Starting phenix.real_space_refine on Mon Jul 6 06:59:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvx_34301/07_2026/8gvx_34301_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvx_34301/07_2026/8gvx_34301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gvx_34301/07_2026/8gvx_34301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvx_34301/07_2026/8gvx_34301.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvx_34301/07_2026/8gvx_34301_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvx_34301/07_2026/8gvx_34301_trim.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.039 sd= 0.121 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 16 5.49 5 S 180 5.16 5 C 21284 2.51 5 N 5392 2.21 5 O 5992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32872 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5590 Classifications: {'peptide': 686} Link IDs: {'PTRANS': 27, 'TRANS': 658} Chain breaks: 3 Chain: "F" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 115 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1274 SG CYS B 176 112.442 71.417 103.189 1.00182.40 S ATOM 1288 SG CYS B 178 114.790 73.922 101.370 1.00194.05 S ATOM 1310 SG CYS B 181 111.047 74.024 100.621 1.00194.94 S Restraints were copied for chains: A, C, D, E, G, H Time building chain proxies: 9.11, per 1000 atoms: 0.28 Number of scatterers: 32872 At special positions: 0 Unit cell: (138.176, 138.176, 179.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 180 16.00 P 16 15.00 O 5992 8.00 N 5392 7.00 C 21284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " 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 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 176 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 176 " pdb=" ZN C 803 " pdb="ZN ZN C 803 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 176 " pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 176 " Number of angles added : 12 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7616 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 8 sheets defined 71.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.940A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.578A pdb=" N HIS B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.889A pdb=" N ARG B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.618A pdb=" N ILE B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.552A pdb=" N SER B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.586A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.551A pdb=" N PHE B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 424 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.915A pdb=" N ILE B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 removed outlier: 3.527A pdb=" N ASP B 439 " --> pdb=" O TRP B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 499 removed outlier: 4.091A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.171A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.693A pdb=" N ASN B 552 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS B 553 " --> pdb=" O PRO B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 553' Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.794A pdb=" N THR B 588 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'B' and resid 615 through 650 removed outlier: 4.187A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE B 637 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 731 Processing helix chain 'B' and resid 740 through 761 Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 62 through 69 removed outlier: 3.670A pdb=" N TYR F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.227A pdb=" N GLY F 89 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 removed outlier: 3.750A pdb=" N ASP F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 Processing helix chain 'F' and resid 133 through 142 Processing helix chain 'F' and resid 143 through 146 Processing helix chain 'F' and resid 151 through 158 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 170 through 176 Processing helix chain 'F' and resid 204 through 215 removed outlier: 4.482A pdb=" N LYS F 209 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 210 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE F 212 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS F 213 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 215 " --> pdb=" O ILE F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 241 through 256 Processing helix chain 'F' and resid 257 through 260 removed outlier: 3.758A pdb=" N THR F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 257 through 260' Processing helix chain 'F' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 295 through 309 Processing helix chain 'F' and resid 328 through 347 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.670A pdb=" N TYR E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.228A pdb=" N GLY E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 110 removed outlier: 3.750A pdb=" N ASP E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 133 through 142 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 151 through 158 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 204 through 215 removed outlier: 4.482A pdb=" N LYS E 209 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 210 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE E 212 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS E 213 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 215 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 241 through 256 Processing helix chain 'E' and resid 257 through 260 removed outlier: 3.758A pdb=" N THR E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 257 through 260' Processing helix chain 'E' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'G' and resid 45 through 58 Processing helix chain 'G' and resid 62 through 69 removed outlier: 3.670A pdb=" N TYR G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.228A pdb=" N GLY G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 110 removed outlier: 3.750A pdb=" N ASP G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 133 through 142 Processing helix chain 'G' and resid 143 through 146 Processing helix chain 'G' and resid 151 through 158 Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 170 through 176 Processing helix chain 'G' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS G 209 " --> pdb=" O SER G 206 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS G 210 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE G 212 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS G 213 " --> pdb=" O LYS G 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE G 215 " --> pdb=" O ILE G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 230 No H-bonds generated for 'chain 'G' and resid 228 through 230' Processing helix chain 'G' and resid 241 through 256 Processing helix chain 'G' and resid 257 through 260 removed outlier: 3.757A pdb=" N THR G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 257 through 260' Processing helix chain 'G' and resid 270 through 279 