1046 " - pdb=" SG CYS H1089 " distance=2.03 Simple disulfide: pdb=" SG CYS H1060 " - pdb=" SG CYS H1084 " distance=2.03 Simple disulfide: pdb=" SG CYS H1071 " - pdb=" SG CYS H1111 " distance=2.02 Simple disulfide: pdb=" SG CYS H1091 " - pdb=" SG CYS H1099 " distance=2.04 Simple disulfide: pdb=" SG CYS H1101 " - pdb=" SG CYS H1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H1130 " - pdb=" SG CYS H1173 " distance=2.03 Simple disulfide: pdb=" SG CYS H1149 " - pdb=" SG CYS H1169 " distance=2.03 Simple disulfide: pdb=" SG CYS H1153 " - pdb=" SG CYS H1165 " distance=2.03 Simple disulfide: pdb=" SG CYS H1157 " - pdb=" SG CYS H1196 " distance=2.04 Simple disulfide: pdb=" SG CYS H1177 " - pdb=" SG CYS H1190 " distance=2.03 Simple disulfide: pdb=" SG CYS H1199 " - pdb=" SG CYS H1227 " distance=2.03 Simple disulfide: pdb=" SG CYS H1222 " - pdb=" SG CYS H1237 " distance=2.04 Simple disulfide: pdb=" SG CYS H1225 " - pdb=" SG CYS H1234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 803 " - " ASN E 156 " " NAG E 804 " - " ASN E 99 " " NAG F1301 " - " ASN F1231 " " NAG F1303 " - " ASN F 857 " " NAG F1304 " - " ASN F1147 " " NAG G 803 " - " ASN G 156 " " NAG G 804 " - " ASN G 99 " " NAG H1301 " - " ASN H1231 " " NAG H1303 " - " ASN H1147 " " NAG H1304 " - " ASN H 857 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 978.1 milliseconds 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 40 sheets defined 17.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'E' and resid 114 through 118 removed outlier: 4.001A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.606A pdb=" N PHE E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 215 through 222 removed outlier: 3.564A pdb=" N LYS E 219 " --> pdb=" O GLY E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 removed outlier: 3.769A pdb=" N SER E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 252 removed outlier: 3.974A pdb=" N LYS E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.532A pdb=" N LEU E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 514 through 517 Processing helix chain 'E' and resid 545 through 551 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 573 through 575 No H-bonds generated for 'chain 'E' and resid 573 through 575' Processing helix chain 'E' and resid 576 through 584 removed outlier: 3.809A pdb=" N CYS E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 593 removed outlier: 3.536A pdb=" N PHE E 592 " --> pdb=" O SER E 589 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU E 593 " --> pdb=" O PRO E 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 589 through 593' Processing helix chain 'E' and resid 601 through 613 removed outlier: 3.565A pdb=" N ARG E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 610 " --> pdb=" O ARG E 606 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E 613 " --> pdb=" O ARG E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 637 removed outlier: 4.100A pdb=" N ALA E 627 " --> pdb=" O CYS E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 673 removed outlier: 4.024A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 668 through 673' Processing helix chain 'F' and resid 1017 through 1023 removed outlier: 3.819A pdb=" N ASN F1023 " --> pdb=" O VAL F1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1026 No H-bonds generated for 'chain 'F' and resid 1024 through 1026' Processing helix chain 'F' and resid 1049 through 1061 removed outlier: 3.562A pdb=" N ASP F1057 " --> pdb=" O GLN F1053 " (cutoff:3.500A) Processing helix chain 'F' and resid 1062 through 1067 removed outlier: 6.742A pdb=" N ASP F1066 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL F1067 " --> pdb=" O THR F1064 " (cutoff:3.500A) Processing helix chain 'F' and resid 1068 through 1073 removed outlier: 3.760A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 removed outlier: 3.680A pdb=" N THR F1088 " --> pdb=" O CYS F1084 " (cutoff:3.500A) Processing helix chain 'F' and resid 1100 through 1114 removed outlier: 3.616A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR F1107 " --> pdb=" O THR F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1131 through 1136 removed outlier: 3.659A pdb=" N ARG F1136 " --> pdb=" O GLU F1132 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 4.000A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 183 through 189 removed outlier: 3.607A pdb=" N PHE G 187 " --> pdb=" O ASP G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 192 No H-bonds generated for 'chain 'G' and resid 190 through 192' Processing helix chain 'G' and resid 215 through 222 removed outlier: 3.565A pdb=" N LYS G 219 " --> pdb=" O GLY G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.769A pdb=" N SER G 230 " --> pdb=" O GLN G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 removed outlier: 3.975A pdb=" N LYS G 252 " --> pdb=" O ALA G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.532A pdb=" N LEU G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 514 through 517 Processing helix chain 'G' and resid 545 through 551 Processing helix chain 'G' and resid 568 through 572 Processing helix chain 'G' and resid 573 through 575 No H-bonds generated for 'chain 'G' and resid 573 through 575' Processing helix chain 'G' and resid 576 through 584 removed outlier: 3.810A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 589 through 593 removed outlier: 3.536A pdb=" N PHE G 592 " --> pdb=" O SER G 589 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU G 593 " --> pdb=" O PRO G 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 589 through 593' Processing helix chain 'G' and resid 601 through 613 removed outlier: 3.565A pdb=" N ARG G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS G 613 " --> pdb=" O ARG G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 637 removed outlier: 4.100A pdb=" N ALA G 627 " --> pdb=" O CYS G 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 673 removed outlier: 4.023A pdb=" N LEU G 672 " --> pdb=" O THR G 668 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER G 673 " --> pdb=" O CYS G 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 668 through 673' Processing helix chain 'H' and resid 1017 through 1023 removed outlier: 3.819A pdb=" N ASN H1023 " --> pdb=" O VAL H1019 " (cutoff:3.500A) Processing helix chain 'H' and resid 1024 through 1026 No H-bonds generated for 'chain 'H' and resid 1024 through 1026' Processing helix chain 'H' and resid 1049 through 1061 removed outlier: 3.639A pdb=" N ASP H1057 " --> pdb=" O GLN H1053 " (cutoff:3.500A) Processing helix chain 'H' and resid 1062 through 1067 removed outlier: 6.742A pdb=" N ASP H1066 " --> pdb=" O LEU H1063 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL H1067 " --> pdb=" O THR H1064 " (cutoff:3.500A) Processing helix chain 'H' and resid 1068 through 1073 removed outlier: 3.761A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 removed outlier: 3.681A pdb=" N THR H1088 " --> pdb=" O CYS H1084 " (cutoff:3.500A) Processing helix chain 'H' and resid 1100 through 1114 removed outlier: 3.615A pdb=" N ILE H1104 " --> pdb=" O PHE H1100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR H1107 " --> pdb=" O THR H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1131 through 1136 removed outlier: 3.659A pdb=" N ARG H1136 " --> pdb=" O GLU H1132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 32 through 37 removed outlier: 3.526A pdb=" N LEU E 150 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.810A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN E 107 " --> pdb=" O GLN E 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 300 through 305 removed