Starting phenix.real_space_refine on Sat Mar 7 09:29:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zwh_14998/03_2026/7zwh_14998_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zwh_14998/03_2026/7zwh_14998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zwh_14998/03_2026/7zwh_14998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zwh_14998/03_2026/7zwh_14998.map" model { file = "/net/cci-nas-00/data/ceres_data/7zwh_14998/03_2026/7zwh_14998_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zwh_14998/03_2026/7zwh_14998_neut_trim.cif" } resolution = 3.2 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= 0.003 sd= 0.027 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 272 5.16 5 C 12862 2.51 5 N 3570 2.21 5 O 4020 1.98 5 H 19501 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40231 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 16768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 16768 Classifications: {'peptide': 1131} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1070} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 16765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 16765 Classifications: {'peptide': 1131} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1070} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3251 Classifications: {'peptide': 199} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3251 Classifications: {'peptide': 199} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.50, per 1000 atoms: 0.16 Number of scatterers: 40231 At special positions: 0 Unit cell: (176.023, 127.679, 172.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 272 16.00 O 4020 8.00 N 3570 7.00 C 12862 6.00 H 19501 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=110, symmetry=0 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 225 " - pdb=" SG CYS D 250 " distance=2.03 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 263 " distance=2.03 Simple disulfide: pdb=" SG CYS D 265 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 295 " - pdb=" SG CYS D 329 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 325 " distance=2.03 Simple disulfide: pdb=" SG CYS D 308 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 312 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 342 " distance=2.03 Simple disulfide: pdb=" SG CYS D 350 " - pdb=" SG CYS D 372 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 384 " distance=2.03 Simple disulfide: pdb=" SG CYS D 370 " - pdb=" SG CYS D 379 " distance=2.03 Simple disulfide: pdb=" SG CYS D 388 " - pdb=" SG CYS D 524 " distance=2.03 Simple disulfide: pdb=" SG CYS D 410 " - pdb=" SG CYS D 559 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 440 " distance=2.03 Simple disulfide: pdb=" SG CYS D 570 " - pdb=" SG CYS D 613 " distance=2.03 Simple disulfide: pdb=" SG CYS D 584 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 633 " distance=2.03 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 621 " distance=2.03 Simple disulfide: pdb=" SG CYS D 623 " - pdb=" SG CYS D 648 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 687 " distance=2.03 Simple disulfide: pdb=" SG CYS D 661 " - pdb=" SG CYS D 683 " distance=2.03 Simple disulfide: pdb=" SG CYS D 665 " - pdb=" SG CYS D 679 " distance=2.03 Simple disulfide: pdb=" SG CYS D 669 " - pdb=" SG CYS D 707 " distance=2.03 Simple disulfide: pdb=" SG CYS D 689 " - pdb=" SG CYS D 701 " distance=2.02 Simple disulfide: pdb=" SG CYS D 709 " - pdb=" SG CYS D 731 " distance=2.02 Simple disulfide: pdb=" SG CYS D 729 " - pdb=" SG CYS D 738 " distance=2.03 Simple disulfide: pdb=" SG CYS D 776 " - pdb=" SG CYS D 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 788 " - pdb=" SG CYS D 799 " distance=2.04 Simple disulfide: pdb=" SG CYS D 792 " - pdb=" SG CYS D 827 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 821 " distance=2.03 Simple disulfide: pdb=" SG CYS D 829 " - pdb=" SG CYS D 851 " distance=2.03 Simple disulfide: pdb=" SG CYS D 846 " - pdb=" SG CYS D 863 " distance=2.03 Simple disulfide: pdb=" SG CYS D 849 " - pdb=" SG CYS D 858 " distance=2.03 Simple disulfide: pdb=" SG CYS D 867 " - pdb=" SG CYS D 996 " distance=2.02 Simple disulfide: pdb=" SG CYS D 889 " - pdb=" SG CYS D1031 " distance=2.03 Simple disulfide: pdb=" SG CYS D 898 " - pdb=" SG CYS D 993 " distance=2.03 Simple disulfide: pdb=" SG CYS D 914 " - pdb=" SG CYS D 921 " distance=2.03 Simple disulfide: pdb=" SG CYS D1046 " - pdb=" SG CYS D1089 " distance=2.03 Simple disulfide: pdb=" SG CYS D1060 " - pdb=" SG CYS D1084 " distance=2.03 Simple disulfide: pdb=" SG CYS D1071 " - pdb=" SG CYS D1111 " distance=2.03 Simple disulfide: pdb=" SG CYS D1091 " - pdb=" SG CYS D1099 " distance=2.03 Simple disulfide: pdb=" SG CYS D1097 " - pdb=" SG CYS E1097 " distance=2.03 Simple disulfide: pdb=" SG CYS D1101 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D1130 " - pdb=" SG CYS D1173 " distance=2.03 Simple disulfide: pdb=" SG CYS D1142 " - pdb=" SG CYS E1142 " distance=2.03 Simple disulfide: pdb=" SG CYS D1149 " - pdb=" SG CYS D1169 " distance=2.03 Simple disulfide: pdb=" SG CYS D1153 " - pdb=" SG CYS D1165 " distance=2.03 Simple disulfide: pdb=" SG CYS D1157 " - pdb=" SG CYS D1196 " distance=2.03 Simple disulfide: pdb=" SG CYS D1177 " - pdb=" SG CYS D1190 " distance=2.03 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=2.03 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=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 440 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.03 Simple disulfide: pdb=" SG CYS E 595 " - pdb=" SG CYS E 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 615 " - pdb=" SG CYS E 621 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 689 " - pdb=" SG CYS E 701 " distance=2.03 Simple disulfide: pdb=" SG CYS E 709 " - pdb=" SG CYS E 731 " distance=2.03 Simple disulfide: pdb=" SG CYS E 729 " - pdb=" SG CYS E 738 " distance=2.03 Simple disulfide: pdb=" SG CYS E 776 " - pdb=" SG CYS E 804 " distance=2.03 Simple disulfide: pdb=" SG CYS E 788 " - pdb=" SG CYS E 799 " distance=2.03 Simple disulfide: pdb=" SG CYS E 792 " - pdb=" SG CYS E 827 " distance=2.03 Simple disulfide: pdb=" SG CYS E 810 " - pdb=" SG CYS E 821 " distance=2.03 Simple disulfide: pdb=" SG CYS E 829 " - pdb=" SG CYS E 851 " distance=2.03 Simple disulfide: pdb=" SG CYS E 846 " - pdb=" SG CYS E 863 " distance=2.03 Simple disulfide: pdb=" SG CYS E 849 " - pdb=" SG CYS E 858 " distance=2.03 Simple disulfide: pdb=" SG CYS E 867 " - pdb=" SG CYS E 996 " distance=2.02 Simple disulfide: pdb=" SG CYS E 889 " - pdb=" SG CYS E1031 " distance=2.03 Simple disulfide: pdb=" SG CYS E 898 " - pdb=" SG CYS E 993 " distance=2.03 Simple disulfide: pdb=" SG CYS E 914 " - pdb=" SG CYS E 921 " distance=2.03 Simple disulfide: pdb=" SG CYS E1046 " - pdb=" SG CYS E1089 " distance=2.03 Simple disulfide: pdb=" SG CYS E1060 " - pdb=" SG CYS E1084 " distance=2.03 Simple disulfide: pdb=" SG CYS E1071 " - pdb=" SG CYS E1111 " distance=2.03 Simple disulfide: pdb=" SG CYS E1091 " - pdb=" SG CYS E1099 " distance=2.03 Simple disulfide: pdb=" SG CYS E1101 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E1130 " - pdb=" SG CYS E1173 " distance=2.03 Simple disulfide: pdb=" SG CYS E1149 " - pdb=" SG CYS E1169 " distance=2.03 Simple disulfide: pdb=" SG CYS E1153 " - pdb=" SG CYS E1165 " distance=2.03 