removed outlier: 4.161A pdb=" N LYS G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 286 Processing helix chain 'G' and resid 295 through 309 Processing helix chain 'G' and resid 328 through 347 Processing helix chain 'H' and resid 45 through 58 Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.672A pdb=" N TYR H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.228A pdb=" N GLY H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG H 90 " --> pdb=" O ARG H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.750A pdb=" N ASP H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 132 Processing helix chain 'H' and resid 133 through 142 Processing helix chain 'H' and resid 143 through 146 Processing helix chain 'H' and resid 151 through 158 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 170 through 176 Processing helix chain 'H' and resid 204 through 215 removed outlier: 4.482A pdb=" N LYS H 209 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS H 210 " --> pdb=" O GLU H 207 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE H 212 " --> pdb=" O LYS H 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 213 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE H 215 " --> pdb=" O ILE H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 230 No H-bonds generated for 'chain 'H' and resid 228 through 230' Processing helix chain 'H' and resid 241 through 256 Processing helix chain 'H' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 257 through 260' Processing helix chain 'H' and resid 270 through 279 removed outlier: 4.161A pdb=" N LYS H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 286 Processing helix chain 'H' and resid 295 through 309 Processing helix chain 'H' and resid 328 through 347 Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.941A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.578A pdb=" N HIS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.888A pdb=" N ARG A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.618A pdb=" N ILE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.552A pdb=" N SER A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.587A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.551A pdb=" N PHE A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 424 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.915A pdb=" N ILE A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 removed outlier: 3.528A pdb=" N ASP A 439 " --> pdb=" O TRP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 499 removed outlier: 4.091A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.170A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.694A pdb=" N ASN A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS A 553 " --> pdb=" O PRO A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 553' Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.794A pdb=" N THR A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 615 through 650 removed outlier: 4.187A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 731 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.940A pdb=" N GLU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.578A pdb=" N HIS C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.889A pdb=" N ARG C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.618A pdb=" N ILE C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 removed outlier: 3.552A pdb=" N SER C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.586A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 339 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.551A pdb=" N PHE C 359 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 360 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 424 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.915A pdb=" N ILE C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 removed outlier: 3.527A pdb=" N ASP C 439 " --> pdb=" O TRP C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 499 removed outlier: 4.091A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.170A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.693A pdb=" N ASN C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS C 553 " --> pdb=" O PRO C 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 553' Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 585 through 589 removed outlier: 3.794A pdb=" N THR C 588 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'C' and resid 615 through 650 removed outlier: 4.188A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE C 637 " --> pdb=" O ASP C 633 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 731 Processing helix chain 'C' and resid 740 through 761 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.940A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.579A pdb=" N HIS D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.888A pdb=" N ARG D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.618A pdb=" N ILE D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 removed outlier: 3.552A pdb=" N SER D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.587A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 339 Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.551A pdb=" N PHE D 359 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE D 360 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 424 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 426 through 431 removed outlier: 3.915A pdb=" N ILE D 431 " --> pdb=" O PHE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 460 removed outlier: 3.527A pdb=" N ASP D 439 " --> pdb=" O TRP D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 499 removed outlier: 4.092A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.170A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.692A pdb=" N ASN D 552 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS D 553 " --> pdb=" O PRO D 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 549 through 553' Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 585 through 589 removed outlier: 3.794A pdb=" N THR D 588 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 615 Processing helix chain 'D' and resid 615 through 650 removed outlier: 4.187A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE D 637 " --> pdb=" O ASP D 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 649 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 731 Processing helix chain 'D' and resid 740 through 761 Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AA3, first strand: chain 'F' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL F 34 " --> pdb=" O LYS F 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE F 199 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU F 36 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL F 201 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS F 35 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE F 222 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 37 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS F 224 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU F 39 " --> pdb=" O CYS F 