outlier: 5.803A pdb=" N TYR E 301 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER E 330 " --> pdb=" O TYR E 301 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN E 303 " --> pdb=" O GLY E 328 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY E 328 " --> pdb=" O GLN E 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AA6, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AA8, first strand: chain 'E' and resid 403 through 405 Processing sheet with id=AA9, first strand: chain 'E' and resid 469 through 470 removed outlier: 3.684A pdb=" N GLN E 469 " --> pdb=" O MET E 466 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE E 427 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU E 413 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR E 429 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN E 411 " --> pdb=" O THR E 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 480 through 484 Processing sheet with id=AB2, first strand: chain 'E' and resid 536 through 537 removed outlier: 3.888A pdb=" N LEU E 541 " --> pdb=" O THR E 537 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 657 through 659 Processing sheet with id=AB4, first strand: chain 'E' and resid 721 through 723 Processing sheet with id=AB5, first strand: chain 'F' and resid 772 through 773 Processing sheet with id=AB6, first strand: chain 'F' and resid 841 through 844 Processing sheet with id=AB7, first strand: chain 'F' and resid 865 through 866 removed outlier: 5.898A pdb=" N LEU F 970 " --> pdb=" O LEU F 966 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 961 " --> pdb=" O SER F 958 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 875 through 876 Processing sheet with id=AB9, first strand: chain 'F' and resid 890 through 895 removed outlier: 7.178A pdb=" N ILE F 907 " --> pdb=" O LEU F 893 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLN F 895 " --> pdb=" O PHE F 905 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE F 905 " --> pdb=" O GLN F 895 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 926 " --> pdb=" O LEU F 908 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS F 912 " --> pdb=" O LYS F 922 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS F 922 " --> pdb=" O LYS F 912 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 934 " --> pdb=" O ILE F 927 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU F 933 " --> pdb=" O LYS F 944 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 1144 through 1151 removed outlier: 5.110A pdb=" N TYR F1146 " --> pdb=" O HIS F1174 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N HIS F1174 " --> pdb=" O TYR F1146 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER F1148 " --> pdb=" O GLY F1172 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLY F1172 " --> pdb=" O SER F1148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 1182 through 1183 Processing sheet with id=AC3, first strand: chain 'G' and resid 32 through 37 removed outlier: 3.526A pdb=" N LEU G 150 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 42 through 44 Processing sheet with id=AC5, first strand: chain 'G' and resid 58 through 62 removed outlier: 6.810A pdb=" N ILE G 72 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN G 107 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 300 through 305 removed outlier: 5.802A pdb=" N TYR G 301 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER G 330 " --> pdb=" O TYR G 301 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN G 303 " --> pdb=" O GLY G 328 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY G 328 " --> pdb=" O GLN G 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 336 through 337 Processing sheet with id=AC8, first strand: chain 'G' and resid 350 through 351 Processing sheet with id=AC9, first strand: chain 'G' and resid 362 through 364 Processing sheet with id=AD1, first strand: chain 'G' and resid 403 through 405 Processing sheet with id=AD2, first strand: chain 'G' and resid 469 through 470 removed outlier: 3.684A pdb=" N GLN G 469 " --> pdb=" O MET G 466 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N THR G 441 " --> pdb=" O VAL G 430 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL G 430 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 443 " --> pdb=" O GLU G 428 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR G 429 " --> pdb=" O GLN G 411 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN G 411 " --> pdb=" O THR G 429 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 480 through 484 Processing sheet with id=AD4, first strand: chain 'G' and resid 536 through 537 removed outlier: 3.887A pdb=" N LEU G 541 " --> pdb=" O THR G 537 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 657 through 659 Processing sheet with id=AD6, first strand: chain 'G' and resid 721 through 723 Processing sheet with id=AD7, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AD8, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AD9, first strand: chain 'H' and resid 865 through 866 removed outlier: 5.898A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR H 961 " --> pdb=" O SER H 958 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 875 through 876 Processing sheet with id=AE2, first strand: chain 'H' and resid 890 through 895 removed outlier: 7.177A pdb=" N ILE H 907 " --> pdb=" O LEU H 893 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN H 895 " --> pdb=" O PHE H 905 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE H 905 " --> pdb=" O GLN H 895 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 926 " --> pdb=" O LEU H 908 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS H 912 " --> pdb=" O LYS H 922 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS H 922 " --> pdb=" O LYS H 912 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 934 " --> pdb=" O ILE H 927 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU H 933 " --> pdb=" O LYS H 944 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 1144 through 1151 removed outlier: 5.111A pdb=" N TYR H1146 " --> pdb=" O HIS H1174 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N HIS H1174 " --> pdb=" O TYR H1146 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER H1148 " --> pdb=" O GLY H1172 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY H1172 " --> pdb=" O SER H1148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 1182 through 1183 446 hydrogen bonds defined for protein. 1163 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6156 1.34 - 1.47: 4334 1.47 - 1.59: 7841 1.59 - 1.71: 0 1.71 - 1.84: 320 Bond restraints: 18651 Sorted by residual: bond pdb=" N LYS G 157 " pdb=" CA LYS G 157 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 9.20e+00 bond pdb=" N CYS H 858 " pdb=" CA CYS H 858 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.88e+00 bond pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.81e+00 bond pdb=" N PHE E 155 " pdb=" CA PHE E 155 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.30e-02 5.92e+03 7.20e+00 bond pdb=" N ASN E 156 " pdb=" CA ASN E 156 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.05e+00 ... (remaining 18646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 24380 2.75 - 5.50: 754 5.50 - 8.24: 133 8.24 - 10.99: 26 10.99 - 13.74: 16 Bond angle restraints: 25309 Sorted by residual: angle pdb=" C THR E 175 " pdb=" N GLN E 176 " pdb=" CA GLN E 176 " ideal model delta sigma weight residual 120.60 132.28 -11.68 1.60e+00 3.91e-01 5.33e+01 angle pdb=" C ALA E 267 " pdb=" N LEU E 268 " pdb=" CA LEU E 268 " ideal model delta sigma weight residual 120.29 130.62 -10.33 1.42e+00 4.96e-01 5.29e+01 angle pdb=" C ALA