Simple disulfide: pdb=" SG CYS E1157 " - pdb=" SG CYS E1196 " distance=2.03 Simple disulfide: pdb=" SG CYS E1177 " - pdb=" SG CYS E1190 " distance=2.03 Simple disulfide: pdb=" SG CYS G1272 " - pdb=" SG CYS G1458 " distance=2.04 Simple disulfide: pdb=" SG CYS H1272 " - pdb=" SG CYS H1458 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 1 " - " ASN D 99 " " NAG B 1 " - " ASN E 99 " " NAG D1202 " - " ASN D1147 " " NAG E1202 " - " ASN E1147 " " NAG E1204 " - " ASN E 666 " Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 38 sheets defined 23.9% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 243 through 257 removed outlier: 4.103A pdb=" N GLU D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'D' and resid 513 through 517 Processing helix chain 'D' and resid 531 through 536 removed outlier: 3.538A pdb=" N ASP D 534 " --> pdb=" O GLN D 531 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE D 535 " --> pdb=" O GLY D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 553 removed outlier: 3.763A pdb=" N TRP D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 575 Proline residue: D 574 - end of helix Processing helix chain 'D' and resid 576 through 585 Processing helix chain 'D' and resid 586 through 591 Proline residue: D 590 - end of helix Processing helix chain 'D' and resid 592 through 597 removed outlier: 4.039A pdb=" N ARG D 597 " --> pdb=" O GLU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 615 Processing helix chain 'D' and resid 617 through 637 Processing helix chain 'D' and resid 668 through 674 Processing helix chain 'D' and resid 985 through 989 Processing helix chain 'D' and resid 1003 through 1007 removed outlier: 4.222A pdb=" N LEU D1007 " --> pdb=" O ASN D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1024 removed outlier: 3.517A pdb=" N PHE D1021 " --> pdb=" O ASP D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1043 through 1048 removed outlier: 3.929A pdb=" N ASN D1048 " --> pdb=" O ALA D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1060 Processing helix chain 'D' and resid 1061 through 1064 Processing helix chain 'D' and resid 1065 through 1073 removed outlier: 4.052A pdb=" N ASP D1070 " --> pdb=" O ASP D1066 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N CYS D1071 " --> pdb=" O VAL D1067 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D1073 " --> pdb=" O GLN D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1086 Processing helix chain 'D' and resid 1097 through 1114 removed outlier: 3.957A pdb=" N THR D1103 " --> pdb=" O CYS D1099 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D1104 " --> pdb=" O PHE D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1130 through 1134 removed outlier: 3.944A pdb=" N ASN D1134 " --> pdb=" O CYS D1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1130 through 1134' Processing helix chain 'E' and resid 152 through 155 Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.578A pdb=" N ARG E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 Processing helix chain 'E' and resid 260 through 263 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 513 through 517 Processing helix chain 'E' and resid 531 through 536 removed outlier: 3.951A pdb=" N PHE E 535 " --> pdb=" O GLY E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 553 removed outlier: 3.507A pdb=" N PHE E 549 " --> pdb=" O ARG E 545 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP E 553 " --> pdb=" O PHE E 549 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 592 through 597 removed outlier: 4.197A pdb=" N ARG E 597 " --> pdb=" O GLU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 613 Processing helix chain 'E' and resid 617 through 635 Processing helix chain 'E' and resid 669 through 674 Processing helix chain 'E' and resid 791 through 796 removed outlier: 3.809A pdb=" N ASP E 796 " --> pdb=" O CYS E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 825 through 827 No H-bonds generated for 'chain 'E' and resid 825 through 827' Processing helix chain 'E' and resid 985 through 989 Processing helix chain 'E' and resid 1003 through 1008 removed outlier: 3.545A pdb=" N ASP E1006 " --> pdb=" O GLN E1003 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU E1007 " --> pdb=" O ASN E1004 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR E1008 " --> pdb=" O ASN E1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1003 through 1008' Processing helix chain 'E' and resid 1017 through 1025 removed outlier: 3.630A pdb=" N SER E1024 " --> pdb=" O ASP E1020 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TRP E1025 " --> pdb=" O PHE E1021 " (cutoff:3.500A) Processing helix chain 'E' and resid 1050 through 1060 Processing helix chain 'E' and resid 1061 through 1064 Processing helix chain 'E' and resid 1065 through 1075 removed outlier: 4.250A pdb=" N ASP E1070 " --> pdb=" O ASP E1066 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N CYS E1071 " --> pdb=" O VAL E1067 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E1073 " --> pdb=" O GLN E1069 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU E1074 " --> pdb=" O ASP E1070 " (cutoff:3.500A) Processing helix chain 'E' and resid 1077 through 1086 Processing helix chain 'E' and resid 1097 through 1114 removed outlier: 4.215A pdb=" N CYS E1101 " --> pdb=" O CYS E1097 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR E1103 " --> pdb=" O CYS E1099 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS E1114 " --> pdb=" O VAL E1110 " (cutoff:3.500A) Processing helix chain 'E' and resid 1130 through 1134 Processing helix chain 'E' and resid 1192 through 1196 Processing helix chain 'G' and resid 1289 through 1305 Processing helix chain 'G' and resid 1336 through 1346 Processing helix chain 'G' and resid 1356 through 1367 Processing helix chain 'G' and resid 1390 through 1394 Processing helix chain 'G' and resid 1396 through 1407 Processing helix chain 'G' and resid 1426 through 1431 Processing helix chain 'G' and resid 1443 through 1460 removed outlier: 4.084A pdb=" N GLU G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G1448 " --> pdb=" O ASP G1444 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP G1451 " --> pdb=" O GLU G1447 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU G1452 " --> pdb=" O GLN G1448 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G1460 " --> pdb=" O TYR G1456 " (cutoff:3.500A) Processing helix chain 'H' and resid 1289 through 1305 Processing helix chain 'H' and resid 1336 through 1346 Processing helix chain 'H' and resid 1356 through 1367 Processing helix chain 'H' and resid 1390 through 1394 Processing helix chain 'H' and resid 1396 through 1407 Processing helix chain 'H' and resid 1426 through 1431 Processing helix chain 'H' and resid 1443 through 1460 removed outlier: 4.084A pdb=" N GLU H1447 " --> pdb=" O VAL H1443 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN H1448 " --> pdb=" O ASP H1444 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP H1451 " --> pdb=" O GLU H1447 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU H1452 " --> pdb=" O GLN H1448 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU H1460 " --> pdb=" O TYR H1456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'D' and resid 59 through 62 removed outlier: 6.808A pdb=" N ILE D 72 