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA F 226 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE F 264 " --> pdb=" O TYR F 320 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS F 322 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU F 266 " --> pdb=" O HIS F 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 184 through 191 removed outlier: 6.407A pdb=" N VAL E 34 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE E 199 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU E 36 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL E 201 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU E 38 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS E 35 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE E 222 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU E 37 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N CYS E 224 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 39 " --> pdb=" O CYS E 224 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ALA E 226 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE E 264 " --> pdb=" O TYR E 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS E 322 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 266 " --> pdb=" O HIS E 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL G 34 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE G 199 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU G 36 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL G 201 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU G 38 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS G 35 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE G 222 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU G 37 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS G 224 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU G 39 " --> pdb=" O CYS G 224 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ALA G 226 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE G 264 " --> pdb=" O TYR G 320 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS G 322 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU G 266 " --> pdb=" O HIS G 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 184 through 191 removed outlier: 6.407A pdb=" N VAL H 34 " --> pdb=" O LYS H 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE H 199 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU H 36 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL H 201 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU H 38 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS H 35 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE H 222 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU H 37 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS H 224 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU H 39 " --> pdb=" O CYS H 224 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ALA H 226 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE H 264 " --> pdb=" O TYR H 320 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS H 322 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU H 266 " --> pdb=" O HIS H 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA8, first strand: chain 'C' and resid 18 through 19 1916 hydrogen bonds defined for protein. 5556 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: 7.39 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5670 1.32 - 1.45: 8799 1.45 - 1.58: 18751 1.58 - 1.70: 76 1.70 - 1.83: 284 Bond restraints: 33580 Sorted by residual: bond pdb=" C SER E 263 " pdb=" N ILE E 264 " ideal model delta sigma weight residual 1.329 1.448 -0.120 1.31e-02 5.83e+03 8.33e+01 bond pdb=" C SER F 263 " pdb=" N ILE F 264 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.31e-02 5.83e+03 8.30e+01 bond pdb=" C SER G 263 " pdb=" N ILE G 264 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.31e-02 5.83e+03 8.29e+01 bond pdb=" C SER H 263 " pdb=" N ILE H 264 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.31e-02 5.83e+03 8.25e+01 bond pdb=" CA VAL E 50 " pdb=" CB VAL E 50 " ideal model delta sigma weight residual 1.540 1.597 -0.057 1.25e-02 6.40e+03 2.07e+01 ... (remaining 33575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 44324 2.82 - 5.63: 924 5.63 - 8.45: 128 8.45 - 11.26: 44 11.26 - 14.08: 4 Bond angle restraints: 45424 Sorted by residual: angle pdb=" C ASP H 133 " pdb=" N GLY H 134 " pdb=" CA GLY H 134 " ideal model delta sigma weight residual 120.00 111.74 8.26 1.10e+00 8.26e-01 5.64e+01 angle pdb=" C ASP F 133 " pdb=" N GLY F 134 " pdb=" CA GLY F 134 " ideal model delta sigma weight residual 120.00 111.75 8.25 1.10e+00 8.26e-01 5.63e+01 angle pdb=" C ASP E 133 " pdb=" N GLY E 134 " pdb=" CA GLY E 134 " ideal model delta sigma weight residual 120.00 111.79 8.21 1.10e+00 8.26e-01 5.58e+01 angle pdb=" O ASP H 133 " pdb=" C ASP H 133 " pdb=" N GLY H 134 " ideal model delta sigma weight residual 122.86 131.66 -8.80 1.18e+00 7.18e-01 5.56e+01 angle pdb=" C ASP G 133 " pdb=" N GLY G 134 " pdb=" CA GLY G 134 " ideal model delta sigma weight residual 120.00 111.80 8.20 1.10e+00 8.26e-01 5.56e+01 ... (remaining 45419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 19888 35.30 - 70.60: 440 70.60 - 105.89: 24 105.89 - 141.19: 28 141.19 - 176.49: 12 Dihedral angle restraints: 20392 sinusoidal: 8668 harmonic: 11724 Sorted by residual: dihedral pdb=" CB CYS A 553 " pdb=" SG CYS A 553 " pdb=" SG CYS A 558 " pdb=" CB CYS A 558 " ideal model delta sinusoidal sigma weight residual 93.00 152.35 -59.35 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS D 553 " pdb=" SG CYS D 553 " pdb=" SG CYS D 558 " pdb=" CB CYS D 558 " ideal model delta sinusoidal sigma weight residual 93.00 152.35 -59.35 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS B 553 " pdb=" SG CYS B 553 " pdb=" SG CYS B 558 " pdb=" CB CYS B 558 " ideal model delta sinusoidal sigma weight residual 93.00 152.35 -59.35 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 20389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4276 0.077 - 0.155: 658 0.155 - 0.232: 126 0.232 - 0.309: 16 0.309 - 0.387: 12 Chirality restraints: 5088 Sorted by residual: chirality pdb=" CA GLU G 58 " pdb=" N GLU G 58 " pdb=" C GLU G 58 " pdb=" CB GLU G 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA GLU H 58 " pdb=" N GLU H 58 " pdb=" C GLU H 58 " pdb=" CB GLU H 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA GLU E 58 " pdb=" N GLU E 58 " pdb=" C GLU E 58 " pdb=" CB GLU E 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 5085 not shown) Planarity restraints: 5644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 743 " 0.034 2.00e-02 2.50e+03 6.05e-02 6.41e+01 pdb=" CG PHE A 743 " -0.133 2.00e-02 2.50e+03 pdb=" CD1 PHE A 743 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE A 743 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE A 743 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 743 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 743 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 743 " -0.033 2.00e-02 2.50e+03 6.05e-02 6.40e+01 pdb=" CG PHE C 743 " 0.133 2.00e-02 2.50e+03 