Starting phenix.real_space_refine on Mon Jun 16 01:11:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wn4_32621/06_2025/7wn4_32621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wn4_32621/06_2025/7wn4_32621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wn4_32621/06_2025/7wn4_32621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wn4_32621/06_2025/7wn4_32621.map" model { file = "/net/cci-nas-00/data/ceres_data/7wn4_32621/06_2025/7wn4_32621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wn4_32621/06_2025/7wn4_32621.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 276 5.16 5 C 11242 2.51 5 N 3127 2.21 5 O 3573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18224 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5427 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 675} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5427 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 3629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3692 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.17, per 1000 atoms: 0.67 Number of scatterers: 18224 At special positions: 0 Unit cell: (159.08, 161.02, 146.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 276 16.00 O 3573 8.00 N 3127 7.00 C 11242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=116, symmetry=0 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 200 " distance=2.02 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.04 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 255 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 250 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 257 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 329 " distance=2.02 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 348 " distance=2.02 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 372 " distance=2.02 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 384 " distance=2.03 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 524 " distance=2.02 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 440 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.02 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.03 Simple disulfide: pdb=" SG CYS E 595 " - pdb=" SG CYS E 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 615 " - pdb=" SG CYS E 621 " distance=2.02 Simple disulfide: pdb=" SG CYS E 623 " - pdb=" SG CYS E 648 " distance=2.02 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 687 " distance=2.03 Simple disulfide: pdb=" SG CYS E 661 " - pdb=" SG CYS E 683 " distance=2.03 Simple disulfide: pdb=" SG CYS E 665 " - pdb=" SG CYS E 679 " distance=2.03 Simple disulfide: pdb=" SG CYS E 669 " - pdb=" SG CYS E 707 " distance=2.03 Simple disulfide: pdb=" SG CYS E 689 " - pdb=" SG CYS E 701 " distance=2.03 Simple disulfide: pdb=" SG CYS E 709 " - pdb=" SG CYS E 731 " distance=2.03 Simple disulfide: pdb=" SG CYS E 729 " - pdb=" SG CYS E 738 " distance=2.05 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 808 " distance=2.04 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 804 " distance=2.02 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 799 " distance=2.03 Simple disulfide: pdb=" SG CYS F 792 " - pdb=" SG CYS F 827 " distance=2.03 Simple disulfide: pdb=" SG CYS F 810 " - pdb=" SG CYS F 821 " distance=2.03 Simple disulfide: pdb=" SG CYS F 829 " - pdb=" SG CYS F 851 " distance=2.02 Simple disulfide: pdb=" SG CYS F 846 " - pdb=" SG CYS F 863 " distance=2.03 Simple disulfide: pdb=" SG CYS F 849 " - pdb=" SG CYS F 858 " distance=2.03 Simple disulfide: pdb=" SG CYS F 867 " - pdb=" SG CYS F 996 " distance=2.02 Simple disulfide: pdb=" SG CYS F 889 " - pdb=" SG CYS F1031 " distance=2.02 Simple disulfide: pdb=" SG CYS F 898 " - pdb=" SG CYS F 993 " distance=2.03 Simple disulfide: pdb=" SG CYS F 914 " - pdb=" SG CYS F 921 " distance=2.02 Simple disulfide: pdb=" SG CYS F1046 " - pdb=" SG CYS F1089 " distance=2.03 Simple disulfide: pdb=" SG CYS F1060 " - pdb=" SG CYS F1084 " distance=2.03 Simple disulfide: pdb=" SG CYS F1071 " - pdb=" SG CYS F1111 " distance=2.02 Simple disulfide: pdb=" SG CYS F1091 " - pdb=" SG CYS F1099 " distance=2.03 Simple disulfide: pdb=" SG CYS F1097 " - pdb=" SG CYS H1097 " distance=2.03 Simple disulfide: pdb=" SG CYS F1101 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F1130 " - pdb=" SG CYS F1173 " distance=2.03 Simple disulfide: pdb=" SG CYS F1142 " - pdb=" SG CYS H1142 " distance=2.02 Simple disulfide: pdb=" SG CYS F1149 " - pdb=" SG CYS F1169 " distance=2.03 Simple disulfide: pdb=" SG CYS F1153 " - pdb=" SG CYS F1165 " distance=2.03 Simple disulfide: pdb=" SG CYS F1157 " - pdb=" SG CYS F1196 " distance=2.03 Simple disulfide: pdb=" SG CYS F1177 " - pdb=" SG CYS F1190 " distance=2.03 Simple disulfide: pdb=" SG CYS F1199 " - pdb=" SG CYS F1227 " distance=2.03 Simple disulfide: pdb=" SG CYS F1222 " - pdb=" SG CYS F1237 " distance=2.03 Simple disulfide: pdb=" SG CYS F1225 " - pdb=" SG CYS F1234 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 57 " - pdb=" SG CYS G 200 " distance=2.02 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 255 " distance=2.03 Simple disulfide: pdb=" SG CYS G 225 " - pdb=" SG CYS G 250 " distance=2.03 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 275 " distance=2.03 Simple disulfide: pdb=" SG CYS G 257 " - pdb=" SG CYS G 263 " distance=2.03 Simple disulfide: pdb=" SG CYS G 265 " - pdb=" SG CYS G 291 " distance=2.03 Simple disulfide: pdb=" SG CYS G 295 " - pdb=" SG CYS G 329 " distance=2.03 Simple disulfide: pdb=" SG CYS G 304 " - pdb=" SG CYS G 325 " distance=2.03 Simple disulfide: pdb=" SG CYS G 308 " - pdb=" SG CYS G 321 " distance=2.02 Simple disulfide: pdb=" SG CYS G 312 " - pdb=" SG CYS G 348 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 342 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 372 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 384 " distance=2.03 Simple disulfide: pdb=" SG CYS G 370 " - pdb=" SG CYS G 379 " distance=2.03 Simple disulfide: pdb=" SG CYS G 388 " - pdb=" SG CYS G 524 " distance=2.02 Simple disulfide: pdb=" SG CYS G 410 " - pdb=" SG CYS G 559 " distance=2.03 Simple