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER D 83 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN D 77 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 119 through 122 Processing sheet with id=AA4, first strand: chain 'D' and resid 302 through 305 removed outlier: 4.048A pdb=" N CYS D 304 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL D 326 " --> pdb=" O CYS D 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 352 Processing sheet with id=AA7, first strand: chain 'D' and resid 386 through 387 Processing sheet with id=AA8, first strand: chain 'D' and resid 411 through 413 removed outlier: 6.561A pdb=" N VAL D 426 " --> pdb=" O VAL D 444 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D 444 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU D 428 " --> pdb=" O ARG D 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 722 through 724 removed outlier: 3.840A pdb=" N THR D 727 " --> pdb=" O ASP D 724 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET D 728 " --> pdb=" O THR D 739 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 829 through 831 Processing sheet with id=AB2, first strand: chain 'D' and resid 841 through 844 Processing sheet with id=AB3, first strand: chain 'D' and resid 865 through 868 Processing sheet with id=AB4, first strand: chain 'D' and resid 874 through 876 Processing sheet with id=AB5, first strand: chain 'D' and resid 892 through 895 Processing sheet with id=AB6, first strand: chain 'D' and resid 911 through 912 removed outlier: 3.737A pdb=" N LYS D 922 " --> pdb=" O LYS D 912 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 936 through 937 Processing sheet with id=AB8, first strand: chain 'D' and resid 1135 through 1136 Processing sheet with id=AB9, first strand: chain 'D' and resid 1144 through 1147 Processing sheet with id=AC1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC2, first strand: chain 'E' and resid 59 through 60 removed outlier: 5.969A pdb=" N GLN E 77 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG E 81 " --> pdb=" O GLN E 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 120 through 122 Processing sheet with id=AC4, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AC5, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AC6, first strand: chain 'E' and resid 370 through 373 Processing sheet with id=AC7, first strand: chain 'E' and resid 411 through 416 removed outlier: 7.129A pdb=" N ILE E 425 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL E 426 " --> pdb=" O VAL E 444 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL E 444 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU E 428 " --> pdb=" O ARG E 442 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 465 through 466 Processing sheet with id=AC9, first strand: chain 'E' and resid 483 through 484 removed outlier: 3.620A pdb=" N GLN E 483 " --> pdb=" O ARG E 491 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 728 through 729 removed outlier: 3.587A pdb=" N MET E 728 " --> pdb=" O THR E 739 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 814 through 815 removed outlier: 3.517A pdb=" N VAL E 815 " --> pdb=" O VAL E 822 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 829 through 830 Processing sheet with id=AD4, first strand: chain 'E' and resid 841 through 842 Processing sheet with id=AD5, first strand: chain 'E' and resid 866 through 868 Processing sheet with id=AD6, first strand: chain 'E' and resid 874 through 876 Processing sheet with id=AD7, first strand: chain 'E' and resid 892 through 895 removed outlier: 3.530A pdb=" N VAL E 894 " --> pdb=" O ILE E 907 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 911 through 912 removed outlier: 3.525A pdb=" N LYS E 922 " --> pdb=" O LYS E 912 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 1145 through 1147 Processing sheet with id=AE1, first strand: chain 'G' and resid 1325 through 1329 removed outlier: 4.060A pdb=" N GLU G1320 " --> pdb=" O HIS G1326 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL G1318 " --> pdb=" O TYR G1328 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G1282 " --> pdb=" O VAL G1319 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR G1321 " --> pdb=" O LEU G1282 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP G1277 " --> pdb=" O ILE G1380 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEU G1382 " --> pdb=" O ASP G1277 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL G1279 " --> pdb=" O LEU G1382 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU G1384 " --> pdb=" O VAL G1279 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU G1281 " --> pdb=" O LEU G1384 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG G1379 " --> pdb=" O ILE G1410 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 1325 through 1329 removed outlier: 4.059A pdb=" N GLU H1320 " --> pdb=" O HIS H1326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL H1318 " --> pdb=" O TYR H1328 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU H1282 " --> pdb=" O VAL H1319 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR H1321 " --> pdb=" O LEU H1282 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP H1277 " --> pdb=" O ILE H1380 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEU H1382 " --> pdb=" O ASP H1277 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL H1279 " --> pdb=" O LEU H1382 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU H1384 " --> pdb=" O VAL H1279 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU H1281 " --> pdb=" O LEU H1384 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG H1379 " --> pdb=" O ILE H1410 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1251 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: 9.29 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 19497 1.04 - 1.24: 2784 1.24 - 1.44: 6318 1.44 - 1.64: 11750 1.64 - 1.84: 320 Bond restraints: 40669 Sorted by residual: bond pdb=" N SER E 31 " pdb=" CA SER E 31 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N SER D 31 " pdb=" CA SER D 31 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N SER E 31 " pdb=" H SER E 31 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" N SER D 31 " pdb=" H SER D 31 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG E1204 " pdb=" O5 NAG E1204 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 40664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.55: 73254 7.55 - 15.11: 1 15.11 - 22.66: 0 22.66 - 30.21: 0 30.21 - 37.77: 3 Bond angle restraints: 73258 Sorted by residual: angle pdb=" N MET D 111 " pdb=" CA MET D 111 " pdb=" HA MET D 111 " ideal model delta sigma weight residual 110.00 72.23 37.77 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C MET D 111 " pdb=" CA MET D 111 " pdb=" HA MET D 111 " ideal model delta sigma weight residual 110.00 78.04 31.96 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CB MET D 111 " pdb=" CA MET D 111 " pdb=" HA MET D 111 " ideal model delta sigma weight residual 109.00 77.39 31.61 3.00e+00 1.11e-01 1.11e+02 angle pdb=" N MET D 111 " pdb=" CA MET D 111 " pdb=" C MET D 111 " ideal model delta sigma weight residual 109.81 119.31 -9.50 2.21e+00 2.05e-01 1.85e+01 angle pdb=" N GLU E 644 " pdb=" CA GLU E 644 " pdb=" C GLU E 644 " ideal model delta sigma weight residual 108.13 111.17 -3.04 9.00e-01 1.23e+00 