pdb=" CD1 PHE C 743 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE C 743 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE C 743 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 743 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 743 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 743 " -0.034 2.00e-02 2.50e+03 6.05e-02 6.40e+01 pdb=" CG PHE B 743 " 0.133 2.00e-02 2.50e+03 pdb=" CD1 PHE B 743 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE B 743 " -0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE B 743 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 743 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 743 " 0.006 2.00e-02 2.50e+03 ... (remaining 5641 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 989 2.72 - 3.26: 33980 3.26 - 3.81: 53043 3.81 - 4.35: 67339 4.35 - 4.90: 112320 Nonbonded interactions: 267671 Sorted by model distance: nonbonded pdb=" OE1 GLN B 537 " pdb=" OG SER C 385 " model vdw 2.173 3.040 nonbonded pdb=" OG SER B 385 " pdb=" OE1 GLN A 537 " model vdw 2.174 3.040 nonbonded pdb=" OE1 GLN C 537 " pdb=" OG SER D 385 " model vdw 2.175 3.040 nonbonded pdb=" OG SER A 385 " pdb=" OE1 GLN D 537 " model vdw 2.175 3.040 nonbonded pdb=" O ILE C 209 " pdb=" OG SER C 213 " model vdw 2.199 3.040 ... (remaining 267666 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: 0.11 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.980 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.008 0.120 33600 Z= 0.482 Angle : 1.011 14.076 45444 Z= 0.617 Chirality : 0.061 0.387 5088 Planarity : 0.006 0.067 5644 Dihedral : 16.267 176.489 12764 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.68 % Allowed : 2.37 % Favored : 96.96 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.11), residues: 3916 helix: -0.45 (0.08), residues: 2552 sheet: -1.41 (0.48), residues: 116 loop : -0.68 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 176 TYR 0.024 0.003 TYR H 155 PHE 0.133 0.003 PHE A 743 TRP 0.020 0.002 TRP C 416 HIS 0.007 0.001 HIS H 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.48 (33580) covalent geometry : angle 1.01045 / 0.62 (45424) SS BOND : bond 0.00187 / 0.09 ( 4) SS BOND : angle 0.90673 / 0.56 ( 8) hydrogen bonds : bond 0.16370 / 10.90 ( 1916) hydrogen bonds : angle 6.12982 / 4.36 ( 5556) metal coordination : bond 0.00635 / 0.51 ( 16) metal coordination : angle 2.23740 / 1.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 MET cc_start: 0.7805 (mmp) cc_final: 0.7327 (mmm) REVERT: B 344 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7379 (tp) REVERT: B 743 PHE cc_start: 0.7836 (m-10) cc_final: 0.7478 (m-80) REVERT: F 243 MET cc_start: 0.7828 (tpp) cc_final: 0.7376 (tpp) REVERT: F 247 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8387 (mtt) REVERT: G 247 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8392 (mtt) REVERT: H 243 MET cc_start: 0.7783 (tpp) cc_final: 0.6963 (tpp) REVERT: H 247 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8351 (mtt) REVERT: A 335 MET cc_start: 0.7776 (mmp) cc_final: 0.7374 (mmm) REVERT: A 344 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7420 (tp) REVERT: A 437 LEU cc_start: 0.8304 (mt) cc_final: 0.8098 (tt) REVERT: A 524 TYR cc_start: 0.8634 (t80) cc_final: 0.8430 (t80) REVERT: A 648 MET cc_start: 0.9225 (mtm) cc_final: 0.8979 (mtm) REVERT: A 743 PHE cc_start: 0.7974 (m-10) cc_final: 0.7576 (m-80) REVERT: C 319 PHE cc_start: 0.9095 (m-80) cc_final: 0.8793 (m-10) REVERT: C 335 MET cc_start: 0.7847 (mmp) cc_final: 0.7351 (mmm) REVERT: C 524 TYR cc_start: 0.8645 (t80) cc_final: 0.8329 (t80) REVERT: C 603 THR cc_start: 0.8929 (m) cc_final: 0.8516 (p) REVERT: C 648 MET cc_start: 0.9236 (mtm) cc_final: 0.9017 (mtp) REVERT: C 743 PHE cc_start: 0.7965 (m-10) cc_final: 0.7625 (m-80) REVERT: D 335 MET cc_start: 0.7807 (mmp) cc_final: 0.7392 (mmm) REVERT: D 344 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7401 (tp) REVERT: D 437 LEU cc_start: 0.8329 (mt) cc_final: 0.8122 (tt) REVERT: D 524 TYR cc_start: 0.8665 (t80) cc_final: 0.8213 (t80) REVERT: D 743 PHE cc_start: 0.7883 (m-10) cc_final: 0.7525 (m-80) outliers start: 24 outliers final: 5 residues processed: 224 average time/residue: 0.2415 time to fit residues: 86.4044 Evaluate side-chains 147 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 HIS B 742 ASN H 306 GLN A 443 ASN A 533 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 HIS A 709 GLN A 742 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 533 ASN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 634 HIS C 742 ASN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN D 533 ASN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 HIS D 709 GLN D 742 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.061438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050512 restraints weight = 172461.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052201 restraints weight = 85754.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.053338 restraints weight = 53614.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.054076 restraints weight = 38882.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.054566 restraints weight = 31303.732| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33600 Z= 0.166 Angle : 0.562 10.545 45444 Z= 0.295 Chirality : 0.039 0.137 5088 Planarity : 0.004 0.049 5644 Dihedral : 13.365 167.644 4934 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.39 % Allowed : 5.92 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.13), residues: 3916 helix: 1.54 (0.10), residues: 2596 sheet: -1.08 (0.41), residues: 152 loop : -0.13 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 132 TYR 0.016 0.001 TYR C 524 PHE 0.014 0.001 PHE H 196 TRP 0.016 0.001 TRP A 327 HIS 0.007 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (33580) covalent geometry : angle 0.56105 / 0.30 (45424) SS BOND : bond 0.00183 / 0.09 ( 4) SS BOND : angle 0.84539 / 0.52 ( 8) hydrogen bonds : bond 0.04658 / 3.11 ( 1916) hydrogen bonds : angle 4.15742 / 2.94 ( 5556) metal coordination : bond 0.01449 / 1.16 ( 16) metal coordination : angle 2.21152 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 MET cc_start: 0.8045 (mmp) cc_final: 0.7687 (mmm) REVERT: B 380 MET cc_start: 0.9163 (mmm) cc_final: 0.8864 (tpp) REVERT: B 406 MET cc_start: 0.8761 (ppp) cc_final: 0.8195 (ppp) REVERT: B 460 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7238 (t80) REVERT: F 53 MET cc_start: 0.8379 (tmm) cc_final: 0.7923 (tmm) REVERT: F 243 MET cc_start: 0.9047 (tpp) cc_final: 0.8624 (tpp) REVERT: F 247 MET cc_start: 0.9028 (mtp) cc_final: 0.8530 (tmm) REVERT: E 53 MET cc_start: 0.8357 (tmm) cc_final: 0.7968 (tmm) REVERT: E 247 MET cc_start: 0.9046 (mtp) cc_final: 0.8596 (tmm) REVERT: G 53 MET cc_start: 0.8345 (tmm) cc_final: 0.8095 (tmm) REVERT: G 243 MET cc_start: 0.9194 (tpp) cc_final: 0.8983 (tpp) REVERT: G 247 MET cc_start: 0.9050 (mtp) cc_final: 0.8481 (tmm) REVERT: G 310 LEU cc_start: 0.8982 (mt) cc_final: 0.7966 (mt) REVERT: H 187 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.7155 (m) REVERT: H 243 MET cc_start: 0.9027 (tpp) cc_final: 