disulfide: pdb=" SG CYS G 418 " - pdb=" SG CYS G 521 " distance=2.02 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 440 " distance=2.03 Simple disulfide: pdb=" SG CYS G 570 " - pdb=" SG CYS G 613 " distance=2.03 Simple disulfide: pdb=" SG CYS G 584 " - pdb=" SG CYS G 608 " distance=2.03 Simple disulfide: pdb=" SG CYS G 595 " - pdb=" SG CYS G 633 " distance=2.03 Simple disulfide: pdb=" SG CYS G 615 " - pdb=" SG CYS G 621 " distance=2.02 Simple disulfide: pdb=" SG CYS G 623 " - pdb=" SG CYS G 648 " distance=2.03 Simple disulfide: pdb=" SG CYS G 652 " - pdb=" SG CYS G 687 " distance=2.03 Simple disulfide: pdb=" SG CYS G 661 " - pdb=" SG CYS G 683 " distance=2.03 Simple disulfide: pdb=" SG CYS G 665 " - pdb=" SG CYS G 679 " distance=2.03 Simple disulfide: pdb=" SG CYS G 669 " - pdb=" SG CYS G 707 " distance=2.04 Simple disulfide: pdb=" SG CYS G 689 " - pdb=" SG CYS G 701 " distance=2.04 Simple disulfide: pdb=" SG CYS G 709 " - pdb=" SG CYS G 731 " distance=2.03 Simple disulfide: pdb=" SG CYS G 729 " - pdb=" SG CYS G 738 " distance=2.04 Simple disulfide: pdb=" SG CYS H 767 " - pdb=" SG CYS H 808 " distance=2.03 Simple disulfide: pdb=" SG CYS H 776 " - pdb=" SG CYS H 804 " distance=2.03 Simple disulfide: pdb=" SG CYS H 788 " - pdb=" SG CYS H 799 " distance=2.03 Simple disulfide: pdb=" SG CYS H 792 " - pdb=" SG CYS H 827 " distance=2.03 Simple disulfide: pdb=" SG CYS H 810 " - pdb=" SG CYS H 821 " distance=2.03 Simple disulfide: pdb=" SG CYS H 829 " - pdb=" SG CYS H 851 " distance=2.03 Simple disulfide: pdb=" SG CYS H 846 " - pdb=" SG CYS H 863 " distance=2.03 Simple disulfide: pdb=" SG CYS H 849 " - pdb=" SG CYS H 858 " distance=2.03 Simple disulfide: pdb=" SG CYS H 867 " - pdb=" SG CYS H 996 " distance=2.02 Simple disulfide: pdb=" SG CYS H 889 " - pdb=" SG CYS H1031 " distance=2.02 Simple disulfide: pdb=" SG CYS H 898 " - pdb=" SG CYS H 993 " distance=2.03 Simple disulfide: pdb=" SG CYS H 914 " - pdb=" SG CYS H 921 " distance=2.03 Simple disulfide: pdb=" SG CYS H1046 " - pdb=" SG CYS H1089 " distance=2.03 Simple disulfide: pdb=" SG CYS H1060 " - pdb=" SG CYS H1084 " distance=2.03 Simple disulfide: pdb=" SG CYS H1071 " - pdb=" SG CYS H1111 " distance=2.02 Simple disulfide: pdb=" SG CYS H1091 " - pdb=" SG CYS H1099 " distance=2.03 Simple disulfide: pdb=" SG CYS H1101 " - pdb=" SG CYS H1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H1130 " - pdb=" SG CYS H1173 " distance=2.03 Simple disulfide: pdb=" SG CYS H1149 " - pdb=" SG CYS H1169 " distance=2.03 Simple disulfide: pdb=" SG CYS H1153 " - pdb=" SG CYS H1165 " distance=2.03 Simple disulfide: pdb=" SG CYS H1157 " - pdb=" SG CYS H1196 " distance=2.03 Simple disulfide: pdb=" SG CYS H1177 " - pdb=" SG CYS H1190 " distance=2.03 Simple disulfide: pdb=" SG CYS H1199 " - pdb=" SG CYS H1227 " distance=2.02 Simple disulfide: pdb=" SG CYS H1222 " - pdb=" SG CYS H1237 " distance=2.03 Simple disulfide: pdb=" SG CYS H1225 " - pdb=" SG CYS H1234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 803 " - " ASN E 99 " " NAG E 804 " - " ASN E 156 " " NAG F1302 " - " ASN F 857 " " NAG F1303 " - " ASN F1147 " " NAG G 803 " - " ASN G 99 " " NAG G 804 " - " ASN G 156 " " NAG H1302 " - " ASN H 857 " " NAG H1303 " - " ASN H1147 " Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 2.7 seconds 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 40 sheets defined 21.1% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.657A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.584A pdb=" N ARG E 236 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 252 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 284 through 290 removed outlier: 4.414A pdb=" N HIS E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 289 " --> pdb=" O TRP E 285 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 290' Processing helix chain 'E' and resid 513 through 517 Processing helix chain 'E' and resid 531 through 535 removed outlier: 3.596A pdb=" N ASP E 534 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE E 535 " --> pdb=" O GLY E 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 531 through 535' Processing helix chain 'E' and resid 545 through 552 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 573 through 575 No H-bonds generated for 'chain 'E' and resid 573 through 575' Processing helix chain 'E' and resid 576 through 586 removed outlier: 4.079A pdb=" N VAL E 586 " --> pdb=" O GLU E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 598 Proline residue: E 590 - end of helix removed outlier: 4.875A pdb=" N ALA E 594 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS E 596 " --> pdb=" O GLU E 593 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG E 597 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 615 Processing helix chain 'E' and resid 617 through 637 removed outlier: 3.599A pdb=" N CYS E 623 " --> pdb=" O ARG E 619 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 628 " --> pdb=" O GLY E 624 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG E 636 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 674 removed outlier: 4.137A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 789 removed outlier: 3.603A pdb=" N THR F 789 " --> pdb=" O LEU F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 791 through 797 removed outlier: 4.323A pdb=" N ASP F 796 " --> pdb=" O CYS F 792 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU F 797 " --> pdb=" O GLN F 793 " (cutoff:3.500A) Processing helix chain 'F' and resid 1003 through 1008 removed outlier: 3.604A pdb=" N ASP F1006 " --> pdb=" O GLN F1003 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU F1007 " --> pdb=" O ASN F1004 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR F1008 " --> pdb=" O ASN F1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1003 through 1008' Processing helix chain 'F' and resid 1017 through 1025 Processing helix chain 'F' and resid 1049 through 1061 Processing helix chain 'F' and resid 1062 through 1065 Processing helix chain 'F' and resid 1068 through 1075 removed outlier: 3.606A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU F1074 " --> pdb=" O