G 267 " pdb=" N LEU G 268 " pdb=" CA LEU G 268 " ideal model delta sigma weight residual 120.29 130.62 -10.33 1.42e+00 4.96e-01 5.29e+01 angle pdb=" C THR G 175 " pdb=" N GLN G 176 " pdb=" CA GLN G 176 " ideal model delta sigma weight residual 120.60 132.22 -11.62 1.60e+00 3.91e-01 5.28e+01 angle pdb=" C LEU G 228 " pdb=" N LYS G 229 " pdb=" CA LYS G 229 " ideal model delta sigma weight residual 121.81 134.64 -12.83 1.83e+00 2.99e-01 4.91e+01 ... (remaining 25304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10938 17.94 - 35.88: 563 35.88 - 53.82: 127 53.82 - 71.75: 41 71.75 - 89.69: 16 Dihedral angle restraints: 11685 sinusoidal: 4861 harmonic: 6824 Sorted by residual: dihedral pdb=" CB CYS E 312 " pdb=" SG CYS E 312 " pdb=" SG CYS E 348 " pdb=" CB CYS E 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.03 -80.03 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS G 312 " pdb=" SG CYS G 312 " pdb=" SG CYS G 348 " pdb=" CB CYS G 348 " ideal model delta sinusoidal sigma weight residual 93.00 172.99 -79.99 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS F 810 " pdb=" SG CYS F 810 " pdb=" SG CYS F 821 " pdb=" CB CYS F 821 " ideal model delta sinusoidal sigma weight residual 93.00 172.08 -79.08 1 1.00e+01 1.00e-02 7.78e+01 ... (remaining 11682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 2711 0.304 - 0.608: 20 0.608 - 0.911: 27 0.911 - 1.215: 0 1.215 - 1.519: 9 Chirality restraints: 2767 Sorted by residual: chirality pdb=" CB THR G 181 " pdb=" CA THR G 181 " pdb=" OG1 THR G 181 " pdb=" CG2 THR G 181 " both_signs ideal model delta sigma weight residual False 2.55 1.03 1.52 2.00e-01 2.50e+01 5.77e+01 chirality pdb=" CB THR E 181 " pdb=" CA THR E 181 " pdb=" OG1 THR E 181 " pdb=" CG2 THR E 181 " both_signs ideal model delta sigma weight residual False 2.55 1.04 1.52 2.00e-01 2.50e+01 5.74e+01 chirality pdb=" CB THR E 175 " pdb=" CA THR E 175 " pdb=" OG1 THR E 175 " pdb=" CG2 THR E 175 " both_signs ideal model delta sigma weight residual False 2.55 1.07 1.49 2.00e-01 2.50e+01 5.52e+01 ... (remaining 2764 not shown) Planarity restraints: 3370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 804 " 0.333 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG E 804 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG E 804 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG E 804 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG E 804 " 0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H1303 " 0.323 2.00e-02 2.50e+03 2.77e-01 9.62e+02 pdb=" C7 NAG H1303 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG H1303 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG H1303 " -0.490 2.00e-02 2.50e+03 pdb=" O7 NAG H1303 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 803 " -0.301 2.00e-02 2.50e+03 2.52e-01 7.97e+02 pdb=" C7 NAG E 803 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG E 803 " -0.193 2.00e-02 2.50e+03 pdb=" N2 NAG E 803 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG E 803 " -0.017 2.00e-02 2.50e+03 ... (remaining 3367 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 221 2.61 - 3.18: 16044 3.18 - 3.76: 26595 3.76 - 4.33: 37449 4.33 - 4.90: 61322 Nonbonded interactions: 141631 Sorted by model distance: nonbonded pdb=" OG SER F1009 " pdb=" OD1 ASN F1011 " model vdw 2.041 3.040 nonbonded pdb=" OG SER H1009 " pdb=" OD1 ASN H1011 " model vdw 2.041 3.040 nonbonded pdb=" O GLU E 270 " pdb=" OG1 THR E 274 " model vdw 2.057 3.040 nonbonded pdb=" O GLU G 270 " pdb=" OG1 THR G 274 " model vdw 2.058 3.040 nonbonded pdb=" O SER F1093 " pdb=" OG SER H1093 " model vdw 2.068 3.040 ... (remaining 141626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and (resid 767 through 1052 or resid 1054 through 1304)) selection = (chain 'H' and (resid 767 through 1052 or resid 1054 through 1304)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.860 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.190 18777 Z= 0.363 Angle : 1.195 17.710 25571 Z= 0.635 Chirality : 0.139 1.519 2767 Planarity : 0.012 0.288 3360 Dihedral : 10.808 89.693 6967 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.98 % Favored : 89.89 % Rotamer: Outliers : 0.74 % Allowed : 2.31 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.14), residues: 2365 helix: -3.60 (0.18), residues: 325 sheet: -2.90 (0.21), residues: 426 loop : -2.84 (0.13), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 960 TYR 0.038 0.003 TYR G 527 PHE 0.026 0.003 PHE G 535 TRP 0.027 0.003 TRP H 974 HIS 0.010 0.002 HIS E 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00871 / 0.36 (18651) covalent geometry : angle 1.17088 / 0.63 (25309) SS BOND : bond 0.00447 / 0.28 ( 116) SS BOND : angle 1.86109 / 1.22 ( 232) hydrogen bonds : bond 0.28096 / 18.48 ( 446) hydrogen bonds : angle 9.45708 / 6.47 ( 1163) link_NAG-ASN : bond 0.06122 / 3.61 ( 10) link_NAG-ASN : angle 5.78050 / 4.27 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 589 time to evaluate : 0.748 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: 0.6505 (tm-30) REVERT: H 795 TYR cc_start: 0.7587 (t80) cc_final: 0.7264 (t80) REVERT: H 842 VAL cc_start: 0.8520 (m) cc_final: 0.8300 (p) outliers start: 14 outliers final: 1 residues processed: 593 average time/residue: 0.5712 time to fit residues: 380.8350 Evaluate side-chains 255 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 181 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 95 HIS E 189 ASN E 368 ASN E 374 ASN F 817 HIS F 942 ASN F 952 HIS F1013 GLN F1174 HIS F1221 HIS G 78 ASN G 95 HIS G 277 GLN G 452 HIS G 596 HIS ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 998 ASN H1013 GLN H1069 GLN H1113 GLN H1221 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132633 restraints weight = 23312.537| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.96 r_work: 0.3354 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 18777 Z= 0.167 Angle : 0.794 18.082 25571 Z= 0.395 Chirality : 0.053 0.774 2767 Planarity : 0.005 0.049 3360 Dihedral : 6.580 59.570 2773 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 3.92 % Allowed : 13.78 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.15), residues: 2365 helix: -1.52 (0.25), residues: 321 sheet: -1.79 (0.23), residues: 438 loop : -2.18 (0.14), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 373 TYR 0.026 0.002 TYR G 711 PHE 0.027 0.002 PHE H 999 TRP 0.015 0.002 TRP F 974 HIS 0.005 0.001 HIS G 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (18651) covalent geometry : angle 0.75566 / 0.38 (25309) SS BOND : bond 0.00476 / 0.29 ( 116) SS BOND : angle 1.97721 / 1.34 ( 232) hydrogen bonds : bond 0.04504 / 2.97 ( 446) hydrogen bonds : angle 5.65764 / 3.84 ( 1163) link_NAG-ASN : bond 0.00667 / 0.35 ( 10) link_NAG-ASN : angle 4.98322 / 3.45 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 273 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 VAL cc_start: 0.8365 (t) cc_final: 0.8104 (m) REVERT: E 132 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7630 (mm-30) REVERT: E 217 MET cc_start: 0.2939 (mtp) cc_final: 0.2411 (ppp) REVERT: E 294 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7471 (p) REVERT: E 320 MET cc_start: 0.5104 (tpt) cc_final: 0.4815 (tpt) REVERT: E 419 GLN cc_start: 0.7450 (pp30) cc_final: 0.7101 (mm110) REVERT: E 602 LEU cc_start: 0.8159 (pp) cc_final: 0.7906 (mt) REVERT: E 649 GLU cc_start: 0.6208 (pt0) cc_final: 0.5172 (mm-30) REVERT: E 696 ASP cc_start: 0.7176 (t0) cc_final: 0.6953 (t70) REVERT: E 712 ASP cc_start: 0.7004 (t0) cc_final: 0.6613 (OUTLIER) REVERT: F 864 ASP cc_start: 0.8546 (m-30) cc_final: 0.8218 (m-30) REVERT: F 912 LYS cc_start: 0.8241 (mppt) cc_final: 0.7962 (mptt) REVERT: F 954 