1.14e+01 ... (remaining 73253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 17827 21.69 - 43.38: 1520 43.38 - 65.07: 425 65.07 - 86.76: 71 86.76 - 108.45: 22 Dihedral angle restraints: 19865 sinusoidal: 10937 harmonic: 8928 Sorted by residual: dihedral pdb=" CB CYS D 432 " pdb=" SG CYS D 432 " pdb=" SG CYS D 440 " pdb=" CB CYS D 440 " ideal model delta sinusoidal sigma weight residual -86.00 -173.73 87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS D1149 " pdb=" SG CYS D1149 " pdb=" SG CYS D1169 " pdb=" CB CYS D1169 " ideal model delta sinusoidal sigma weight residual 93.00 -179.56 -87.44 1 1.00e+01 1.00e-02 9.17e+01 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 -86.00 1.42 -87.42 1 1.00e+01 1.00e-02 9.17e+01 ... (remaining 19862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2981 0.092 - 0.185: 168 0.185 - 0.277: 2 0.277 - 0.369: 1 0.369 - 0.461: 1 Chirality restraints: 3153 Sorted by residual: chirality pdb=" CA MET D 111 " pdb=" N MET D 111 " pdb=" C MET D 111 " pdb=" CB MET D 111 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" C1 NAG E1204 " pdb=" ND2 ASN E 666 " pdb=" C2 NAG E1204 " pdb=" O5 NAG E1204 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 3150 not shown) Planarity restraints: 6293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 642 " 0.016 2.00e-02 2.50e+03 9.21e-03 3.39e+00 pdb=" CG TRP E 642 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP E 642 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP E 642 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 642 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 642 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 642 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 642 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 642 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 642 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP E 642 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP E 642 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP E 642 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 642 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 642 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP E 642 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 702 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO D 703 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 703 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 703 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG G1426 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C ARG G1426 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG G1426 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU G1427 " -0.009 2.00e-02 2.50e+03 ... (remaining 6290 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1420 2.12 - 2.74: 72789 2.74 - 3.36: 117313 3.36 - 3.98: 148190 3.98 - 4.60: 228637 Nonbonded interactions: 568349 Sorted by model distance: nonbonded pdb=" O THR E 668 " pdb=" H SER E 671 " model vdw 1.502 2.450 nonbonded pdb="HD21 ASN E 528 " pdb=" OD2 ASP E 533 " model vdw 1.508 2.450 nonbonded pdb=" OD1 ASP G1283 " pdb=" H SER G1285 " model vdw 1.526 2.450 nonbonded pdb=" OD1 ASP H1283 " pdb=" H SER H1285 " model vdw 1.526 2.450 nonbonded pdb=" O GLN D 890 " pdb=" H VAL D1027 " model vdw 1.549 2.450 ... (remaining 568344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'D' and (resid 31 through 394 or (resid 395 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 396 through 565 or (resid 566 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2) \ ) or resid 567 through 665 or (resid 666 and (name N or name CA or name C or nam \ e O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name H \ B2 or name HB3 or name HD21)) or resid 667 through 1046 or (resid 1047 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 1048 through 1207)) selection = (chain 'E' and (resid 31 through 237 or (resid 238 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 239 through 1207)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 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: 0.240 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.720 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.003 0.034 21287 Z= 0.158 Angle : 0.582 9.501 28925 Z= 0.295 Chirality : 0.042 0.461 3153 Planarity : 0.003 0.045 3772 Dihedral : 17.637 108.446 8038 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.58 % Favored : 84.34 % Rotamer: Outliers : 0.26 % Allowed : 23.37 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.45 (0.16), residues: 2644 helix: 0.78 (0.25), residues: 462 sheet: -2.93 (0.25), residues: 406 loop : -2.08 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 507 TYR 0.010 0.001 TYR E 185 PHE 0.011 0.001 PHE E1100 TRP 0.029 0.001 TRP E 642 HIS 0.005 0.001 HIS E 556 Details of bonding type rmsd covalent geometry : bond 0.00345 (21168) covalent geometry : angle 0.57490 (28678) SS BOND : bond 0.00314 ( 110) SS BOND : angle 1.01586 ( 220) hydrogen bonds : bond 0.20230 ( 492) hydrogen bonds : angle 7.47294 ( 1251) link_BETA1-4 : bond 0.00193 ( 4) link_BETA1-4 : angle 1.46070 ( 12) link_NAG-ASN : bond 0.00627 ( 5) link_NAG-ASN : angle 2.24387 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 280 MET cc_start: 0.8353 (tmm) cc_final: 0.8019 (tmm) REVERT: E 771 MET cc_start: -0.0491 (ptt) cc_final: -0.1328 (tmm) outliers start: 6 outliers final: 3 residues processed: 156 average time/residue: 0.3121 time to fit residues: 77.7113 Evaluate side-chains 119 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 1156 THR Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.2980 chunk 111 optimal weight: 8.9990 overall best weight: 4.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 817 HIS D 890 GLN E 104 GLN E 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.052572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.043544 restraints weight = 609675.128| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 6.45 r_work: 0.3209 rms_B_bonded: 5.87 restraints_weight: 2.0000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21287 Z= 0.159 Angle : 0.613 8.362 28925 Z= 0.317 Chirality : 0.042 0.438 3153 Planarity : 0.004 0.043 3772 Dihedral : 7.043 75.557 3187 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.09 % Favored : 84.80 % Rotamer: Outliers : 1.82 % Allowed : 23.37 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.54 (0.16), residues: 2644 helix: 0.38 (0.24), residues: 494 sheet: -2.82 (0.25), residues: 424 loop : -2.11 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.015 0.001 TYR D 185 PHE 0.018 0.001 PHE H1397 TRP 0.010 0.001 TRP D 642 HIS 0.006 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00334 (21168) covalent geometry : angle 0.60605 (28678) SS BOND : bond 0.00310 ( 110) SS BOND : angle 0.92134 ( 220) hydrogen bonds : bond 0.04502 ( 492) hydrogen bonds : angle 6.01021 ( 1251) link_BETA1-4 : bond 0.00342 ( 4) link_BETA1-4 : angle 2.55500 ( 12) link_NAG-ASN : bond 0.00594 ( 5) link_NAG-ASN : angle 2.23566 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 280 MET cc_start: 0.9109 (tmm) cc_final: 0.8351 (tmm) REVERT: E 771 MET cc_start: 0.6237 (ptt) cc_final: 0.4333 (tmm) REVERT: E 800 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.4282 (ttm) outliers start: 42 outliers final: 23 residues processed: 