ASP F1070 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 Processing helix chain 'F' and resid 1097 through 1114 removed outlier: 4.382A pdb=" N THR F1103 " --> pdb=" O CYS F1099 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR F1107 " --> pdb=" O THR F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1131 through 1136 removed outlier: 3.841A pdb=" N ARG F1136 " --> pdb=" O GLU F1132 " (cutoff:3.500A) Processing helix chain 'F' and resid 1218 through 1222 Processing helix chain 'G' and resid 114 through 118 removed outlier: 4.327A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 209 through 213 removed outlier: 3.791A pdb=" N ILE G 212 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 231 removed outlier: 4.168A pdb=" N GLY G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS G 229 " --> pdb=" O CYS G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 removed outlier: 4.348A pdb=" N ARG G 236 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 237 " --> pdb=" O PHE G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 255 removed outlier: 3.996A pdb=" N CYS G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 263 removed outlier: 3.665A pdb=" N CYS G 263 " --> pdb=" O GLY G 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 260 through 263' Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.639A pdb=" N LEU G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.863A pdb=" N CYS G 348 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 469 removed outlier: 3.559A pdb=" N GLN G 469 " --> pdb=" O MET G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 517 Processing helix chain 'G' and resid 545 through 552 Processing helix chain 'G' and resid 568 through 572 removed outlier: 3.720A pdb=" N ALA G 571 " --> pdb=" O ASP G 568 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU G 572 " --> pdb=" O PRO G 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 568 through 572' Processing helix chain 'G' and resid 576 through 584 removed outlier: 3.877A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 596 Proline residue: G 590 - end of helix removed outlier: 4.911A pdb=" N ALA G 594 " --> pdb=" O THR G 591 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS G 596 " --> pdb=" O GLU G 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 615 Processing helix chain 'G' and resid 617 through 635 removed outlier: 3.825A pdb=" N ALA G 627 " --> pdb=" O CYS G 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 707 No H-bonds generated for 'chain 'G' and resid 705 through 707' Processing helix chain 'H' and resid 785 through 789 Processing helix chain 'H' and resid 1003 through 1008 removed outlier: 3.795A pdb=" N ASP H1006 " --> pdb=" O GLN H1003 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU H1007 " --> pdb=" O ASN H1004 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR H1008 " --> pdb=" O ASN H1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1003 through 1008' Processing helix chain 'H' and resid 1017 through 1024 Processing helix chain 'H' and resid 1049 through 1061 Processing helix chain 'H' and resid 1062 through 1065 Processing helix chain 'H' and resid 1068 through 1073 removed outlier: 3.776A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 Processing helix chain 'H' and resid 1097 through 1114 removed outlier: 4.771A pdb=" N THR H1103 " --> pdb=" O CYS H1099 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR H1107 " --> pdb=" O THR H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1130 through 1134 removed outlier: 3.990A pdb=" N ARG H1133 " --> pdb=" O CYS H1130 " (cutoff:3.500A) Processing helix chain 'H' and resid 1192 through 1196 Processing helix chain 'H' and resid 1218 through 1222 Processing sheet with id=AA1, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'E' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.782A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE E 94 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 300 through 305 removed outlier: 4.173A pdb=" N CYS E 304 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL E 326 " --> pdb=" O CYS E 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 337 through 338 Processing sheet with id=AA6, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AA8, first strand: chain 'E' and resid 403 through 405 Processing sheet with id=AA9, first strand: chain 'E' and resid 455 through 458 removed outlier: 5.084A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE E 425 " --> pdb=" O LEU E 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 465 through 466 removed outlier: 3.515A pdb=" N GLN E 469 " --> pdb=" O MET E 466 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 475 through 476 removed outlier: 3.514A pdb=" N GLN E 483 " --> pdb=" O ARG E 491 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 657 through 659 Processing sheet with id=AB4, first strand: chain 'E' and resid 721 through 723 Processing sheet with id=AB5, first strand: chain 'F' and resid 841 through 844 Processing sheet with id=AB6, first strand: chain 'F' and resid 865 through 866 removed outlier: 4.727A pdb=" N TRP F 974 " --> pdb=" O ILE F 962 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 874 through 876 Processing sheet with id=AB8, first strand: chain 'F' and resid 890 through 891 Processing sheet with id=AB9, first strand: chain 'F' and resid 928 through 929 removed outlier: 3.612A pdb=" N VAL F 929 " --> pdb=" O GLY F 932 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 936 through 937 Processing sheet with id=AC2, first strand: chain 'F' and resid 1144 through 1146 removed outlier: 3.663A pdb=" N ARG F1145 " --> pdb=" O HIS F1174 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 1150 through 1151 Processing sheet with id=AC4, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AC5, first strand: chain 'G' and resid 42 through 44 Processing sheet with id=AC6, first strand: chain 'G' and resid 59 through 62 removed outlier: 5.651A pdb=" N LEU G 60 " --> pdb=" O GLY G 74 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY G 74 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 