GLU cc_start: 0.8267 (tp30) cc_final: 0.8059 (tp30) REVERT: F 1049 ASN cc_start: 0.6097 (t0) cc_final: 0.5855 (t0) REVERT: F 1161 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: G 201 GLU cc_start: 0.7279 (mp0) cc_final: 0.6617 (mm-30) REVERT: G 313 GLN cc_start: 0.6719 (mp10) cc_final: 0.6452 (mp-120) REVERT: G 326 VAL cc_start: 0.7958 (t) cc_final: 0.7662 (p) REVERT: G 343 VAL cc_start: 0.7556 (p) cc_final: 0.7348 (m) REVERT: G 479 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6956 (m-30) REVERT: G 578 ARG cc_start: 0.7600 (mtm110) cc_final: 0.7367 (ttp-110) REVERT: G 602 LEU cc_start: 0.7987 (pp) cc_final: 0.7528 (mt) REVERT: G 695 MET cc_start: 0.7202 (mmp) cc_final: 0.6876 (mmp) REVERT: G 728 MET cc_start: 0.6868 (tmm) cc_final: 0.6550 (tmm) REVERT: H 795 TYR cc_start: 0.7690 (t80) cc_final: 0.7149 (t80) REVERT: H 842 VAL cc_start: 0.8306 (m) cc_final: 0.8000 (p) REVERT: H 862 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7578 (t) REVERT: H 947 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6897 (ptm) REVERT: H 1049 ASN cc_start: 0.6111 (t0) cc_final: 0.5860 (t0) REVERT: H 1061 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7817 (mpt90) outliers start: 79 outliers final: 30 residues processed: 327 average time/residue: 0.4709 time to fit residues: 176.0278 Evaluate side-chains 233 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 294 VAL 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 685 GLU Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 250 CYS Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 479 ASP Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 19 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 138 optimal weight: 0.0020 chunk 177 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 190 optimal weight: 0.4980 chunk 205 optimal weight: 4.9990 chunk 120 optimal weight: 0.0000 chunk 124 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 78 ASN F1003 GLN F1113 GLN F1168 GLN G 78 ASN G 303 GLN G 368 ASN G 453 ASN G 563 GLN H1003 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.179549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134872 restraints weight = 23875.234| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.27 r_work: 0.3360 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18777 Z= 0.110 Angle : 0.650 13.914 25571 Z= 0.323 Chirality : 0.048 0.555 2767 Planarity : 0.004 0.048 3360 Dihedral : 5.693 52.977 2773 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 2.94 % Allowed : 16.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2365 helix: -0.45 (0.27), residues: 327 sheet: -1.32 (0.25), residues: 424 loop : -1.83 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 373 TYR 0.021 0.001 TYR G 711 PHE 0.016 0.001 PHE H 878 TRP 0.013 0.001 TRP H 974 HIS 0.003 0.000 HIS F1176 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (18651) covalent geometry : angle 0.62432 / 0.32 (25309) SS BOND : bond 0.00327 / 0.20 ( 116) SS BOND : angle 1.31462 / 0.82 ( 232) hydrogen bonds : bond 0.03489 / 2.23 ( 446) hydrogen bonds : angle 5.12977 / 3.48 ( 1163) link_NAG-ASN : bond 0.01110 / 0.58 ( 10) link_NAG-ASN : angle 4.23996 / 2.83 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 231 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 VAL cc_start: 0.8277 (t) cc_final: 0.8022 (m) REVERT: E 132 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7643 (mm-30) REVERT: E 217 MET cc_start: 0.2921 (mtp) cc_final: 0.2425 (ppp) REVERT: E 252 LYS cc_start: 0.7280 (ptmt) cc_final: 0.6887 (ptmm) REVERT: E 280 MET cc_start: 0.8074 (ttm) cc_final: 0.7802 (tmm) REVERT: E 302 ARG cc_start: 0.7560 (ttm170) cc_final: 0.6525 (ttt-90) REVERT: E 313 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7079 (mp10) REVERT: E 320 MET cc_start: 0.5008 (tpt) cc_final: 0.4621 (tpt) REVERT: E 419 GLN cc_start: 0.7676 (pp30) cc_final: 0.7291 (mm-40) REVERT: E 694 TYR cc_start: 0.5043 (m-10) cc_final: 0.4785 (m-10) REVERT: E 712 ASP cc_start: 0.7182 (t0) cc_final: 0.6825 (OUTLIER) REVERT: E 728 MET cc_start: 0.7899 (tpp) cc_final: 0.7670 (tpt) REVERT: F 864 ASP cc_start: 0.8607 (m-30) cc_final: 0.8282 (m-30) REVERT: F 912 LYS cc_start: 0.8062 (mppt) cc_final: 0.7763 (mptt) REVERT: F 954 GLU cc_start: 0.8359 (tp30) cc_final: 0.8098 (tp30) REVERT: F 968 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7636 (mtmm) REVERT: F 1049 ASN cc_start: 0.5985 (t0) cc_final: 0.5779 (t0) REVERT: F 1161 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: G 217 MET cc_start: 0.3167 (mtm) cc_final: 0.2048 (pp-130) REVERT: G 280 MET cc_start: 0.8194 (ttm) cc_final: 0.7882 (ttm) REVERT: G 338 ASP cc_start: 0.7853 (t0) cc_final: 0.7632 (t0) REVERT: G 479 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6780 (m-30) REVERT: G 534 ASP cc_start: 0.8527 (m-30) cc_final: 0.8144 (m-30) REVERT: G 564 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8333 (tppt) REVERT: G 578 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7491 (ttp-110) REVERT: G 593 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7271 (pm20) REVERT: G 602 LEU cc_start: 0.7875 (pp) cc_final: 0.7606 (mt) REVERT: H 795 TYR cc_start: 0.7654 (t80) cc_final: 0.7157 (t80) REVERT: H 802 MET cc_start: 0.5017 (mpt) cc_final: 0.4631 (mpt) REVERT: H 862 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7608 (t) REVERT: H 947 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7034 (ptm) REVERT: H 1049 ASN cc_start: 0.6177 (t0) cc_final: 0.5878 (t0) REVERT: H 1061 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7891 (mpt90) outliers start: 59 outliers final: 24 residues processed: 269 average time/residue: 0.5301 time to fit residues: 163.3511 Evaluate side-chains 214 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain F residue 771 MET 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 130 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 479 ASP Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 105 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 0.0010 chunk 177 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 220 optimal weight: 0.2980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 78 ASN F 911 ASN F1188 GLN G 78 ASN G 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.176322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132796 restraints weight = 21314.986| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.90 r_work: 0.3348 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18777 Z= 0.115 Angle : 0.645 13.220 25571 Z= 0.319 Chirality : 0.047 0.493 2767 Planarity : 0.004 0.046 3360 Dihedral : 5.518 53.962 2773 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.56 % Favored : 93.40 % Rotamer: Outliers : 3.53 % Allowed : 17.85 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.16), residues: 2365 helix: -0.08 (0.28), residues: 345 sheet: -0.89 (0.25), residues: 438 loop : -1.73 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 373 TYR 0.020 0.001 TYR G 711 PHE 0.019 0.002 PHE H 999 TRP 0.012 0.001 TRP G 222 HIS 0.002 0.001 HIS E 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (18651) covalent geometry : angle 0.62295 / 0.31 (25309) SS BOND : bond 0.00305 / 0.20 ( 116) SS BOND : angle 1.22561 / 0.78 ( 232) hydrogen bonds : bond 0.03401 / 2.22 ( 446) hydrogen bonds : angle 4.95771 / 3.35 ( 1163) link_NAG-ASN : bond 0.00772 / 0.41 ( 10) link_NAG-ASN : angle 3.89492 / 2.56 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 192 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 VAL cc_start: 0.8315 (t) cc_final: 0.8100 (m) REVERT: E 217 MET cc_start: 0.2954 (mtp) cc_final: 0.2488 (ppp) REVERT: E 280 MET cc_start: 0.7976 (ttm) cc_final: 