158 average time/residue: 0.2889 time to fit residues: 73.8802 Evaluate side-chains 134 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 325 CYS Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 799 CYS Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 1031 CYS Chi-restraints excluded: chain D residue 1097 CYS Chi-restraints excluded: chain D residue 1153 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 310 ARG Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 800 MET Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1017 ASP Chi-restraints excluded: chain E residue 1047 HIS Chi-restraints excluded: chain E residue 1165 CYS Chi-restraints excluded: chain G residue 1277 ASP Chi-restraints excluded: chain H residue 1268 HIS Chi-restraints excluded: chain H residue 1277 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 183 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 192 optimal weight: 30.0000 chunk 168 optimal weight: 0.1980 chunk 126 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.052308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.043217 restraints weight = 609980.988| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 6.64 r_work: 0.3207 rms_B_bonded: 5.88 restraints_weight: 2.0000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21287 Z= 0.139 Angle : 0.577 9.053 28925 Z= 0.295 Chirality : 0.041 0.435 3153 Planarity : 0.004 0.044 3772 Dihedral : 5.831 56.654 3183 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.96 % Favored : 85.89 % Rotamer: Outliers : 1.56 % Allowed : 23.68 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.53 (0.16), residues: 2644 helix: 0.36 (0.24), residues: 486 sheet: -2.81 (0.24), residues: 424 loop : -2.09 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.016 0.001 TYR G1321 PHE 0.016 0.001 PHE H1397 TRP 0.010 0.001 TRP D 642 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00300 (21168) covalent geometry : angle 0.56478 (28678) SS BOND : bond 0.00305 ( 110) SS BOND : angle 1.32341 ( 220) hydrogen bonds : bond 0.04317 ( 492) hydrogen bonds : angle 5.79121 ( 1251) link_BETA1-4 : bond 0.00395 ( 4) link_BETA1-4 : angle 2.04366 ( 12) link_NAG-ASN : bond 0.00516 ( 5) link_NAG-ASN : angle 1.97833 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 280 MET cc_start: 0.9279 (ppp) cc_final: 0.9019 (ppp) REVERT: E 280 MET cc_start: 0.9150 (tmm) cc_final: 0.8402 (tmm) REVERT: E 320 MET cc_start: 0.9042 (ppp) cc_final: 0.8703 (ppp) REVERT: E 800 MET cc_start: 0.5306 (ttm) cc_final: 0.4346 (ttm) REVERT: G 1385 MET cc_start: 0.8009 (ptp) cc_final: 0.7758 (ptm) outliers start: 36 outliers final: 31 residues processed: 145 average time/residue: 0.3346 time to fit residues: 76.9690 Evaluate side-chains 141 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 325 CYS Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 799 CYS Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 1009 SER Chi-restraints excluded: chain D residue 1031 CYS Chi-restraints excluded: chain D residue 1046 CYS Chi-restraints excluded: chain D residue 1091 CYS Chi-restraints excluded: chain D residue 1097 CYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 310 ARG Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1017 ASP Chi-restraints excluded: chain E residue 1047 HIS Chi-restraints excluded: chain E residue 1165 CYS Chi-restraints excluded: chain G residue 1268 HIS Chi-restraints excluded: chain G residue 1277 ASP Chi-restraints excluded: chain G residue 1371 LYS Chi-restraints excluded: chain H residue 1268 HIS Chi-restraints excluded: chain H residue 1277 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 87 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 556 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.051763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.042600 restraints weight = 611525.152| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 6.78 r_work: 0.3186 rms_B_bonded: 5.89 restraints_weight: 2.0000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21287 Z= 0.149 Angle : 0.562 9.153 28925 Z= 0.289 Chirality : 0.040 0.421 3153 Planarity : 0.004 0.048 3772 Dihedral : 4.999 46.968 3183 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.30 % Favored : 85.59 % Rotamer: Outliers : 2.17 % Allowed : 23.76 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.52 (0.16), residues: 2644 helix: 0.28 (0.24), residues: 486 sheet: -2.73 (0.24), residues: 436 loop : -2.07 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.015 0.001 TYR E 185 PHE 0.019 0.001 PHE H1299 TRP 0.010 0.001 TRP D 642 HIS 0.006 0.001 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00316 (21168) covalent geometry : angle 0.55600 (28678) SS BOND : bond 0.00426 ( 110) SS BOND : angle 0.91411 ( 220) hydrogen bonds : bond 0.03548 ( 492) hydrogen bonds : angle 5.55707 ( 1251) link_BETA1-4 : bond 0.00337 ( 4) link_BETA1-4 : angle 1.75906 ( 12) link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 1.93646 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 157 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.9339 (mmmm) REVERT: D 280 MET cc_start: 0.9258 (ppp) cc_final: 0.9036 (ppp) REVERT: D 501 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8750 (t0) REVERT: E 83 SER cc_start: 0.9286 (OUTLIER) cc_final: 0.8862 (m) REVERT: E 280 MET cc_start: 0.9176 (tmm) cc_final: 0.8438 (tmm) REVERT: E 800 MET cc_start: 0.5423 (ttm) cc_final: 0.4782 (ttm) outliers start: 50 outliers final: 33 residues processed: 153 average time/residue: 0.3372 time to fit residues: 82.6732 Evaluate side-chains 145 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 325 CYS Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 799 CYS Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 1031 CYS Chi-restraints excluded: chain D residue 1046 CYS Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1091 CYS Chi-restraints excluded: chain D residue 1097 CYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 310 ARG Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1017 ASP Chi-restraints excluded: chain E residue 1047 HIS Chi-restraints excluded: chain E residue 1055 MET Chi-restraints excluded: chain E residue 1165 CYS Chi-restraints excluded: chain G residue 1268 HIS Chi-restraints excluded: chain G residue 1277 ASP Chi-restraints excluded: chain H residue 1268 HIS Chi-restraints excluded: chain H residue 1277 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 overall best weight: 7.