62 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER G 83 " --> pdb=" O ASP G 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 300 through 305 removed outlier: 4.438A pdb=" N CYS G 304 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL G 326 " --> pdb=" O CYS G 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 350 through 351 Processing sheet with id=AC9, first strand: chain 'G' and resid 362 through 364 Processing sheet with id=AD1, first strand: chain 'G' and resid 386 through 389 Processing sheet with id=AD2, first strand: chain 'G' and resid 395 through 398 Processing sheet with id=AD3, first strand: chain 'G' and resid 454 through 458 removed outlier: 6.881A pdb=" N GLU G 428 " --> pdb=" O ARG G 442 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL G 444 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL G 426 " --> pdb=" O VAL G 444 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL G 446 " --> pdb=" O SER G 424 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER G 424 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 415 " --> pdb=" O ILE G 425 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR G 429 " --> pdb=" O GLN G 411 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN G 411 " --> pdb=" O THR G 429 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 657 through 658 Processing sheet with id=AD5, first strand: chain 'G' and resid 693 through 695 Processing sheet with id=AD6, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AD7, first strand: chain 'H' and resid 815 through 817 Processing sheet with id=AD8, first strand: chain 'H' and resid 829 through 830 Processing sheet with id=AD9, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AE1, first strand: chain 'H' and resid 865 through 866 removed outlier: 4.614A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 874 through 876 Processing sheet with id=AE3, first strand: chain 'H' and resid 890 through 891 Processing sheet with id=AE4, first strand: chain 'H' and resid 1144 through 1151 removed outlier: 4.101A pdb=" N CYS H1149 " --> pdb=" O VAL H1170 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL H1170 " --> pdb=" O CYS H1149 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6170 1.34 - 1.47: 4292 1.47 - 1.59: 7840 1.59 - 1.72: 1 1.72 - 1.84: 320 Bond restraints: 18623 Sorted by residual: bond pdb=" CA ASP F 975 " pdb=" C ASP F 975 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.66e-02 3.63e+03 1.46e+01 bond pdb=" CA ASP H 975 " pdb=" C ASP H 975 " ideal model delta sigma weight residual 1.525 1.473 0.052 1.38e-02 5.25e+03 1.41e+01 bond pdb=" N VAL H 850 " pdb=" CA VAL H 850 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.85e+00 bond pdb=" N VAL E 102 " pdb=" CA VAL E 102 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.20e-02 6.94e+03 8.61e+00 bond pdb=" N CYS H 851 " pdb=" CA CYS H 851 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.15e-02 7.56e+03 7.97e+00 ... (remaining 18618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 23781 1.89 - 3.78: 1289 3.78 - 5.67: 164 5.67 - 7.56: 33 7.56 - 9.45: 4 Bond angle restraints: 25271 Sorted by residual: angle pdb=" C TRP H 974 " pdb=" N ASP H 975 " pdb=" CA ASP H 975 " ideal model delta sigma weight residual 122.83 113.38 9.45 1.54e+00 4.22e-01 3.77e+01 angle pdb=" N VAL H1230 " pdb=" CA VAL H1230 " pdb=" C VAL H1230 " ideal model delta sigma weight residual 113.71 109.22 4.49 9.50e-01 1.11e+00 2.23e+01 angle pdb=" CA PRO H1038 " pdb=" N PRO H1038 " pdb=" CD PRO H1038 " ideal model delta sigma weight residual 112.00 105.61 6.39 1.40e+00 5.10e-01 2.08e+01 angle pdb=" N LYS E 157 " pdb=" CA LYS E 157 " pdb=" C LYS E 157 " ideal model delta sigma weight residual 113.55 107.82 5.73 1.26e+00 6.30e-01 2.07e+01 angle pdb=" C TRP F 974 " pdb=" N ASP F 975 " pdb=" CA ASP F 975 " ideal model delta sigma weight residual 122.65 115.35 7.30 1.66e+00 3.63e-01 1.93e+01 ... (remaining 25266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10352 17.94 - 35.88: 1008 35.88 - 53.81: 206 53.81 - 71.75: 46 71.75 - 89.69: 31 Dihedral angle restraints: 11643 sinusoidal: 4819 harmonic: 6824 Sorted by residual: dihedral pdb=" CA MET E 111 " pdb=" C MET E 111 " pdb=" N PRO E 112 " pdb=" CA PRO E 112 " ideal model delta harmonic sigma weight residual 180.00 121.65 58.35 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CB CYS E 65 " pdb=" SG CYS E 65 " pdb=" SG CYS E 159 " pdb=" CB CYS E 159 " ideal model delta sinusoidal sigma weight residual -86.00 2.79 -88.79 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS H1130 " pdb=" SG CYS H1130 " pdb=" SG CYS H1173 " pdb=" CB CYS H1173 " ideal model delta sinusoidal sigma weight residual -86.00 -173.61 87.61 1 1.00e+01 1.00e-02 9.20e+01 ... (remaining 11640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2728 0.146 - 0.292: 26 0.292 - 0.438: 1 0.438 - 0.584: 1 0.584 - 0.730: 1 Chirality restraints: 2757 Sorted by residual: chirality pdb=" C1 NAG G 804 " pdb=" ND2 ASN G 156 " pdb=" C2 NAG G 804 " pdb=" O5 NAG G 804 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG F1302 " pdb=" ND2 ASN F 857 " pdb=" C2 NAG F1302 " pdb=" O5 NAG F1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.87 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" C1 NAG G 803 " pdb=" ND2 ASN G 99 " pdb=" C2 NAG G 803 " pdb=" O5 NAG G 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2754 not shown) Planarity restraints: 3366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H1037 " 0.075 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO H1038 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO H1038 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO H1038 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 804 " 0.045 2.00e-02 2.50e+03 3.67e-02 1.69e+01 pdb=" C7 NAG G 804 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG G 804 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG G 804 " -0.059 2.00e-02 2.50e+03 pdb=" O7 NAG G 804 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H1303 " 0.044 2.00e-02 2.50e+03 3.65e-02 1.67e+01 pdb=" C7 NAG H1303 