0.7653 (tmm) REVERT: E 302 ARG cc_start: 0.7465 (ttm170) cc_final: 0.6478 (ttt-90) REVERT: E 313 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: E 419 GLN cc_start: 0.7634 (pp30) cc_final: 0.7313 (mm110) REVERT: E 466 MET cc_start: 0.8758 (ttt) cc_final: 0.8542 (mtp) REVERT: E 712 ASP cc_start: 0.7223 (t0) cc_final: 0.6823 (OUTLIER) REVERT: E 728 MET cc_start: 0.7715 (tpp) cc_final: 0.7487 (tpt) REVERT: F 864 ASP cc_start: 0.8539 (m-30) cc_final: 0.8188 (m-30) REVERT: F 920 LYS cc_start: 0.5788 (OUTLIER) cc_final: 0.5113 (mtmt) REVERT: F 954 GLU cc_start: 0.8267 (tp30) cc_final: 0.8001 (tp30) REVERT: F 968 LYS cc_start: 0.8032 (mmtm) cc_final: 0.7598 (mtmm) REVERT: F 1049 ASN cc_start: 0.5910 (t0) cc_final: 0.5708 (t0) REVERT: F 1051 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7227 (tmm) REVERT: G 107 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7217 (pp30) REVERT: G 201 GLU cc_start: 0.7390 (mp0) cc_final: 0.6668 (mm-30) REVERT: G 217 MET cc_start: 0.3176 (mtm) cc_final: 0.1974 (pp-130) REVERT: G 373 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7421 (ttm110) REVERT: G 479 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7159 (t0) REVERT: G 564 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8564 (tptt) REVERT: G 578 ARG cc_start: 0.7959 (mtm110) cc_final: 0.7748 (ttp-110) REVERT: G 609 ARG cc_start: 0.8521 (mtp85) cc_final: 0.8280 (mpt-90) REVERT: H 795 TYR cc_start: 0.7582 (t80) cc_final: 0.7114 (t80) REVERT: H 802 MET cc_start: 0.5392 (mpt) cc_final: 0.4906 (mpt) REVERT: H 862 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7735 (t) REVERT: H 930 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: H 936 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7800 (pp) REVERT: H 947 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6855 (ptm) REVERT: H 1049 ASN cc_start: 0.6181 (t0) cc_final: 0.5862 (t0) REVERT: H 1061 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7869 (mpt90) outliers start: 71 outliers final: 32 residues processed: 241 average time/residue: 0.5356 time to fit residues: 146.8578 Evaluate side-chains 214 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 1051 MET 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 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 454 SER 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 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 800 MET Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 930 GLU Chi-restraints excluded: chain H residue 936 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 226 GLN E 393 GLN F1003 GLN F1188 GLN G 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.170776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122866 restraints weight = 30340.849| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.57 r_work: 0.3239 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5015 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= 0.171 Angle : 0.699 11.958 25571 Z= 0.350 Chirality : 0.051 0.524 2767 Planarity : 0.005 0.044 3360 Dihedral : 5.998 57.048 2773 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.32 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.16), residues: 2365 helix: 0.16 (0.28), residues: 341 sheet: -0.65 (0.25), residues: 446 loop : -1.71 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 373 TYR 0.025 0.002 TYR H 897 PHE 0.025 0.002 PHE H 999 TRP 0.011 0.002 TRP G 222 HIS 0.004 0.001 HIS E 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (18651) covalent geometry : angle 0.67640 / 0.34 (25309) SS BOND : bond 0.00385 / 0.25 ( 116) SS BOND : angle 1.45606 / 0.94 ( 232) hydrogen bonds : bond 0.03970 / 2.60 ( 446) hydrogen bonds : angle 5.00737 / 3.38 ( 1163) link_NAG-ASN : bond 0.00976 / 0.51 ( 10) link_NAG-ASN : angle 3.82479 / 2.50 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 195 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 GLN cc_start: 0.7910 (mm-40) cc_final: 0.6344 (pm20) REVERT: E 98 VAL cc_start: 0.8456 (t) cc_final: 0.8248 (m) REVERT: E 217 MET cc_start: 0.3111 (mtp) cc_final: 0.2523 (ppp) REVERT: E 252 LYS cc_start: 0.7484 (ptmt) cc_final: 0.6926 (ptmt) REVERT: E 302 ARG cc_start: 0.7599 (ttm170) cc_final: 0.6474 (ttt-90) REVERT: E 313 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: E 341 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6943 (pt) REVERT: E 346 THR cc_start: 0.7411 (m) cc_final: 0.7072 (p) REVERT: E 347 GLU cc_start: 0.7733 (tp30) cc_final: 0.7512 (tp30) REVERT: E 419 GLN cc_start: 0.7796 (pp30) cc_final: 0.7249 (mm-40) REVERT: F 911 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.7796 (p0) REVERT: F 912 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7836 (mptt) REVERT: F 920 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.5038 (mtmt) REVERT: F 954 GLU cc_start: 0.8348 (tp30) cc_final: 0.8020 (tp30) REVERT: F 1036 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7581 (mptm) REVERT: F 1049 ASN cc_start: 0.6014 (t0) cc_final: 0.5630 (t0) REVERT: F 1051 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7224 (tmm) REVERT: G 107 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7167 (pp30) REVERT: G 265 CYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7217 (m) REVERT: G 501 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7608 (t0) REVERT: G 503 ASP cc_start: 0.4474 (t0) cc_final: 0.4157 (t0) REVERT: G 564 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8431 (tptt) REVERT: G 578 ARG cc_start: 0.7788 (mtm110) cc_final: 0.7417 (ttp-110) REVERT: G 736 MET cc_start: 0.6932 (tpt) cc_final: 0.6650 (tpt) REVERT: H 862 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7829 (t) REVERT: H 930 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: H 947 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6734 (ptm) REVERT: H 1049 ASN cc_start: 0.6228 (t0) cc_final: 0.5859 (t160) REVERT: H 1061 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7822 (mpt90) outliers start: 87 outliers final: 44 residues processed: 256 average time/residue: 0.5348 time to fit residues: 155.4363 Evaluate side-chains 232 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 341 LEU 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 E residue 736 MET 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 911 ASN Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 935 GLU Chi-restraints excluded: chain F residue 1036 LYS 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 41 ASP 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 351 VAL Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 454 SER Chi-restraints excluded: chain G residue 479 ASP Chi-restraints excluded: chain G residue 498 LEU 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 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 927 ILE Chi-restraints excluded: chain H residue 930 GLU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 179 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 78 ASN E 107 GLN G 78 ASN G 313 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.168558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125050 restraints weight = 22785.012| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.90 r_work: 0.3225 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18777 Z= 0.192 Angle : 0.726 12.381 25571 Z= 0.364 Chirality : 0.052 0.620 2767 Planarity : 0.005 0.050 3360 Dihedral : 6.291 59.031 2773 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.86 % Allowed : 17.66 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.16), residues: 2365 helix: -0.03 (0.28), residues: 347 sheet: -0.63 (0.26), residues: 424 loop : -1.67 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 