0.8607 (tpp) REVERT: H 247 MET cc_start: 0.9040 (mtp) cc_final: 0.8483 (tmm) REVERT: H 310 LEU cc_start: 0.8993 (mt) cc_final: 0.8000 (mt) REVERT: A 335 MET cc_start: 0.8013 (mmp) cc_final: 0.7677 (mmm) REVERT: A 380 MET cc_start: 0.9163 (mmm) cc_final: 0.8905 (tpp) REVERT: A 406 MET cc_start: 0.8778 (ppp) cc_final: 0.8134 (ppp) REVERT: C 319 PHE cc_start: 0.9099 (m-80) cc_final: 0.8767 (m-10) REVERT: C 335 MET cc_start: 0.8053 (mmp) cc_final: 0.7749 (mmm) REVERT: C 336 THR cc_start: 0.9297 (t) cc_final: 0.9030 (p) REVERT: D 319 PHE cc_start: 0.9117 (m-80) cc_final: 0.8783 (m-10) REVERT: D 335 MET cc_start: 0.8019 (mmp) cc_final: 0.7689 (mmm) REVERT: D 344 LEU cc_start: 0.7939 (tp) cc_final: 0.7523 (tp) outliers start: 14 outliers final: 3 residues processed: 167 average time/residue: 0.2070 time to fit residues: 59.5735 Evaluate side-chains 149 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain D residue 604 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 323 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 354 optimal weight: 4.9990 chunk 243 optimal weight: 0.0000 chunk 122 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.060320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048984 restraints weight = 192067.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050582 restraints weight = 100161.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051592 restraints weight = 66085.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052235 restraints weight = 50695.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052619 restraints weight = 42841.415| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 33600 Z= 0.279 Angle : 0.646 7.390 45444 Z= 0.343 Chirality : 0.041 0.151 5088 Planarity : 0.004 0.043 5644 Dihedral : 12.849 166.269 4908 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.73 % Allowed : 8.09 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.13), residues: 3916 helix: 1.90 (0.10), residues: 2592 sheet: -0.82 (0.38), residues: 172 loop : -0.35 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 208 TYR 0.019 0.002 TYR C 524 PHE 0.030 0.002 PHE C 341 TRP 0.023 0.002 TRP C 327 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.28 (33580) covalent geometry : angle 0.64577 / 0.34 (45424) SS BOND : bond 0.00370 / 0.19 ( 4) SS BOND : angle 1.00660 / 0.67 ( 8) hydrogen bonds : bond 0.05013 / 3.37 ( 1916) hydrogen bonds : angle 4.41919 / 3.13 ( 5556) metal coordination : bond 0.02704 / 2.20 ( 16) metal coordination : angle 1.50978 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LYS cc_start: 0.9276 (tttt) cc_final: 0.9038 (ttpt) REVERT: B 335 MET cc_start: 0.8322 (mmp) cc_final: 0.7853 (mmm) REVERT: B 344 LEU cc_start: 0.7948 (tp) cc_final: 0.7484 (tp) REVERT: B 380 MET cc_start: 0.9186 (mmm) cc_final: 0.8106 (tpp) REVERT: B 634 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8099 (m90) REVERT: F 53 MET cc_start: 0.8443 (tmm) cc_final: 0.7936 (tmm) REVERT: F 243 MET cc_start: 0.9162 (tpp) cc_final: 0.8367 (tpp) REVERT: F 247 MET cc_start: 0.8989 (mtp) cc_final: 0.8638 (tmm) REVERT: E 247 MET cc_start: 0.8959 (mtp) cc_final: 0.8741 (tmm) REVERT: G 53 MET cc_start: 0.8415 (tmm) cc_final: 0.8211 (tmm) REVERT: G 243 MET cc_start: 0.9283 (tpp) cc_final: 0.8538 (tpp) REVERT: G 247 MET cc_start: 0.8972 (mtp) cc_final: 0.8729 (tmm) REVERT: H 198 MET cc_start: 0.7649 (ppp) cc_final: 0.7308 (ppp) REVERT: H 243 MET cc_start: 0.9118 (tpp) cc_final: 0.8396 (tpp) REVERT: H 247 MET cc_start: 0.8934 (mtp) cc_final: 0.8626 (tmm) REVERT: H 310 LEU cc_start: 0.9167 (mt) cc_final: 0.8865 (mt) REVERT: A 49 LYS cc_start: 0.9259 (tttt) cc_final: 0.9028 (ttpt) REVERT: A 324 ARG cc_start: 0.8236 (mtt180) cc_final: 0.7702 (mtm180) REVERT: A 335 MET cc_start: 0.8280 (mmp) cc_final: 0.7869 (mmm) REVERT: A 344 LEU cc_start: 0.7987 (tp) cc_final: 0.7524 (tp) REVERT: A 380 MET cc_start: 0.9171 (mmm) cc_final: 0.8143 (tpp) REVERT: A 743 PHE cc_start: 0.8719 (m-80) cc_final: 0.8498 (t80) REVERT: C 335 MET cc_start: 0.8337 (mmp) cc_final: 0.7923 (mmm) REVERT: C 336 THR cc_start: 0.9389 (t) cc_final: 0.9165 (p) REVERT: C 344 LEU cc_start: 0.7967 (tp) cc_final: 0.7512 (tp) REVERT: C 380 MET cc_start: 0.9167 (mmm) cc_final: 0.8780 (tpp) REVERT: C 406 MET cc_start: 0.8615 (ppp) cc_final: 0.7963 (ppp) REVERT: D 49 LYS cc_start: 0.9244 (tttt) cc_final: 0.9018 (ttpt) REVERT: D 319 PHE cc_start: 0.9182 (m-80) cc_final: 0.8902 (m-10) REVERT: D 335 MET cc_start: 0.8300 (mmp) cc_final: 0.7840 (mmm) REVERT: D 344 LEU cc_start: 0.8103 (tp) cc_final: 0.7689 (tp) REVERT: D 743 PHE cc_start: 0.8682 (m-80) cc_final: 0.8480 (t80) outliers start: 26 outliers final: 12 residues processed: 179 average time/residue: 0.2099 time to fit residues: 63.6833 Evaluate side-chains 160 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 613 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 153 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 391 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 366 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 345 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.061212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.049940 restraints weight = 189900.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.051528 restraints weight = 99038.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.052562 restraints weight = 65729.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053203 restraints weight = 50350.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.053636 restraints weight = 42563.084| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33600 Z= 0.151 Angle : 0.511 7.064 45444 Z= 0.269 Chirality : 0.038 0.125 5088 Planarity : 0.004 0.038 5644 Dihedral : 12.316 169.418 4908 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.56 % Allowed : 9.16 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.14), residues: 3916 helix: 2.22 (0.10), residues: 2600 sheet: -0.81 (0.38), residues: 172 loop : -0.23 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 208 TYR 0.016 0.001 TYR C 524 PHE 0.015 0.001 PHE D 341 TRP 0.018 0.001 TRP C 327 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (33580) covalent geometry : angle 0.51069 / 0.27 (45424) SS BOND : bond 0.00239 / 0.12 ( 4) SS BOND : angle 0.71155 / 0.48 ( 8) hydrogen bonds : bond 0.04249 / 2.84 ( 1916) hydrogen bonds : angle 4.00885 / 2.83 ( 5556) metal coordination : bond 0.01299 / 1.04 ( 16) metal coordination : angle 1.40646 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 MET cc_start: 0.8302 (mmp) cc_final: 0.7826 (mmm) REVERT: B 344 LEU cc_start: 0.7841 (tp) cc_final: 0.7353 (tp) REVERT: B 380 MET cc_start: 0.9152 (mmm) cc_final: 0.8035 (tpp) REVERT: B 406 MET cc_start: 0.8851 (ppp) cc_final: 0.8568 (ppp) REVERT: B 619 MET cc_start: 0.8170 (tmm) cc_final: 0.7774 (tmm) REVERT: B 634 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.8231 (m90) REVERT: B 743 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8493 (t80) REVERT: F 53 MET cc_start: 0.8416 (tmm) cc_final: 0.7941 (tmm) REVERT: F 188 HIS cc_start: 0.7232 (m90) cc_final: 0.6946 (m90) REVERT: F 243 MET