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 GLN D 303 GLN D 556 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN E1158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.050759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.041711 restraints weight = 616620.498| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 6.72 r_work: 0.3151 rms_B_bonded: 5.99 restraints_weight: 2.0000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21287 Z= 0.229 Angle : 0.616 8.515 28925 Z= 0.318 Chirality : 0.040 0.419 3153 Planarity : 0.004 0.050 3772 Dihedral : 4.990 42.665 3183 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.98 % Favored : 84.80 % Rotamer: Outliers : 2.56 % Allowed : 23.29 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.73 (0.16), residues: 2644 helix: -0.00 (0.23), residues: 494 sheet: -2.86 (0.24), residues: 438 loop : -2.18 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 545 TYR 0.016 0.002 TYR D 185 PHE 0.022 0.002 PHE G1280 TRP 0.010 0.001 TRP E 199 HIS 0.005 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00471 (21168) covalent geometry : angle 0.60864 (28678) SS BOND : bond 0.00429 ( 110) SS BOND : angle 1.08219 ( 220) hydrogen bonds : bond 0.03743 ( 492) hydrogen bonds : angle 5.67147 ( 1251) link_BETA1-4 : bond 0.00439 ( 4) link_BETA1-4 : angle 2.02759 ( 12) link_NAG-ASN : bond 0.00494 ( 5) link_NAG-ASN : angle 1.98110 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 111 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 736 MET cc_start: 0.8987 (tpp) cc_final: 0.8746 (tpp) REVERT: D 884 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8766 (tp) REVERT: E 34 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8901 (tpt-90) REVERT: E 83 SER cc_start: 0.9379 (OUTLIER) cc_final: 0.9021 (m) REVERT: E 280 MET cc_start: 0.9239 (tmm) cc_final: 0.8457 (tmm) REVERT: E 800 MET cc_start: 0.5583 (OUTLIER) cc_final: 0.4575 (ttm) REVERT: E 947 MET cc_start: 0.7370 (ptm) cc_final: 0.7169 (ptm) REVERT: E 1035 ARG cc_start: 0.9297 (tpp80) cc_final: 0.9064 (mmm-85) REVERT: G 1385 MET cc_start: 0.8247 (ptp) cc_final: 0.7913 (ptm) outliers start: 59 outliers final: 40 residues processed: 164 average time/residue: 0.3303 time to fit residues: 85.1510 Evaluate side-chains 152 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 325 CYS Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 654 LYS Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 799 CYS Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1009 SER Chi-restraints excluded: chain D residue 1031 CYS Chi-restraints excluded: chain D residue 1046 CYS Chi-restraints excluded: chain D residue 1091 CYS Chi-restraints excluded: chain D residue 1097 CYS Chi-restraints excluded: chain D residue 1153 CYS Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain E residue 800 MET Chi-restraints excluded: chain E residue 952 HIS Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1013 GLN Chi-restraints excluded: chain E residue 1017 ASP Chi-restraints excluded: chain E residue 1047 HIS Chi-restraints excluded: chain E residue 1051 MET Chi-restraints excluded: chain E residue 1165 CYS Chi-restraints excluded: chain G residue 1268 HIS Chi-restraints excluded: chain G residue 1277 ASP Chi-restraints excluded: chain G residue 1371 LYS Chi-restraints excluded: chain H residue 1268 HIS Chi-restraints excluded: chain H residue 1277 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 219 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 251 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 483 GLN D 556 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** G1326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.050917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.041913 restraints weight = 614882.401| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 6.48 r_work: 0.3154 rms_B_bonded: 5.85 restraints_weight: 2.0000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21287 Z= 0.158 Angle : 0.561 8.273 28925 Z= 0.289 Chirality : 0.040 0.418 3153 Planarity : 0.004 0.051 3772 Dihedral : 4.836 43.449 3183 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.96 % Favored : 85.93 % Rotamer: Outliers : 2.12 % Allowed : 23.81 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.69 (0.16), residues: 2644 helix: 0.23 (0.24), residues: 484 sheet: -2.93 (0.23), residues: 458 loop : -2.16 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H1341 TYR 0.016 0.001 TYR E 185 PHE 0.020 0.001 PHE H1299 TRP 0.012 0.001 TRP E 199 HIS 0.004 0.001 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00328 (21168) covalent geometry : angle 0.55479 (28678) SS BOND : bond 0.00331 ( 110) SS BOND : angle 0.97741 ( 220) hydrogen bonds : bond 0.03469 ( 492) hydrogen bonds : angle 5.49691 ( 1251) link_BETA1-4 : bond 0.00267 ( 4) link_BETA1-4 : angle 1.57950 ( 12) link_NAG-ASN : bond 0.00382 ( 5) link_NAG-ASN : angle 1.70296 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 729 CYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8121 (m) REVERT: D 884 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8735 (tp) REVERT: E 280 MET cc_start: 0.9253 (tmm) cc_final: 0.8459 (tmm) REVERT: E 771 MET cc_start: 0.6886 (ptt) cc_final: 0.4844 (ppp) REVERT: G 1385 MET cc_start: 0.8408 (ptp) cc_final: 0.8093 (ptm) outliers start: 49 outliers final: 38 residues processed: 151 average time/residue: 0.3492 time to fit residues: 82.2161 Evaluate side-chains 145 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 325 CYS Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 654 LYS Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 729 CYS Chi-restraints excluded: chain D residue 799 CYS Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 1031 CYS Chi-restraints excluded: chain D residue 1046 CYS Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1091 CYS Chi-restraints excluded: chain D residue 1097 CYS Chi-restraints excluded: chain D residue 1165 CYS Chi-restraints excluded: chain D residue 1174 HIS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 310 ARG Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain E residue 952 HIS Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1013 GLN Chi-restraints excluded: chain E residue 1047 HIS Chi-restraints excluded: chain E residue 1165 CYS Chi-restraints excluded: chain G residue 1268 HIS Chi-restraints excluded: chain G residue 1277 ASP Chi-restraints excluded: chain H residue 1268 HIS Chi-restraints excluded: chain H residue 1277 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 154 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 57 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 556 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.050878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.041972 restraints weight = 611634.553| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 6.37 r_work: 0.3161 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21287 Z= 0.140 Angle : 0.553 8.327 28925 Z= 0.282 Chirality : 0.040 0.409 3153 Planarity : 0.004 0.050 3772 Dihedral : 4.696 42.737 3183 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.33 % Favored : 85.55 % Rotamer: Outliers : 1.95 % Allowed : 23.98 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.62 (0.16), residues: 2644 helix: 0.34 (0.24), residues: 484 sheet: -2.92 (0.23), residues: 462 loop : -2.11 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1035 TYR 0.014 0.001 TYR E 185 PHE 0.019 0.001 PHE H1299 TRP 0.011 0.001 TRP E 199 HIS 0.005 0.001 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00299 (21168) covalent geometry : angle 0.54703 (28678) SS BOND : bond 0.00291 ( 110) SS BOND : angle 0.90764 ( 220) hydrogen bonds : bond 0.03387 ( 492) hydrogen bonds : angle 5.37631 ( 1251) link_BETA1-4 : bond 0.00387 ( 4) link_BETA1-4 : angle 1.60237 ( 12) link_NAG-ASN : bond 0.00406 ( 5) link_NAG-ASN : angle 1.64477 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 250 CYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8640 (t) REVERT: D 736 MET cc_start: 0.8986 (tpp) cc_final: 0.8784 (tpp) REVERT: D 884 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8753 (tp) REVERT: E 280 MET cc_start: 0.9272 (tmm) cc_final: 0.8509 (tmm) REVERT: E 771 MET cc_start: 0.6805 (ptt) cc_final: 0.4738 (ppp) REVERT: E 800 MET cc_start: 0.4044 (tpp) cc_final: 0.3755 (tpp) REVERT: G 1385 MET cc_start: 0.8357 (ptp) cc_final: 0.8046 (ptm) outliers start: 45 outliers final: 38 residues processed: 148 average time/residue: 0.2964 time to fit residues: 71.6643 Evaluate side-chains 147 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 325 CYS Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 799 CYS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 1031 CYS Chi-restraints excluded: chain D residue 1046 CYS Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1091 CYS Chi-restraints excluded: chain D residue 1097 CYS Chi-restraints excluded: chain D residue 1165 CYS Chi-restraints excluded: chain D residue 1174 HIS Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 952 HIS Chi-restraints excluded: chain E residue 978 LEU Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1017 ASP Chi-restraints excluded: chain E residue 1047 HIS Chi-restraints excluded: chain E residue 1055 MET Chi-restraints excluded: chain E residue 1165 CYS Chi-restraints excluded: chain G residue 1268 HIS Chi-restraints excluded: chain G residue 1277 ASP Chi-restraints excluded: chain H residue 1268 HIS Chi-restraints excluded: chain H residue 1277 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 15 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 257 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 256 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 overall best weight: 7.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 556 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** G1326 HIS ** 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 = 0.3619 r_free = 0.3619 target = 0.050273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.041219 restraints weight = 620688.436| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 6.79 r_work: 0.3141 rms_B_bonded: 6.03 restraints_weight: 2.0000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21287 Z= 0.205 Angle : 0.580 8.444 28925 Z= 0.299 Chirality : 0.040 0.401 3153 Planarity : 0.004 0.052 3772 Dihedral : 4.771 43.001 3183 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.24 % Favored : 84.64 % Rotamer: Outliers : 2.47 % Allowed : 23.42 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.75 (0.16), residues: 2644 helix: 0.29 (0.24), residues: 478 sheet: -2.94 (0.23), residues: 454 loop : -2.24 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 976 TYR 0.015 0.001 TYR E 185 PHE 0.017 0.001 PHE H1280 TRP 0.010 0.001 TRP E 642 HIS 0.005 0.001 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00417 (21168) covalent geometry : angle 0.57298 (28678) SS BOND : bond 0.00379 ( 110) SS BOND : angle 0.99486 ( 220) hydrogen bonds : bond 0.03430 ( 492) hydrogen bonds : angle 5.44755 ( 1251) link_BETA1-4 : bond 0.00405 ( 4) link_BETA1-4 : angle 1.78034 ( 12) link_NAG-ASN : bond 0.00386 ( 5) link_NAG-ASN : angle 1.74756 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 105 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 250 CYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8601 (t) REVERT: D 729 CYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8275 (m) REVERT: D 884 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8815 (tp) REVERT: E 280 MET cc_start: 0.9262 (tmm) cc_final: 0.8500 (tmm) REVERT: E 320 MET cc_start: 0.9149 (ppp) cc_final: 0.8844 (ppp) REVERT: E 771 MET cc_start: 0.7332 (ptt) cc_final: 0.5588 (ppp) REVERT: E 800 MET cc_start: 0.4522 (tpp) cc_final: 0.4055 (tpp) outliers start: 57 outliers final: 48 residues processed: 157 average time/residue: 0.3255 time to fit residues: 81.2250 Evaluate side-chains 155 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 325 CYS Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 729 CYS Chi-restraints excluded: chain D residue 799 CYS Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 921 CYS Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 1031 CYS Chi-restraints excluded: chain D residue 1046 CYS Chi-restraints excluded: chain D residue 1047 HIS Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1091 CYS Chi-restraints excluded: chain D residue 1097 CYS Chi-restraints excluded: chain D residue 1165 CYS Chi-restraints excluded: chain D residue 1174 HIS Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 321 CYS Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 952 HIS Chi-restraints excluded: chain E residue 978 LEU Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1013 GLN Chi-restraints excluded: chain E residue 1017 ASP Chi-restraints excluded: chain E residue 1047 HIS Chi-restraints excluded: chain E residue 1055 MET Chi-restraints excluded: chain E residue 1165 CYS Chi-restraints excluded: chain G residue 1268 HIS Chi-restraints excluded: chain G residue 1277 ASP Chi-restraints excluded: chain G residue 1371 LYS Chi-restraints excluded: chain H residue 1268 HIS Chi-restraints excluded: chain H residue 1277 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 147 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 138 optimal weight: 0.0570 chunk 194 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 251 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 overall best weight: 6.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 556 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN E 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.050172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.041423 restraints weight = 620241.450| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 6.19 r_work: 0.3137 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21287 Z= 0.181 Angle : 0.575 8.468 28925 Z= 0.297 Chirality : 0.040 0.399 3153 Planarity : 0.004 0.051 3772 Dihedral : 4.792 43.699 3183 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.02 % Favored : 84.87 % Rotamer: Outliers : 2.52 % Allowed : 23.37 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.74 (0.16), residues: 2644 helix: 0.12 (0.23), residues: 494 sheet: -2.90 (0.24), residues: 442 loop : -2.22 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 826 TYR 0.016 0.001 TYR E 134 PHE 0.014 0.001 PHE H1299 TRP 0.013 0.001 TRP G1313 HIS 0.011 0.001 HIS E 817 Details of bonding type rmsd covalent geometry : bond 0.00376 (21168) covalent geometry : angle 0.56902 (28678) SS BOND : bond 0.00321 ( 110) SS BOND : angle 1.01323 ( 220) hydrogen bonds : bond 0.03379 ( 492) hydrogen bonds : angle 5.39886 ( 1251) link_BETA1-4 : bond 0.00416 ( 4) link_BETA1-4 : angle 1.44075 ( 12) link_NAG-ASN : bond 0.00338 ( 5) link_NAG-ASN : angle 1.67961 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 104 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 250 CYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8581 (t) REVERT: D 729 CYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8149 (m) REVERT: D 1093 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.7250 (p) REVERT: D 1141 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.8883 (tp30) REVERT: E 280 MET cc_start: 0.9216 (tmm) cc_final: 0.8514 (tmm) REVERT: E 320 MET cc_start: 0.9130 (ppp) cc_final: 0.8839 (ppp) REVERT: E 771 MET cc_start: 0.6600 (ptt) cc_final: 0.4442 (ppp) REVERT: E 800 MET cc_start: 0.4614 (tpp) cc_final: 