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG H1303 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG H1303 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG H1303 " -0.008 2.00e-02 2.50e+03 ... (remaining 3363 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 622 2.69 - 3.24: 18203 3.24 - 3.79: 27201 3.79 - 4.35: 35952 4.35 - 4.90: 60491 Nonbonded interactions: 142469 Sorted by model distance: nonbonded pdb=" OH TYR F 883 " pdb=" O LEU F 995 " model vdw 2.137 3.040 nonbonded pdb=" NE2 GLN G 431 " pdb=" O ASP G 435 " model vdw 2.164 3.120 nonbonded pdb=" OG SER H1129 " pdb=" OE1 GLU H1131 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR E 311 " pdb=" OE1 GLN E 313 " model vdw 2.183 3.040 nonbonded pdb=" O THR E 668 " pdb=" OG SER E 671 " model vdw 2.190 3.040 ... (remaining 142464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and (resid 767 through 1052 or resid 1054 through 1241 or resid 1301 \ through 1303)) selection = (chain 'H' and (resid 767 through 1052 or resid 1054 through 1241 or resid 1301 \ through 1303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 43.930 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 18747 Z= 0.350 Angle : 0.995 17.026 25527 Z= 0.579 Chirality : 0.054 0.730 2757 Planarity : 0.006 0.110 3358 Dihedral : 14.185 89.689 6925 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.54 % Favored : 86.29 % Rotamer: Outliers : 0.15 % Allowed : 0.44 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.16), residues: 2365 helix: -0.74 (0.28), residues: 335 sheet: -2.69 (0.27), residues: 364 loop : -2.26 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 502 HIS 0.008 0.001 HIS G 726 PHE 0.019 0.002 PHE F1021 TYR 0.026 0.002 TYR E 711 ARG 0.019 0.001 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.01097 ( 8) link_NAG-ASN : angle 7.51701 ( 24) hydrogen bonds : bond 0.19019 ( 466) hydrogen bonds : angle 7.84761 ( 1151) SS BOND : bond 0.00510 ( 116) SS BOND : angle 1.88810 ( 232) covalent geometry : bond 0.00747 (18623) covalent geometry : angle 0.95579 (25271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 593 GLU cc_start: 0.8162 (tp30) cc_final: 0.7927 (mm-30) REVERT: F 1049 ASN cc_start: 0.7047 (t0) cc_final: 0.6780 (t0) REVERT: G 111 MET cc_start: 0.9140 (ttt) cc_final: 0.8808 (ttt) REVERT: G 280 MET cc_start: 0.8270 (tmm) cc_final: 0.7677 (tmm) REVERT: G 737 HIS cc_start: 0.6647 (m90) cc_final: 0.6416 (m90) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.3278 time to fit residues: 111.6012 Evaluate side-chains 173 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 ASN F1226 HIS G 104 GLN ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN H1069 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097417 restraints weight = 27173.544| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.41 r_work: 0.2973 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 18747 Z= 0.230 Angle : 0.766 11.416 25527 Z= 0.391 Chirality : 0.049 0.178 2757 Planarity : 0.006 0.083 3358 Dihedral : 5.995 54.597 2730 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.87 % Favored : 89.00 % Rotamer: Outliers : 1.18 % Allowed : 8.34 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.16), residues: 2365 helix: -0.47 (0.27), residues: 345 sheet: -2.62 (0.27), residues: 340 loop : -2.07 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 502 HIS 0.017 0.001 HIS E 452 PHE 0.021 0.002 PHE E 579 TYR 0.029 0.002 TYR E 711 ARG 0.008 0.001 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 8) link_NAG-ASN : angle 4.83163 ( 24) hydrogen bonds : bond 0.05097 ( 466) hydrogen bonds : angle 5.91369 ( 1151) SS BOND : bond 0.00467 ( 116) SS BOND : angle 1.61435 ( 232) covalent geometry : bond 0.00555 (18623) covalent geometry : angle 0.73978 (25271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8167 (pp) cc_final: 0.7778 (mt) REVERT: E 593 GLU cc_start: 0.8865 (tp30) cc_final: 0.8644 (mm-30) REVERT: E 649 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8048 (mm-30) REVERT: E 740 MET cc_start: 0.7057 (mmm) cc_final: 0.6770 (tpt) REVERT: G 111 MET cc_start: 0.9602 (ttt) cc_final: 0.9301 (ttt) REVERT: G 280 MET cc_start: 0.8832 (tmm) cc_final: 0.7716 (tmm) REVERT: G 737 HIS cc_start: 0.6575 (m90) cc_final: 0.6363 (m90) REVERT: H 897 TYR cc_start: 0.8874 (m-80) cc_final: 0.8631 (m-10) outliers start: 23 outliers final: 16 residues processed: 203 average time/residue: 0.3333 time to fit residues: 101.6129 Evaluate side-chains 181 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 719 GLU Chi-restraints excluded: chain F residue 772 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 64 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 HIS F1215 ASN ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098185 restraints weight = 37249.571| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.21 r_work: 0.2963 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18747 Z= 0.176 Angle : 0.684 8.192 25527 Z= 0.349 Chirality : 0.046 0.180 2757 Planarity : 0.005 0.114 3358 Dihedral : 5.717 59.588 2730 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.41 % Favored : 89.55 % Rotamer: Outliers : 1.91 % Allowed : 11.48 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.16), residues: 2365 helix: -0.17 (0.28), residues: 339 sheet: -2.54 (0.26), residues: 388 loop : -1.93 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 974 HIS 0.018 0.001 HIS E 452 PHE 0.014 0.001 PHE H1100 TYR 0.021 0.001 TYR E 711 ARG 0.007 0.000 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 8) link_NAG-ASN : angle 3.81338 ( 24) hydrogen bonds : bond 0.04432 ( 466) hydrogen bonds : angle 5.54061 ( 1151) SS BOND : bond 0.00394 ( 116) SS BOND : angle 1.41243 ( 232) covalent geometry : bond 0.00426 (18623) covalent geometry : angle 0.66407 (25271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 252 LYS cc_start: 0.8547 (ptpt) cc_final: 0.8237 (ptmm) REVERT: E 711 TYR cc_start: 0.8294 (t80) cc_final: 0.8028 (t80) REVERT: E 714 GLU cc_start: 0.7613 (pt0) cc_final: 0.7401 (pt0) REVERT: F 1215 ASN cc_start: 0.0056 (OUTLIER) cc_final: -0.0244 (m110) REVERT: G 106 ASP cc_start: 