cc_start: 0.9105 (tpp) cc_final: 0.8290 (tpp) REVERT: F 247 MET cc_start: 0.8892 (mtp) cc_final: 0.8544 (tmm) REVERT: E 53 MET cc_start: 0.8322 (tmm) cc_final: 0.7973 (tmm) REVERT: E 247 MET cc_start: 0.8894 (mtp) cc_final: 0.8653 (tmm) REVERT: G 243 MET cc_start: 0.9211 (tpp) cc_final: 0.8447 (tpp) REVERT: G 247 MET cc_start: 0.8924 (mtp) cc_final: 0.8663 (tmm) REVERT: H 243 MET cc_start: 0.9063 (tpp) cc_final: 0.8337 (tpp) REVERT: H 247 MET cc_start: 0.8907 (mtp) cc_final: 0.8628 (tmm) REVERT: A 49 LYS cc_start: 0.9196 (tttt) cc_final: 0.8976 (ttpt) REVERT: A 324 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7989 (mtm180) REVERT: A 335 MET cc_start: 0.8269 (mmp) cc_final: 0.7844 (mmm) REVERT: A 344 LEU cc_start: 0.7847 (tp) cc_final: 0.7341 (tp) REVERT: A 380 MET cc_start: 0.9109 (mmm) cc_final: 0.8088 (tpp) REVERT: A 743 PHE cc_start: 0.8609 (m-80) cc_final: 0.8356 (t80) REVERT: C 335 MET cc_start: 0.8310 (mmp) cc_final: 0.7868 (mmm) REVERT: C 336 THR cc_start: 0.9332 (t) cc_final: 0.9107 (p) REVERT: C 344 LEU cc_start: 0.7885 (tp) cc_final: 0.7430 (tp) REVERT: C 380 MET cc_start: 0.9132 (mmm) cc_final: 0.8393 (tpt) REVERT: C 406 MET cc_start: 0.8562 (ppp) cc_final: 0.8280 (ppp) REVERT: C 743 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8543 (t80) REVERT: D 49 LYS cc_start: 0.9209 (tttt) cc_final: 0.8980 (ttpt) REVERT: D 319 PHE cc_start: 0.9201 (m-80) cc_final: 0.8951 (m-10) REVERT: D 335 MET cc_start: 0.8265 (mmp) cc_final: 0.7798 (mmm) REVERT: D 344 LEU cc_start: 0.8017 (tp) cc_final: 0.7513 (tp) REVERT: D 380 MET cc_start: 0.9089 (mmp) cc_final: 0.8881 (mmm) REVERT: D 406 MET cc_start: 0.8747 (ppp) cc_final: 0.8121 (ppp) outliers start: 20 outliers final: 13 residues processed: 168 average time/residue: 0.2087 time to fit residues: 59.6105 Evaluate side-chains 163 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 743 PHE Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 198 MET Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 743 PHE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 746 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 280 optimal weight: 10.0000 chunk 12 optimal weight: 0.0270 chunk 55 optimal weight: 0.9990 chunk 335 optimal weight: 0.0000 chunk 105 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** D 562 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 = 0.3395 r_free = 0.3395 target = 0.061071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049728 restraints weight = 190568.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051341 restraints weight = 100628.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052375 restraints weight = 66557.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.053007 restraints weight = 50958.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.053438 restraints weight = 43082.939| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33600 Z= 0.154 Angle : 0.506 8.492 45444 Z= 0.265 Chirality : 0.038 0.122 5088 Planarity : 0.003 0.037 5644 Dihedral : 11.901 175.773 4908 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.96 % Allowed : 9.58 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.14), residues: 3916 helix: 2.28 (0.10), residues: 2624 sheet: -0.73 (0.38), residues: 172 loop : -0.12 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.017 0.001 TYR D 118 PHE 0.030 0.001 PHE A 341 TRP 0.020 0.001 TRP B 327 HIS 0.003 0.001 HIS D 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (33580) covalent geometry : angle 0.50560 / 0.27 (45424) SS BOND : bond 0.00237 / 0.12 ( 4) SS BOND : angle 0.60737 / 0.39 ( 8) hydrogen bonds : bond 0.04084 / 2.74 ( 1916) hydrogen bonds : angle 3.95607 / 2.80 ( 5556) metal coordination : bond 0.01222 / 0.97 ( 16) metal coordination : angle 1.43867 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 MET cc_start: 0.8366 (mmp) cc_final: 0.7922 (mmm) REVERT: B 344 LEU cc_start: 0.7852 (tp) cc_final: 0.7303 (tp) REVERT: B 380 MET cc_start: 0.9203 (mmm) cc_final: 0.8056 (tpp) REVERT: B 619 MET cc_start: 0.8157 (tmm) cc_final: 0.7741 (tmm) REVERT: B 634 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.8159 (m90) REVERT: B 743 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8580 (t80) REVERT: F 53 MET cc_start: 0.8479 (tmm) cc_final: 0.8010 (tmm) REVERT: F 188 HIS cc_start: 0.7351 (m90) cc_final: 0.7040 (m90) REVERT: F 243 MET cc_start: 0.9169 (tpp) cc_final: 0.8368 (tpp) REVERT: F 247 MET cc_start: 0.8986 (mtp) cc_final: 0.8588 (tmm) REVERT: E 53 MET cc_start: 0.8433 (tmm) cc_final: 0.8080 (tmm) REVERT: E 247 MET cc_start: 0.8983 (mtp) cc_final: 0.8619 (tmm) REVERT: G 243 MET cc_start: 0.9285 (tpp) cc_final: 0.8365 (tpp) REVERT: G 247 MET cc_start: 0.9005 (mtp) cc_final: 0.8697 (tmm) REVERT: H 187 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8452 (p) REVERT: H 243 MET cc_start: 0.9129 (tpp) cc_final: 0.8397 (tpp) REVERT: H 247 MET cc_start: 0.8964 (mtp) cc_final: 0.8668 (tmm) REVERT: A 335 MET cc_start: 0.8407 (mmp) cc_final: 0.8048 (mmm) REVERT: A 336 THR cc_start: 0.9325 (t) cc_final: 0.9098 (p) REVERT: A 344 LEU cc_start: 0.7857 (tp) cc_final: 0.7312 (tp) REVERT: A 380 MET cc_start: 0.9139 (mmm) cc_final: 0.8128 (tpp) REVERT: C 324 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7739 (mtm180) REVERT: C 335 MET cc_start: 0.8309 (mmp) cc_final: 0.7866 (mmp) REVERT: C 336 THR cc_start: 0.9330 (t) cc_final: 0.9107 (p) REVERT: C 344 LEU cc_start: 0.7839 (tp) cc_final: 0.7305 (tp) REVERT: C 380 MET cc_start: 0.9155 (mmm) cc_final: 0.8008 (tpp) REVERT: C 743 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8608 (t80) REVERT: D 49 LYS cc_start: 0.9295 (tttt) cc_final: 0.9011 (ttpt) REVERT: D 319 PHE cc_start: 0.9234 (m-80) cc_final: 0.9025 (m-10) REVERT: D 335 MET cc_start: 0.8327 (mmp) cc_final: 0.7893 (mmm) REVERT: D 344 LEU cc_start: 0.7859 (tp) cc_final: 0.7351 (tp) REVERT: D 406 MET cc_start: 0.8721 (ppp) cc_final: 0.8256 (ppp) REVERT: D 619 MET cc_start: 0.8184 (tmm) cc_final: 0.7975 (tmm) REVERT: D 743 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8505 (t80) outliers start: 34 outliers final: 18 residues processed: 180 average time/residue: 0.1930 time to fit residues: 59.3800 Evaluate side-chains 174 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 743 PHE Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 743 PHE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 743 PHE Chi-restraints excluded: chain D residue 746 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 299 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 269 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 291 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 356 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 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 = 0.3417 r_free = 0.3417 target = 0.061702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050426 restraints weight = 189630.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052021 restraints weight = 99552.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053051 restraints weight = 66106.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.053711 restraints weight = 50774.