0.4137 (tpp) REVERT: G 1333 ASP cc_start: 0.9207 (m-30) cc_final: 0.8950 (p0) REVERT: G 1385 MET cc_start: 0.8699 (ptp) cc_final: 0.8415 (ptm) outliers start: 58 outliers final: 49 residues processed: 155 average time/residue: 0.3348 time to fit residues: 82.9219 Evaluate side-chains 156 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 103 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 325 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 729 CYS Chi-restraints excluded: chain D residue 799 CYS Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 921 CYS Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 1009 SER Chi-restraints excluded: chain D residue 1031 CYS Chi-restraints excluded: chain D residue 1046 CYS Chi-restraints excluded: chain D residue 1047 HIS Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1091 CYS Chi-restraints excluded: chain D residue 1093 SER Chi-restraints excluded: chain D residue 1097 CYS Chi-restraints excluded: chain D residue 1141 GLU Chi-restraints excluded: chain D residue 1174 HIS Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 321 CYS Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain E residue 952 HIS Chi-restraints excluded: chain E residue 978 LEU Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1017 ASP Chi-restraints excluded: chain E residue 1047 HIS Chi-restraints excluded: chain E residue 1051 MET Chi-restraints excluded: chain E residue 1055 MET Chi-restraints excluded: chain E residue 1165 CYS Chi-restraints excluded: chain G residue 1268 HIS Chi-restraints excluded: chain G residue 1277 ASP Chi-restraints excluded: chain G residue 1371 LYS Chi-restraints excluded: chain H residue 1268 HIS Chi-restraints excluded: chain H residue 1277 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 1 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 250 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 556 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** G1326 HIS ** 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 = 0.3622 r_free = 0.3622 target = 0.050253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.041303 restraints weight = 616245.742| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 6.51 r_work: 0.3145 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21287 Z= 0.156 Angle : 0.558 8.699 28925 Z= 0.286 Chirality : 0.040 0.395 3153 Planarity : 0.004 0.052 3772 Dihedral : 4.702 43.416 3183 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.79 % Favored : 85.14 % Rotamer: Outliers : 2.47 % Allowed : 23.42 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.63 (0.16), residues: 2644 helix: 0.36 (0.24), residues: 482 sheet: -2.87 (0.24), residues: 436 loop : -2.18 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 507 TYR 0.014 0.001 TYR E 185 PHE 0.015 0.001 PHE G1280 TRP 0.012 0.001 TRP E 199 HIS 0.006 0.001 HIS E 817 Details of bonding type rmsd covalent geometry : bond 0.00328 (21168) covalent geometry : angle 0.55165 (28678) SS BOND : bond 0.00306 ( 110) SS BOND : angle 0.98244 ( 220) hydrogen bonds : bond 0.03280 ( 492) hydrogen bonds : angle 5.31710 ( 1251) link_BETA1-4 : bond 0.00287 ( 4) link_BETA1-4 : angle 1.51001 ( 12) link_NAG-ASN : bond 0.00350 ( 5) link_NAG-ASN : angle 1.60358 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Residue LEU 1275 is missing expected H atoms. Skipping. Residue THR 1381 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 102 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 250 CYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8590 (t) REVERT: D 729 CYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7945 (m) REVERT: D 736 MET cc_start: 0.8954 (tpp) cc_final: 0.8695 (tpp) REVERT: E 280 MET cc_start: 0.9270 (tmm) cc_final: 0.8549 (tmm) REVERT: E 320 MET cc_start: 0.9136 (ppp) cc_final: 0.8841 (ppp) REVERT: E 771 MET cc_start: 0.7306 (ptt) cc_final: 0.5681 (ppp) REVERT: E 800 MET cc_start: 0.4302 (tpp) cc_final: 0.3604 (tpp) REVERT: E 1012 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9280 (pt) REVERT: E 1100 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8581 (t80) REVERT: G 1333 ASP cc_start: 0.8992 (m-30) cc_final: 0.8730 (p0) REVERT: G 1385 MET cc_start: 0.8578 (ptp) cc_final: 0.8314 (ptm) outliers start: 57 outliers final: 47 residues processed: 155 average time/residue: 0.3391 time to fit residues: 82.7722 Evaluate side-chains 153 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 325 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 729 CYS Chi-restraints excluded: chain D residue 799 CYS Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 921 CYS Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 1009 SER Chi-restraints excluded: chain D residue 1031 CYS Chi-restraints excluded: chain D residue 1046 CYS Chi-restraints excluded: chain D residue 1047 HIS Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1091 CYS Chi-restraints excluded: chain D residue 1097 CYS Chi-restraints excluded: chain D residue 1174 HIS Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 321 CYS Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 952 HIS Chi-restraints excluded: chain E residue 978 LEU Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1017 ASP Chi-restraints excluded: chain E residue 1047 HIS Chi-restraints excluded: chain E residue 1055 MET Chi-restraints excluded: chain E residue 1100 PHE Chi-restraints excluded: chain E residue 1165 CYS Chi-restraints excluded: chain G residue 1268 HIS Chi-restraints excluded: chain G residue 1277 ASP Chi-restraints excluded: chain G residue 1371 LYS Chi-restraints excluded: chain H residue 1268 HIS Chi-restraints excluded: chain H residue 1277 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 214 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 250 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 556 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** E 352 HIS ** 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 = 0.3607 r_free = 0.3607 target = 0.049823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.041063 restraints weight = 623571.457| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 6.34 r_work: 0.3128 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21287 Z= 0.205 Angle : 0.590 8.788 28925 Z= 0.304 Chirality : 0.040 0.394 3153 Planarity : 0.004 0.052 3772 Dihedral : 4.798 43.479 3183 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.62 % Favored : 84.23 % Rotamer: Outliers : 2.56 % Allowed : 23.29 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.76 (0.16), residues: 2644 helix: 0.15 (0.23), residues: 490 sheet: -2.95 (0.23), residues: 444 loop : -2.23 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 365 TYR 0.018 0.001 TYR G1363 PHE 0.013 0.001 PHE G1280 TRP 0.013 0.001 TRP E 642 HIS 0.007 0.001 HIS E 817 Details of bonding type rmsd covalent geometry : bond 0.00421 (21168) covalent geometry : angle 0.58185 (28678) SS BOND : bond 0.00373 ( 110) SS BOND : angle 1.15014 ( 220) hydrogen bonds : bond 0.03363 ( 492) hydrogen bonds : angle 5.41147 ( 1251) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 1.75636 ( 12) link_NAG-ASN : bond 0.00379 ( 5) link_NAG-ASN : angle 1.73405 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10624.59 seconds wall clock time: 181 minutes 9.41 seconds (10869.41 seconds total)