0.8359 (t0) cc_final: 0.8122 (m-30) REVERT: G 111 MET cc_start: 0.9477 (ttt) cc_final: 0.9144 (ttt) REVERT: G 199 TRP cc_start: 0.8740 (m100) cc_final: 0.8494 (m100) REVERT: G 280 MET cc_start: 0.8635 (tmm) cc_final: 0.8351 (tmm) REVERT: G 333 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: G 365 ARG cc_start: 0.6956 (tpp-160) cc_final: 0.6482 (mmt180) REVERT: G 737 HIS cc_start: 0.6337 (m90) cc_final: 0.6091 (m90) REVERT: H 897 TYR cc_start: 0.8756 (m-80) cc_final: 0.8556 (m-10) outliers start: 38 outliers final: 21 residues processed: 222 average time/residue: 0.3293 time to fit residues: 114.8977 Evaluate side-chains 202 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 719 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 772 VAL Chi-restraints excluded: chain F residue 1055 MET Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain F residue 1215 ASN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 1075 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 235 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 216 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS E 556 HIS F1215 ASN F1226 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 656 GLN ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097738 restraints weight = 39217.445| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.76 r_work: 0.2987 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 18747 Z= 0.171 Angle : 0.673 8.567 25527 Z= 0.343 Chirality : 0.046 0.181 2757 Planarity : 0.005 0.108 3358 Dihedral : 5.614 59.892 2730 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.15 % Favored : 89.81 % Rotamer: Outliers : 2.31 % Allowed : 13.39 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.17), residues: 2365 helix: -0.37 (0.27), residues: 373 sheet: -2.50 (0.26), residues: 382 loop : -1.92 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 502 HIS 0.018 0.001 HIS E 452 PHE 0.015 0.001 PHE H1100 TYR 0.018 0.001 TYR G 629 ARG 0.009 0.000 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 8) link_NAG-ASN : angle 3.41587 ( 24) hydrogen bonds : bond 0.04221 ( 466) hydrogen bonds : angle 5.42206 ( 1151) SS BOND : bond 0.00382 ( 116) SS BOND : angle 1.37122 ( 232) covalent geometry : bond 0.00413 (18623) covalent geometry : angle 0.65537 (25271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8134 (pp) cc_final: 0.7596 (mt) REVERT: E 252 LYS cc_start: 0.8602 (ptpt) cc_final: 0.8279 (ptmm) REVERT: E 581 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7849 (mm-30) REVERT: E 728 MET cc_start: 0.6794 (tmm) cc_final: 0.6580 (tmm) REVERT: F 771 MET cc_start: 0.5968 (mmm) cc_final: 0.5711 (mmm) REVERT: F 957 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8300 (mt-10) REVERT: G 106 ASP cc_start: 0.8551 (t0) cc_final: 0.8271 (m-30) REVERT: G 111 MET cc_start: 0.9557 (ttt) cc_final: 0.9239 (ttt) REVERT: G 199 TRP cc_start: 0.8810 (m100) cc_final: 0.8586 (m100) REVERT: G 280 MET cc_start: 0.8809 (tmm) cc_final: 0.8384 (tmm) REVERT: G 333 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: G 503 ASP cc_start: 0.7446 (t0) cc_final: 0.7153 (t0) REVERT: H 897 TYR cc_start: 0.8875 (m-80) cc_final: 0.8630 (m-10) outliers start: 46 outliers final: 27 residues processed: 228 average time/residue: 0.4739 time to fit residues: 173.9676 Evaluate side-chains 210 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 719 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 772 VAL Chi-restraints excluded: chain F residue 1055 MET Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 110 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 221 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099364 restraints weight = 37408.522| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.53 r_work: 0.2927 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18747 Z= 0.170 Angle : 0.673 8.650 25527 Z= 0.343 Chirality : 0.046 0.182 2757 Planarity : 0.005 0.101 3358 Dihedral : 5.542 58.737 2730 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.98 % Favored : 89.97 % Rotamer: Outliers : 2.26 % Allowed : 14.66 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.17), residues: 2365 helix: -0.34 (0.27), residues: 373 sheet: -2.37 (0.25), residues: 396 loop : -1.85 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP G 502 HIS 0.021 0.001 HIS E 452 PHE 0.014 0.001 PHE H1100 TYR 0.017 0.001 TYR E 711 ARG 0.010 0.000 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 3.21346 ( 24) hydrogen bonds : bond 0.04083 ( 466) hydrogen bonds : angle 5.34893 ( 1151) SS BOND : bond 0.00382 ( 116) SS BOND : angle 1.42611 ( 232) covalent geometry : bond 0.00410 (18623) covalent geometry : angle 0.65483 (25271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8119 (pp) cc_final: 0.7675 (mt) REVERT: E 252 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8243 (ptmm) REVERT: E 581 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7733 (mm-30) REVERT: F 771 MET cc_start: 0.6161 (mmm) cc_final: 0.5841 (mmm) REVERT: G 106 ASP cc_start: 0.8434 (t0) cc_final: 0.8199 (m-30) REVERT: G 111 MET cc_start: 0.9494 (ttt) cc_final: 0.9260 (ttt) REVERT: G 280 MET cc_start: 0.8710 (tmm) cc_final: 0.8282 (tmm) REVERT: G 333 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: G 365 ARG cc_start: 0.6790 (tpp-160) cc_final: 0.6410 (mmt180) outliers start: 45 outliers final: 28 residues processed: 227 average time/residue: 0.3120 time to fit residues: 110.4779 Evaluate side-chains 213 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 719 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 116 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 112 optimal weight: 0.0030 chunk 156 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100039 restraints weight = 39690.559| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.80 r_work: 0.3027 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18747 Z= 0.122 Angle : 0.639 10.382 25527 Z= 0.325 Chirality : 0.044 0.205 2757 Planarity : 0.005 0.094 3358 Dihedral : 5.330 56.583 2730 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.06 % Allowed : 15.94 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 