643 TYR 0.024 0.002 TYR G 711 PHE 0.024 0.002 PHE H 999 TRP 0.013 0.002 TRP G 222 HIS 0.005 0.001 HIS E 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (18651) covalent geometry : angle 0.70130 / 0.36 (25309) SS BOND : bond 0.00433 / 0.28 ( 116) SS BOND : angle 1.59672 / 1.02 ( 232) hydrogen bonds : bond 0.04103 / 2.70 ( 446) hydrogen bonds : angle 5.01082 / 3.39 ( 1163) link_NAG-ASN : bond 0.00738 / 0.40 ( 10) link_NAG-ASN : angle 3.88999 / 2.53 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 179 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7552 (mm-40) REVERT: E 154 TYR cc_start: 0.8596 (m-80) cc_final: 0.8309 (m-80) REVERT: E 217 MET cc_start: 0.3166 (mtp) cc_final: 0.2049 (ptt) REVERT: E 252 LYS cc_start: 0.7588 (ptmt) cc_final: 0.7091 (ptmm) REVERT: E 302 ARG cc_start: 0.7808 (ttm170) cc_final: 0.6874 (ttt-90) REVERT: E 313 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: E 341 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7096 (pt) REVERT: E 347 GLU cc_start: 0.7891 (tp30) cc_final: 0.7601 (tp30) REVERT: E 419 GLN cc_start: 0.7886 (pp30) cc_final: 0.7434 (mm110) REVERT: E 483 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: E 543 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: E 597 ARG cc_start: 0.7835 (ptp-110) cc_final: 0.7353 (ptm-80) REVERT: E 620 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6872 (tp30) REVERT: E 712 ASP cc_start: 0.7742 (t0) cc_final: 0.7431 (t0) REVERT: F 793 GLN cc_start: 0.7164 (pp30) cc_final: 0.6795 (tm-30) REVERT: F 911 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8026 (p0) REVERT: F 912 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7844 (mptt) REVERT: F 920 LYS cc_start: 0.5746 (OUTLIER) cc_final: 0.5161 (mtmt) REVERT: F 1036 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7677 (mptm) REVERT: F 1049 ASN cc_start: 0.6047 (t0) cc_final: 0.5792 (t0) REVERT: G 67 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7970 (ptmt) REVERT: G 107 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7223 (pp30) REVERT: G 302 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7818 (tpp-160) REVERT: G 326 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7515 (p) REVERT: G 382 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6550 (pt0) REVERT: G 503 ASP cc_start: 0.4476 (t0) cc_final: 0.4039 (t0) REVERT: G 578 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7627 (ttp-110) REVERT: G 700 ASP cc_start: 0.6406 (t0) cc_final: 0.6131 (p0) REVERT: G 736 MET cc_start: 0.7328 (tpt) cc_final: 0.7061 (tpt) REVERT: H 862 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8045 (t) REVERT: H 947 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6990 (ptm) REVERT: H 1049 ASN cc_start: 0.6335 (t0) cc_final: 0.5985 (t160) REVERT: H 1061 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7867 (mpt90) outliers start: 98 outliers final: 52 residues processed: 248 average time/residue: 0.5107 time to fit residues: 143.6655 Evaluate side-chains 234 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 167 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 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 804 CYS Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 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 41 ASP 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 302 ARG 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 432 CYS Chi-restraints excluded: chain G residue 454 SER Chi-restraints excluded: chain G residue 479 ASP Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 927 ILE Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 123 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 138 optimal weight: 0.0970 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 303 GLN G 78 ASN G 313 GLN ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 952 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.173100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127564 restraints weight = 25091.521| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.22 r_work: 0.3273 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18777 Z= 0.104 Angle : 0.608 11.992 25571 Z= 0.303 Chirality : 0.047 0.538 2767 Planarity : 0.004 0.045 3360 Dihedral : 5.583 54.971 2773 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.24 % Allowed : 19.67 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.17), residues: 2365 helix: 0.12 (0.27), residues: 361 sheet: -0.56 (0.24), residues: 482 loop : -1.54 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 373 TYR 0.025 0.001 TYR G 711 PHE 0.013 0.001 PHE H 878 TRP 0.021 0.001 TRP G 222 HIS 0.003 0.000 HIS F 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (18651) covalent geometry : angle 0.58887 / 0.30 (25309) SS BOND : bond 0.00255 / 0.16 ( 116) SS BOND : angle 1.07404 / 0.68 ( 232) hydrogen bonds : bond 0.03144 / 2.05 ( 446) hydrogen bonds : angle 4.72290 / 3.19 ( 1163) link_NAG-ASN : bond 0.00835 / 0.43 ( 10) link_NAG-ASN : angle 3.75156 / 2.41 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8684 (mtp) cc_final: 0.8365 (mtm) REVERT: E 66 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7503 (mm-40) REVERT: E 107 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7527 (mm110) REVERT: E 217 MET cc_start: 0.3152 (mtp) cc_final: 0.2538 (ppp) REVERT: E 252 LYS cc_start: 0.7548 (ptmt) cc_final: 0.7041 (ptmm) REVERT: E 280 MET cc_start: 0.7975 (ttm) cc_final: 0.7707 (tmm) REVERT: E 302 ARG cc_start: 0.7852 (ttm170) cc_final: 0.6885 (ttt-90) REVERT: E 341 LEU cc_start: 0.7441 (pt) cc_final: 0.7163 (pt) REVERT: E 347 GLU cc_start: 0.8042 (tp30) cc_final: 0.7611 (tp30) REVERT: E 419 GLN cc_start: 0.7849 (pp30) cc_final: 0.7400 (mm110) REVERT: E 500 MET cc_start: 0.8832 (mtt) cc_final: 0.8591 (mtt) REVERT: E 620 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6822 (tp30) REVERT: E 712 ASP cc_start: 0.7367 (t0) cc_final: 0.7062 (t0) REVERT: F 912 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7734 (mptt) REVERT: F 920 LYS cc_start: 0.5640 (OUTLIER) cc_final: 0.5075 (mtpt) REVERT: F 954 GLU cc_start: 0.8438 (tp30) cc_final: 0.8198 (tp30) REVERT: F 1049 ASN cc_start: 0.5937 (t0) cc_final: 0.5635 (t0) REVERT: F 1051 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7402 (tmm) REVERT: G 67 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7843 (ptmm) REVERT: G 108 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7587 (mtp-110) REVERT: G 170 GLU cc_start: 0.7303 (pm20) cc_final: 0.6856 (pm20) REVERT: G 302 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7899 (ttp-170) REVERT: G 347 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: G 363 LEU cc_start: 0.8405 (mp) cc_final: 0.8195 (mp) REVERT: G 503 ASP cc_start: 0.3860 (t0) cc_final: 0.3567 (t70) REVERT: G 578 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7599 (ttp-170) REVERT: G 609 ARG cc_start: 0.8782 (mtp85) cc_final: 0.8378 (mtt-85) REVERT: G 736 MET cc_start: 0.6915 (tpt) cc_final: 0.6603 (tpt) REVERT: H 862 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8031 (t) REVERT: H 947 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6760 (ptm) REVERT: H 1049 ASN cc_start: 0.6285 (t0) cc_final: 0.5939 (t160) REVERT: H 1061 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7971 (mpt90) outliers start: 65 outliers final: 29 residues processed: 231 average time/residue: 0.5348 time to fit residues: 140.1214 Evaluate side-chains 207 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 SER 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 314 SER Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 1051 MET Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain G residue 347 GLU Chi-restraints excluded: chain G residue 432 CYS 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 616 SER Chi-restraints excluded: chain G residue 707 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 188 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 206 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 148 optimal weight: 0.0870 overall best weight: 2.