2365 helix: -0.16 (0.27), residues: 367 sheet: -2.14 (0.27), residues: 338 loop : -1.78 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP G 502 HIS 0.025 0.001 HIS E 452 PHE 0.017 0.001 PHE H1100 TYR 0.025 0.001 TYR E 711 ARG 0.011 0.000 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 8) link_NAG-ASN : angle 2.77947 ( 24) hydrogen bonds : bond 0.03641 ( 466) hydrogen bonds : angle 5.22235 ( 1151) SS BOND : bond 0.00309 ( 116) SS BOND : angle 1.20335 ( 232) covalent geometry : bond 0.00284 (18623) covalent geometry : angle 0.62563 (25271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8189 (pp) cc_final: 0.7878 (mt) REVERT: E 252 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8306 (ptmm) REVERT: E 581 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7669 (mm-30) REVERT: E 714 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7427 (pt0) REVERT: G 106 ASP cc_start: 0.8267 (t0) cc_final: 0.8038 (m-30) REVERT: G 111 MET cc_start: 0.9413 (ttt) cc_final: 0.9193 (ttt) REVERT: G 280 MET cc_start: 0.8594 (tmm) cc_final: 0.8274 (tmm) REVERT: G 333 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: G 365 ARG cc_start: 0.6801 (tpp-160) cc_final: 0.6546 (mmt180) REVERT: G 740 MET cc_start: 0.5120 (ttp) cc_final: 0.4877 (tmm) outliers start: 41 outliers final: 28 residues processed: 236 average time/residue: 0.3156 time to fit residues: 117.4223 Evaluate side-chains 215 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 714 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 149 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 23 optimal weight: 0.0030 chunk 153 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100287 restraints weight = 26994.651| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.57 r_work: 0.2987 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18747 Z= 0.168 Angle : 0.678 12.632 25527 Z= 0.342 Chirality : 0.046 0.300 2757 Planarity : 0.005 0.098 3358 Dihedral : 5.377 57.389 2730 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.31 % Allowed : 15.30 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.17), residues: 2365 helix: -0.09 (0.27), residues: 365 sheet: -2.15 (0.27), residues: 360 loop : -1.75 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP G 502 HIS 0.013 0.001 HIS E 452 PHE 0.040 0.001 PHE E 70 TYR 0.015 0.001 TYR G 629 ARG 0.012 0.000 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 8) link_NAG-ASN : angle 2.83560 ( 24) hydrogen bonds : bond 0.03927 ( 466) hydrogen bonds : angle 5.13381 ( 1151) SS BOND : bond 0.00389 ( 116) SS BOND : angle 1.40904 ( 232) covalent geometry : bond 0.00408 (18623) covalent geometry : angle 0.66172 (25271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8186 (pp) cc_final: 0.7685 (mt) REVERT: E 252 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8306 (ptmm) REVERT: E 581 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7708 (mm-30) REVERT: G 106 ASP cc_start: 0.8163 (t0) cc_final: 0.7955 (m-30) REVERT: G 111 MET cc_start: 0.9415 (ttt) cc_final: 0.9198 (ttt) REVERT: G 280 MET cc_start: 0.8591 (tmm) cc_final: 0.8159 (tmm) REVERT: G 333 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7191 (tp30) REVERT: G 365 ARG cc_start: 0.6821 (tpp-160) cc_final: 0.6587 (mmt180) outliers start: 46 outliers final: 33 residues processed: 220 average time/residue: 0.2896 time to fit residues: 99.2001 Evaluate side-chains 216 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 957 GLU Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1173 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 117 optimal weight: 0.0270 chunk 64 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 178 optimal weight: 7.9990 chunk 235 optimal weight: 30.0000 chunk 22 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS F 901 ASN F1226 HIS G 238 HIS ** G 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1011 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101938 restraints weight = 26975.186| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.56 r_work: 0.3040 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18747 Z= 0.114 Angle : 0.634 13.016 25527 Z= 0.320 Chirality : 0.044 0.254 2757 Planarity : 0.005 0.090 3358 Dihedral : 5.125 55.507 2730 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.86 % Allowed : 16.09 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2365 helix: 0.00 (0.27), residues: 367 sheet: -1.93 (0.27), residues: 368 loop : -1.69 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP G 502 HIS 0.012 0.001 HIS E 452 PHE 0.027 0.001 PHE E 70 TYR 0.015 0.001 TYR G 629 ARG 0.013 0.000 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 8) link_NAG-ASN : angle 2.48870 ( 24) hydrogen bonds : bond 0.03435 ( 466) hydrogen bonds : angle 5.01586 ( 1151) SS BOND : bond 0.00290 ( 116) SS BOND : angle 1.18739 ( 232) covalent geometry : bond 0.00264 (18623) covalent geometry : angle 0.62263 (25271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8266 (pp) cc_final: 0.7678 (mt) REVERT: E 252 LYS cc_start: 0.8412 (ptpt) cc_final: 0.8206 (ptmm) REVERT: E 254 LEU cc_start: 0.7494 (mt) cc_final: 0.7240 (mt) REVERT: E 581 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7781 (mm-30) REVERT: G 106 ASP cc_start: 0.8099 (t0) cc_final: 0.7894 (m-30) REVERT: G 111 MET cc_start: 0.9371 (ttt) cc_final: 0.9159 (ttt) REVERT: G 226 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7800 (mm-40) REVERT: G 280 MET cc_start: 0.8562 (tmm) cc_final: 0.8252 (tmm) REVERT: G 333 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7068 (tp30) REVERT: G 365 ARG cc_start: 0.6795 (tpp-160) cc_final: 0.6567 (mmt180) REVERT: H 840 GLU cc_start: 0.8779 (mp0) cc_final: 0.8465 (mp0) outliers start: 37 outliers final: 31 residues processed: 217 average time/residue: 0.2977 time to fit residues: 100.8565 Evaluate side-chains 215 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 714 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1173 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 92 optimal weight: 0.0670 chunk 32 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 901 ASN 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 = 0.134528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101382 restraints weight = 37002.870| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.27 r_work: 0.3006 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 18747 Z= 0.133 Angle : 0.649 10.115 25527 Z= 0.327 Chirality : 0.045 0.252 2757 Planarity : 0.005 0.096 3358 Dihedral : 5.074 56.108 2730 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 1.81 % Allowed : 16.38 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.17), residues: 2365 helix: 0.05 (0.27), residues: 367 sheet: -1.94 (0.27), residues: 370 loop : -1.66 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP G 502 HIS 0.005 0.001 HIS G 737 PHE 0.025 0.001 PHE E 70 TYR 0.013 0.001 TYR G 629 ARG 0.013 0.000 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 8) link_NAG-ASN : angle 2.49185 ( 24) hydrogen bonds : bond 0.03578 ( 466) hydrogen bonds : angle 4.95637 ( 1151) SS BOND : bond 0.00315 ( 116) SS BOND : angle 1.27809 ( 232) covalent geometry : bond 0.00318 (18623) covalent geometry : angle 0.63569 (25271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8041 (mtp) cc_final: 0.7653 (ttm) REVERT: E 249 LEU cc_start: 0.8313 (pp) cc_final: 0.7469 (mt) REVERT: E 252 LYS cc_start: 0.8382 (ptpt) cc_final: 0.8167 (ptmm) REVERT: E 254 LEU cc_start: 0.7509 (mt) cc_final: 0.7282 (mt) REVERT: E 536 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8900 (mp) REVERT: E 581 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7811 (mm-30) REVERT: E 728 MET cc_start: 0.6564 (tmm) cc_final: 0.6284 (ptm) REVERT: F 947 MET cc_start: 0.8553 (mmm) cc_final: 0.8230 (mmm) REVERT: G 106 ASP cc_start: 0.8116 (t0) cc_final: 0.7908 (m-30) REVERT: G 217 MET cc_start: 0.5381 (pmm) cc_final: 0.5144 (pmm) REVERT: G 226 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7801 (mm-40) REVERT: G 280 MET cc_start: 0.8563 (tmm) cc_final: 0.8216 (tmm) REVERT: G 333 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7078 (tp30) outliers start: 36 outliers final: 32 residues processed: 210 average time/residue: 0.3008 time to fit residues: 98.0652 Evaluate side-chains 214 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 452 HIS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 714 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1173 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 219 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 230 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099164 restraints weight = 26815.169| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.35 r_work: 0.3044 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 18747 Z= 0.152 Angle : 0.660 10.127 25527 Z= 0.334 Chirality : 0.045 0.256 2757 Planarity : 0.005 0.093 3358 Dihedral : 5.164 56.808 2730 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.96 % Allowed : 16.67 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.17), residues: 2365 helix: 0.09 (0.27), residues: 365 sheet: -1.95 (0.27), residues: 370 loop : -1.67 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP G 502 HIS 0.005 0.001 HIS G 726 PHE 0.027 0.001 PHE E 70 TYR 0.014 0.001 TYR F 988 ARG 0.015 0.000 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 8) link_NAG-ASN : angle 2.51824 ( 24) hydrogen bonds : bond 0.03714 ( 466) hydrogen bonds : angle 4.95313 ( 1151) SS BOND : bond 0.00330 ( 116) SS BOND : angle 1.32805 ( 232) covalent geometry : bond 0.00368 (18623) covalent geometry : angle 0.64679 (25271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8301 (mtp) cc_final: 0.7862 (ttm) REVERT: E 249 LEU cc_start: 0.8307 (pp) cc_final: 0.7485 (mt) REVERT: E 252 LYS cc_start: 0.8440 (ptpt) cc_final: 0.8219 (ptmm) REVERT: E 452 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8001 (t-170) REVERT: E 536 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8960 (mp) REVERT: E 581 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7938 (mm-30) REVERT: E 728 MET cc_start: 0.6649 (tmm) cc_final: 0.6385 (ptm) REVERT: G 217 MET cc_start: 0.5413 (pmm) cc_final: 0.5172 (pmm) REVERT: G 226 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7789 (mm-40) REVERT: G 280 MET cc_start: 0.8670 (tmm) cc_final: 0.8256 (tmm) REVERT: G 333 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7105 (tp30) outliers start: 39 outliers final: 32 residues processed: 213 average time/residue: 0.2993 time to fit residues: 98.7121 Evaluate side-chains 218 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 237 CYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 452 HIS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 800 MET Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1173 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 189 optimal weight: 0.0670 chunk 110 optimal weight: 0.0470 chunk 77 optimal weight: 2.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 HIS G 95 HIS G 145 ASN G 737 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104939 restraints weight = 31849.277| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.00 r_work: 0.3051 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 18747 Z= 0.111 Angle : 0.632 10.309 25527 Z= 0.319 Chirality : 0.044 0.249 2757 Planarity : 0.005 0.093 3358 Dihedral : 4.941 54.813 2730 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.62 % Allowed : 17.12 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.17), residues: 2365 helix: 0.17 (0.27), residues: 367 sheet: -1.81 (0.27), residues: 368 loop : -1.61 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP G 502 HIS 0.004 0.001 HIS G 737 PHE 0.021 0.001 PHE E 70 TYR 0.014 0.001 TYR E 658 ARG 0.014 0.000 ARG E 597 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 8) link_NAG-ASN : angle 2.59166 ( 24) hydrogen bonds : bond 0.03256 ( 466) hydrogen bonds : angle 4.84160 ( 1151) SS BOND : bond 0.00260 ( 116) SS BOND : angle 1.11246 ( 232) covalent geometry : bond 0.00251 (18623) covalent geometry : angle 0.62133 (25271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11554.65 seconds wall clock time: 203 minutes 22.77 seconds (12202.77 seconds total)