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 78 ASN F 952 HIS G 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.169017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.122001 restraints weight = 30237.096| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.42 r_work: 0.3235 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18777 Z= 0.167 Angle : 0.683 11.699 25571 Z= 0.342 Chirality : 0.050 0.612 2767 Planarity : 0.005 0.056 3360 Dihedral : 5.991 57.766 2773 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.92 % Allowed : 19.52 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.16), residues: 2365 helix: 0.20 (0.28), residues: 347 sheet: -0.47 (0.26), residues: 430 loop : -1.57 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 643 TYR 0.026 0.002 TYR G 711 PHE 0.018 0.002 PHE H 999 TRP 0.020 0.002 TRP G 222 HIS 0.005 0.001 HIS H 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (18651) covalent geometry : angle 0.66018 / 0.33 (25309) SS BOND : bond 0.00376 / 0.24 ( 116) SS BOND : angle 1.43827 / 0.92 ( 232) hydrogen bonds : bond 0.03842 / 2.51 ( 446) hydrogen bonds : angle 4.83832 / 3.28 ( 1163) link_NAG-ASN : bond 0.00729 / 0.39 ( 10) link_NAG-ASN : angle 3.76277 / 2.42 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 176 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7418 (mm110) REVERT: E 217 MET cc_start: 0.3154 (mtp) cc_final: 0.2296 (ptt) REVERT: E 252 LYS cc_start: 0.7618 (ptmt) cc_final: 0.7112 (ptmm) REVERT: E 280 MET cc_start: 0.8019 (ttm) cc_final: 0.7653 (tmm) REVERT: E 302 ARG cc_start: 0.7782 (ttm170) cc_final: 0.6654 (ttt-90) REVERT: E 313 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: E 341 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6917 (pt) REVERT: E 419 GLN cc_start: 0.7911 (pp30) cc_final: 0.7315 (mm-40) REVERT: E 452 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6655 (m-70) REVERT: E 500 MET cc_start: 0.8945 (mtt) cc_final: 0.8699 (mtt) REVERT: E 620 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6841 (tp30) REVERT: E 712 ASP cc_start: 0.7524 (t0) cc_final: 0.7106 (t0) REVERT: F 793 GLN cc_start: 0.7056 (pp30) cc_final: 0.6687 (tm-30) REVERT: F 911 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.7835 (p0) REVERT: F 912 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7798 (mptt) REVERT: F 920 LYS cc_start: 0.5623 (OUTLIER) cc_final: 0.5068 (mtmt) REVERT: F 952 HIS cc_start: 0.6426 (m170) cc_final: 0.6211 (m-70) REVERT: F 1030 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7125 (pt0) REVERT: F 1049 ASN cc_start: 0.5969 (t0) cc_final: 0.5648 (t0) REVERT: G 67 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7831 (ptmt) REVERT: G 107 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7052 (pp30) REVERT: G 170 GLU cc_start: 0.7330 (pm20) cc_final: 0.6916 (pm20) REVERT: G 302 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7847 (ttp-170) REVERT: G 503 ASP cc_start: 0.4349 (t0) cc_final: 0.4030 (t0) REVERT: G 578 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7424 (ttp-110) REVERT: G 609 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8212 (mtt-85) REVERT: G 660 GLN cc_start: 0.6836 (tp40) cc_final: 0.5952 (tp-100) REVERT: G 736 MET cc_start: 0.7088 (tpt) cc_final: 0.6821 (tpt) REVERT: H 862 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8038 (t) REVERT: H 947 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6614 (ptm) REVERT: H 1061 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7823 (mpt90) REVERT: H 1092 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6375 (mp0) outliers start: 79 outliers final: 51 residues processed: 235 average time/residue: 0.5472 time to fit residues: 147.1943 Evaluate side-chains 235 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 169 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 452 HIS Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 661 CYS 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 804 CYS Chi-restraints excluded: chain F residue 822 VAL 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 911 ASN 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 1030 GLN 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 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 302 ARG Chi-restraints excluded: chain G residue 341 LEU 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 454 SER Chi-restraints excluded: chain G residue 480 LEU Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 926 THR Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 978 LEU Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1093 SER Chi-restraints excluded: chain H residue 1124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.9980 chunk 202 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 78 ASN G 78 ASN ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123741 restraints weight = 28762.683| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.30 r_work: 0.3214 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18777 Z= 0.120 Angle : 0.632 13.678 25571 Z= 0.313 Chirality : 0.047 0.556 2767 Planarity : 0.005 0.047 3360 Dihedral : 5.682 55.550 2773 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.24 % Allowed : 20.26 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.17), residues: 2365 helix: 0.10 (0.27), residues: 363 sheet: -0.40 (0.27), residues: 404 loop : -1.50 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 643 TYR 0.026 0.001 TYR G 711 PHE 0.016 0.002 PHE H 999 TRP 0.022 0.001 TRP G 222 HIS 0.003 0.001 HIS F 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (18651) covalent geometry : angle 0.61160 / 0.31 (25309) SS BOND : bond 0.00280 / 0.17 ( 116) SS BOND : angle 1.18624 / 0.75 ( 232) hydrogen bonds : bond 0.03378 / 2.22 ( 446) hydrogen bonds : angle 4.69871 / 3.18 ( 1163) link_NAG-ASN : bond 0.00793 / 0.42 ( 10) link_NAG-ASN : angle 3.69424 / 2.37 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 178 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8759 (mtp) cc_final: 0.8405 (mtm) REVERT: E 107 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7503 (mm110) REVERT: E 217 MET cc_start: 0.3155 (mtp) cc_final: 0.2277 (ptt) REVERT: E 252 LYS cc_start: 0.7610 (ptmt) cc_final: 0.7118 (ptmm) REVERT: E 280 MET cc_start: 0.8046 (ttm) cc_final: 0.7673 (tmm) REVERT: E 302 ARG cc_start: 0.7919 (ttm170) cc_final: 0.6944 (ttt-90) REVERT: E 313 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: E 341 LEU cc_start: 0.7479 (pt) cc_final: 0.7163 (pp) REVERT: E 419 GLN cc_start: 0.7916 (pp30) cc_final: 0.7487 (mm-40) REVERT: E 500 MET cc_start: 0.8841 (mtt) cc_final: 0.8615 (mtt) REVERT: E 620 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6905 (tp30) REVERT: E 674 TYR cc_start: 0.6881 (m-80) cc_final: 0.6669 (m-80) REVERT: E 684 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7490 (tt) REVERT: E 712 ASP cc_start: 0.7443 (t0) cc_final: 0.7097 (t0) REVERT: F 912 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7823 (mptt) REVERT: F 920 LYS cc_start: 0.5643 (OUTLIER) cc_final: 0.5047 (mtmt) REVERT: F 954 GLU cc_start: 0.8513 (tp30) cc_final: 0.8277 (tp30) REVERT: F 1030 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7159 (pt0) REVERT: F 1049 ASN cc_start: 0.5920 (t0) cc_final: 0.5606 (t0) REVERT: F 1051 MET cc_start: 0.8063 (mmm) cc_final: 0.7402 (tmm) REVERT: G 67 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7900 (ptmt) REVERT: G 107 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7176 (pp30) REVERT: G 170 GLU cc_start: 0.7399 (pm20) cc_final: 0.6983 (pm20) REVERT: G 302 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7872 (ttp-170) REVERT: G 578 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7705 (ptm-80) REVERT: G 609 ARG cc_start: 0.8787 (mtp85) cc_final: 0.8390 (mtt-85) REVERT: G 660 GLN cc_start: 0.6938 (tp40) cc_final: 0.6128 (tp40) REVERT: G 736 MET cc_start: 0.7123 (tpt) cc_final: 0.6911 (tpt) REVERT: H 862 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8120 (t) REVERT: H 947 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6568 (ptm) REVERT: H 949 ASP cc_start: 0.7703 (t0) cc_final: 0.7490 (t70) REVERT: H 1061 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7959 (mpt90) outliers start: 65 outliers final: 43 residues processed: 226 average time/residue: 0.5201 time to fit residues: 133.6736 Evaluate side-chains 225 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 661 CYS 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 804 CYS Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 862 VAL 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 1030 GLN Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 364 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 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 926 THR Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 1 optimal weight: 6.9990 chunk 162 optimal weight: 0.1980 chunk 179 optimal weight: 30.0000 chunk 215 optimal weight: 0.0010 chunk 92 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 112 optimal weight: 0.0470 chunk 193 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 78 ASN F 911 ASN F 952 HIS F1003 GLN G 78 ASN ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.175010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129986 restraints weight = 23254.219| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.04 r_work: 0.3313 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18777 Z= 0.100 Angle : 0.605 13.525 25571 Z= 0.298 Chirality : 0.046 0.504 2767 Planarity : 0.004 0.046 3360 Dihedral : 5.342 58.517 2773 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.84 % Allowed : 20.65 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2365 helix: 0.33 (0.28), residues: 363 sheet: -0.23 (0.26), residues: 434 loop : -1.38 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 373 TYR 0.027 0.001 TYR G 711 PHE 0.012 0.001 PHE E 76 TRP 0.026 0.001 TRP G 222 HIS 0.003 0.000 HIS F 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (18651) covalent geometry : angle 0.58755 / 0.29 (25309) SS BOND : bond 0.00283 / 0.15 ( 116) SS BOND : angle 1.01224 / 0.65 ( 232) hydrogen bonds : bond 0.03008 / 1.98 ( 446) hydrogen bonds : angle 4.62898 / 3.13 ( 1163) link_NAG-ASN : bond 0.00810 / 0.42 ( 10) link_NAG-ASN : angle 3.59590 / 2.29 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8691 (mtp) cc_final: 0.8378 (mtm) REVERT: E 107 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7475 (mm110) REVERT: E 217 MET cc_start: 0.3056 (mtp) cc_final: 0.2522 (ppp) REVERT: E 280 MET cc_start: 0.7914 (ttm) cc_final: 0.7575 (tmm) REVERT: E 302 ARG cc_start: 0.7637 (ttm170) cc_final: 0.6761 (ttt-90) REVERT: E 324 ARG cc_start: 0.7488 (ttt-90) cc_final: 0.7062 (ttt180) REVERT: E 341 LEU cc_start: 0.7383 (pt) cc_final: 0.7078 (pp) REVERT: E 419 GLN cc_start: 0.7855 (pp30) cc_final: 0.7474 (mm-40) REVERT: E 620 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6755 (tp30) REVERT: E 644 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5728 (mm-30) REVERT: E 674 TYR cc_start: 0.6850 (m-80) cc_final: 0.6640 (m-80) REVERT: E 685 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: E 712 ASP cc_start: 0.7281 (t0) cc_final: 0.6953 (t0) REVERT: F 912 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7612 (mptt) REVERT: F 952 HIS cc_start: 0.6077 (m170) cc_final: 0.5855 (m-70) REVERT: F 954 GLU cc_start: 0.8400 (tp30) cc_final: 0.8089 (tp30) REVERT: F 1049 ASN cc_start: 0.5879 (t0) cc_final: 0.5646 (t0) REVERT: F 1051 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7374 (tmm) REVERT: F 1185 GLU cc_start: 0.6679 (mp0) cc_final: 0.6477 (mp0) REVERT: G 107 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7107 (pp30) REVERT: G 170 GLU cc_start: 0.7378 (pm20) cc_final: 0.6969 (pm20) REVERT: G 201 GLU cc_start: 0.7639 (mp0) cc_final: 0.7036 (mm-30) REVERT: G 265 CYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7162 (m) REVERT: G 302 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7820 (ttp-170) REVERT: G 387 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7959 (mt-10) REVERT: G 503 ASP cc_start: 0.4033 (t0) cc_final: 0.3804 (t0) REVERT: G 578 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7696 (ptm-80) REVERT: G 609 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8321 (mtt-85) REVERT: G 660 GLN cc_start: 0.6865 (tp40) cc_final: 0.6054 (tp-100) REVERT: G 736 MET cc_start: 0.6654 (tpt) cc_final: 0.6431 (tpt) REVERT: H 862 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8045 (t) REVERT: H 947 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6443 (ptm) REVERT: H 1061 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7947 (mpt90) REVERT: H 1128 GLN cc_start: 0.7914 (tp40) cc_final: 0.7283 (tp40) outliers start: 57 outliers final: 32 residues processed: 229 average time/residue: 0.5441 time to fit residues: 141.2921 Evaluate side-chains 221 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 661 CYS Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain F residue 804 CYS Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 1051 MET 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 302 ARG Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 454 SER Chi-restraints excluded: chain G residue 480 LEU Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 221 optimal weight: 0.0060 chunk 186 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 192 optimal weight: 0.2980 chunk 210 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 78 ASN F 911 ASN F1168 GLN G 78 ASN ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.174282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129155 restraints weight = 30522.358| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.42 r_work: 0.3273 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 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 = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18777 Z= 0.103 Angle : 0.612 13.466 25571 Z= 0.300 Chirality : 0.046 0.504 2767 Planarity : 0.004 0.045 3360 Dihedral : 5.315 56.778 2773 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.75 % Allowed : 20.99 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.17), residues: 2365 helix: 0.43 (0.28), residues: 361 sheet: -0.10 (0.27), residues: 414 loop : -1.36 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 373 TYR 0.028 0.001 TYR G 711 PHE 0.013 0.001 PHE H 878 TRP 0.028 0.001 TRP G 222 HIS 0.003 0.001 HIS F 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (18651) covalent geometry : angle 0.59308 / 0.29 (25309) SS BOND : bond 0.00236 / 0.15 ( 116) SS BOND : angle 1.13990 / 0.78 ( 232) hydrogen bonds : bond 0.03143 / 2.06 ( 446) hydrogen bonds : angle 4.58169 / 3.10 ( 1163) link_NAG-ASN : bond 0.00785 / 0.41 ( 10) link_NAG-ASN : angle 3.53484 / 2.25 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8670.47 seconds wall clock time: 147 minutes 40.23 seconds (8860.23 seconds total)