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054130 restraints weight = 42883.887| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 33600 Z= 0.112 Angle : 0.480 8.755 45444 Z= 0.249 Chirality : 0.037 0.130 5088 Planarity : 0.003 0.037 5644 Dihedral : 11.424 174.779 4908 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.96 % Allowed : 9.84 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.14), residues: 3916 helix: 2.41 (0.10), residues: 2604 sheet: -0.65 (0.39), residues: 172 loop : -0.02 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 86 TYR 0.014 0.001 TYR B 524 PHE 0.028 0.001 PHE B 341 TRP 0.017 0.001 TRP D 327 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (33580) covalent geometry : angle 0.47935 / 0.25 (45424) SS BOND : bond 0.00168 / 0.08 ( 4) SS BOND : angle 0.45231 / 0.29 ( 8) hydrogen bonds : bond 0.03749 / 2.51 ( 1916) hydrogen bonds : angle 3.76108 / 2.65 ( 5556) metal coordination : bond 0.00646 / 0.49 ( 16) metal coordination : angle 1.42782 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 1.366 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: B 86 MET cc_start: 0.8765 (ttm) cc_final: 0.8495 (mmt) REVERT: B 335 MET cc_start: 0.8343 (mmp) cc_final: 0.7885 (mmm) REVERT: B 344 LEU cc_start: 0.7632 (tp) cc_final: 0.7050 (tp) REVERT: B 380 MET cc_start: 0.9174 (mmm) cc_final: 0.8077 (tpp) REVERT: B 619 MET cc_start: 0.8106 (tmm) cc_final: 0.7666 (tmm) REVERT: B 634 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8120 (m90) REVERT: F 53 MET cc_start: 0.8432 (tmm) cc_final: 0.7988 (tmm) REVERT: F 188 HIS cc_start: 0.7407 (m90) cc_final: 0.7093 (m90) REVERT: F 243 MET cc_start: 0.9128 (tpp) cc_final: 0.8429 (tpp) REVERT: F 247 MET cc_start: 0.8947 (mtp) cc_final: 0.8515 (tmm) REVERT: E 53 MET cc_start: 0.8376 (tmm) cc_final: 0.8005 (tmm) REVERT: E 247 MET cc_start: 0.8894 (mtp) cc_final: 0.8463 (tmm) REVERT: G 243 MET cc_start: 0.9245 (tpp) cc_final: 0.8333 (tpp) REVERT: G 247 MET cc_start: 0.8934 (mtp) cc_final: 0.8636 (tmm) REVERT: H 53 MET cc_start: 0.8319 (tmm) cc_final: 0.8024 (tmm) REVERT: H 243 MET cc_start: 0.9102 (tpp) cc_final: 0.8366 (tpp) REVERT: H 247 MET cc_start: 0.8951 (mtp) cc_final: 0.8688 (tmm) REVERT: A 335 MET cc_start: 0.8344 (mmp) cc_final: 0.7983 (mmm) REVERT: A 336 THR cc_start: 0.9304 (t) cc_final: 0.9050 (p) REVERT: A 344 LEU cc_start: 0.7679 (tp) cc_final: 0.7091 (tp) REVERT: A 380 MET cc_start: 0.9138 (mmm) cc_final: 0.8155 (tpp) REVERT: A 743 PHE cc_start: 0.8740 (m-80) cc_final: 0.8493 (t80) REVERT: C 147 MET cc_start: 0.8358 (ptp) cc_final: 0.8106 (ptt) REVERT: C 324 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7755 (mtm180) REVERT: C 335 MET cc_start: 0.8277 (mmp) cc_final: 0.7835 (mmp) REVERT: C 336 THR cc_start: 0.9298 (t) cc_final: 0.9064 (p) REVERT: C 380 MET cc_start: 0.9124 (mmm) cc_final: 0.8009 (tpp) REVERT: C 613 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8692 (mm) REVERT: C 743 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8531 (t80) REVERT: D 49 LYS cc_start: 0.9233 (tttt) cc_final: 0.8985 (ttpt) REVERT: D 335 MET cc_start: 0.8332 (mmp) cc_final: 0.7881 (mmm) REVERT: D 344 LEU cc_start: 0.7809 (tp) cc_final: 0.7261 (tp) REVERT: D 380 MET cc_start: 0.9028 (mmm) cc_final: 0.8040 (tpp) REVERT: D 619 MET cc_start: 0.8133 (tmm) cc_final: 0.7834 (tmm) REVERT: D 743 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8464 (t80) outliers start: 34 outliers final: 16 residues processed: 185 average time/residue: 0.2010 time to fit residues: 63.5149 Evaluate side-chains 168 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 743 PHE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 743 PHE Chi-restraints excluded: chain D residue 746 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 216 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 247 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 742 ASN ** D 562 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 = 0.3399 r_free = 0.3399 target = 0.061115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049708 restraints weight = 190786.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.051319 restraints weight = 101091.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.052353 restraints weight = 67032.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053012 restraints weight = 51394.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.053375 restraints weight = 43364.611| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33600 Z= 0.151 Angle : 0.511 11.597 45444 Z= 0.263 Chirality : 0.038 0.184 5088 Planarity : 0.003 0.037 5644 Dihedral : 10.986 171.825 4908 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.73 % Allowed : 10.48 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.14), residues: 3916 helix: 2.42 (0.10), residues: 2628 sheet: -0.53 (0.39), residues: 172 loop : 0.01 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 86 TYR 0.015 0.001 TYR B 524 PHE 0.033 0.001 PHE A 341 TRP 0.019 0.001 TRP D 327 HIS 0.003 0.001 HIS D 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (33580) covalent geometry : angle 0.51041 / 0.26 (45424) SS BOND : bond 0.00197 / 0.10 ( 4) SS BOND : angle 0.53656 / 0.36 ( 8) hydrogen bonds : bond 0.03866 / 2.59 ( 1916) hydrogen bonds : angle 3.83515 / 2.70 ( 5556) metal coordination : bond 0.01113 / 0.88 ( 16) metal coordination : angle 1.38101 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.305 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: B 324 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7650 (mtm180) REVERT: B 335 MET cc_start: 0.8324 (mmp) cc_final: 0.7807 (mmm) REVERT: B 344 LEU cc_start: 0.7722 (tp) cc_final: 0.7149 (tp) REVERT: B 380 MET cc_start: 0.9160 (mmm) cc_final: 0.8071 (tpp) REVERT: B 406 MET cc_start: 0.8791 (ppp) cc_final: 0.8575 (ppp) REVERT: B 619 MET cc_start: 0.8040 (tmm) cc_final: 0.7594 (tmm) REVERT: B 634 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8167 (m90) REVERT: F 53 MET cc_start: 0.8400 (tmm) cc_final: 0.7992 (tmm) REVERT: F 188 HIS cc_start: 0.7308 (m90) cc_final: 0.7017 (m90) REVERT: F 243 MET cc_start: 0.9058 (tpp) cc_final: 0.8273 (tpp) REVERT: F 247 MET cc_start: 0.8886 (mtp) cc_final: 0.8562 (tmm) REVERT: E 53 MET cc_start: 0.8343 (tmm) cc_final: 0.8003 (tmm) REVERT: E 247 MET cc_start: 0.8801 (mtp) cc_final: 0.8523 (tmm) REVERT: G 243 MET cc_start: 0.9183 (tpp) cc_final: 0.8300 (tpp) REVERT: G 247 MET cc_start: 0.8892 (mtp) cc_final: 0.8627 (tmm) REVERT: H 53 MET cc_start: 0.8315 (tmm) cc_final: 0.7765 (tmm) REVERT: H 243 MET cc_start: 0.9035 (tpp) cc_final: 0.8318 (tpp) REVERT: A 335 MET cc_start: 0.8329 (mmp) cc_final: 0.7964 (mmm) REVERT: A 336 THR cc_start: 0.9286 (t) cc_final: 0.9045 (p) REVERT: A 344 LEU cc_start: 0.7764 (tp) cc_final: 0.7158 (tp) REVERT: A 380 MET cc_start: 0.9100 (mmm) cc_final: 0.8084 (tpp) REVERT: A 743 PHE cc_start: 0.8698 (m-80) cc_final: 0.8443 (t80) REVERT: C 324 ARG cc_start: 0.8369 (mtt180) cc_final: 0.7749 (mtm180) REVERT: C 335 MET cc_start: 0.8101 (mmp) cc_final: 0.7678 (mmp) REVERT: C 336 THR cc_start: 0.9290 (t) cc_final: 0.9053 (p) REVERT: C 380 MET cc_start: 0.9131 (mmm) cc_final: 0.7993 (tpp) REVERT: C 743 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8557 (t80) REVERT: D 240 GLU cc_start: 0.8463 (mp0) cc_final: 0.8219 (mp0) REVERT: D 335 MET cc_start: 0.8128 (mmp) cc_final: 0.7664 (mmm) REVERT: D 336 THR cc_start: 0.9338 (t) cc_final: 0.9114 (p) REVERT: D 344 LEU cc_start: 0.7658 (tp) cc_final: 0.7122 (tp) REVERT: D 380 MET cc_start: 0.9088 (mmm) cc_final: 0.8109 (tpp) REVERT: D 619 MET cc_start: 0.8074 (tmm) cc_final: 0.7757 (tmm) REVERT: D 743 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8445 (t80) outliers start: 26 outliers final: 17 residues processed: 178 average time/residue: 0.1881 time to fit residues: 57.2337 Evaluate side-chains 168 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 743 PHE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 743 PHE Chi-restraints excluded: chain D residue 746 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 164 optimal weight: 9.9990 chunk 378 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 327 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.061118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049714 restraints weight = 189914.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051271 restraints weight = 100460.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.052315 restraints weight = 67101.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.052947 restraints weight = 51536.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053380 restraints weight = 43646.844| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33600 Z= 0.151 Angle : 0.523 13.899 45444 Z= 0.268 Chirality : 0.038 0.189 5088 Planarity : 0.003 0.036 5644 Dihedral : 10.790 168.620 4908 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.76 % Allowed : 10.68 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.14), residues: 3916 helix: 2.40 (0.10), residues: 2628 sheet: -0.50 (0.39), residues: 172 loop : 0.04 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 208 TYR 0.018 0.001 TYR D 118 PHE 0.030 0.001 PHE D 341 TRP 0.024 0.001 TRP B 327 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (33580) covalent geometry : angle 0.52303 / 0.27 (45424) SS BOND : bond 0.00207 / 0.10 ( 4) SS BOND : angle 0.55520 / 0.37 ( 8) hydrogen bonds : bond 0.03868 / 2.59 ( 1916) hydrogen bonds : angle 3.82866 / 2.70 ( 5556) metal coordination : bond 0.01031 / 0.81 ( 16) metal coordination : angle 1.27994 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 ARG cc_start: 0.8285 (mtm180) cc_final: 0.7673 (mtm180) REVERT: B 335 MET cc_start: 0.8362 (mmp) cc_final: 0.7879 (mmm) REVERT: B 336 THR cc_start: 0.9350 (t) cc_final: 0.9113 (p) REVERT: B 380 MET cc_start: 0.9157 (mmm) cc_final: 0.8060 (tpp) REVERT: B 406 MET cc_start: 0.8787 (ppp) cc_final: 0.8587 (ppp) REVERT: B 619 MET cc_start: 0.8055 (tmm) cc_final: 0.7596 (tmm) REVERT: B 634 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8164 (m90) REVERT: F 188 HIS cc_start: 0.7315 (m90) cc_final: 0.7010 (m90) REVERT: F 243 MET cc_start: 0.9008 (tpp) cc_final: 0.8251 (tpp) REVERT: F 247 MET cc_start: 0.8892 (mtp) cc_final: 0.8564 (tmm) REVERT: E 53 MET cc_start: 0.8336 (tmm) cc_final: 0.7963 (tmm) REVERT: E 198 MET cc_start: 0.7526 (ppp) cc_final: 0.7240 (ppp) REVERT: E 247 MET cc_start: 0.8778 (mtp) cc_final: 0.8431 (tmm) REVERT: G 243 MET cc_start: 0.9173 (tpp) cc_final: 0.8287 (tpp) REVERT: G 247 MET cc_start: 0.8856 (mtp) cc_final: 0.8596 (tmm) REVERT: H 243 MET cc_start: 0.9043 (tpp) cc_final: 0.7372 (tpp) REVERT: A 335 MET cc_start: 0.8359 (mmp) cc_final: 0.7990 (mmm) REVERT: A 336 THR cc_start: 0.9289 (t) cc_final: 0.9049 (p) REVERT: A 380 MET cc_start: 0.9111 (mmm) cc_final: 0.8132 (tpp) REVERT: A 743 PHE cc_start: 0.8672 (m-80) cc_final: 0.8431 (t80) REVERT: C 335 MET cc_start: 0.8132 (mmp) cc_final: 0.7704 (mmp) REVERT: C 336 THR cc_start: 0.9266 (t) cc_final: 0.9051 (p) REVERT: C 380 MET cc_start: 0.9116 (mmm) cc_final: 0.8058 (tpp) REVERT: C 406 MET cc_start: 0.8759 (ppp) cc_final: 0.8345 (ppp) REVERT: C 613 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8721 (mm) REVERT: C 743 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8572 (t80) REVERT: D 335 MET cc_start: 0.8132 (mmp) cc_final: 0.7665 (mmm) REVERT: D 336 THR cc_start: 0.9334 (t) cc_final: 0.9110 (p) REVERT: D 380 MET cc_start: 0.9108 (mmm) cc_final: 0.8145 (tpp) REVERT: D 619 MET cc_start: 0.8079 (tmm) cc_final: 0.7737 (tmm) outliers start: 27 outliers final: 17 residues processed: 173 average time/residue: 0.1949 time to fit residues: 57.6415 Evaluate side-chains 164 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 743 PHE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 746 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 59 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 321 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 386 optimal weight: 0.0370 chunk 301 optimal weight: 0.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.060719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.049311 restraints weight = 189821.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.050873 restraints weight = 100146.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051897 restraints weight = 66924.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.052553 restraints weight = 51546.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.052934 restraints weight = 43503.045| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33600 Z= 0.171 Angle : 0.551 12.458 45444 Z= 0.281 Chirality : 0.039 0.173 5088 Planarity : 0.003 0.036 5644 Dihedral : 10.728 173.802 4908 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.59 % Allowed : 11.10 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.14), residues: 3916 helix: 2.40 (0.10), residues: 2628 sheet: -0.50 (0.39), residues: 172 loop : 0.02 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 208 TYR 0.014 0.001 TYR D 524 PHE 0.028 0.001 PHE C 341 TRP 0.020 0.001 TRP B 327 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (33580) covalent geometry : angle 0.55061 / 0.28 (45424) SS BOND : bond 0.00223 / 0.11 ( 4) SS BOND : angle 0.63123 / 0.43 ( 8) hydrogen bonds : bond 0.03968 / 2.66 ( 1916) hydrogen bonds : angle 3.90745 / 2.75 ( 5556) metal coordination : bond 0.01288 / 1.02 ( 16) metal coordination : angle 1.18667 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 ARG cc_start: 0.8297 (mtm180) cc_final: 0.7707 (mtm180) REVERT: B 335 MET cc_start: 0.8181 (mmp) cc_final: 0.7671 (mmm) REVERT: B 336 THR cc_start: 0.9339 (t) cc_final: 0.9107 (p) REVERT: B 380 MET cc_start: 0.9154 (mmm) cc_final: 0.8032 (tpp) REVERT: B 619 MET cc_start: 0.8073 (tmm) cc_final: 0.7606 (tmm) REVERT: B 634 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.8213 (m90) REVERT: F 53 MET cc_start: 0.8273 (tmm) cc_final: 0.7962 (tmm) REVERT: F 188 HIS cc_start: 0.7283 (m90) cc_final: 0.6994 (m90) REVERT: F 243 MET cc_start: 0.8994 (tpp) cc_final: 0.8248 (tpp) REVERT: F 247 MET cc_start: 0.8922 (mtp) cc_final: 0.8659 (tmm) REVERT: E 53 MET cc_start: 0.8358 (tmm) cc_final: 0.7985 (tmm) REVERT: E 198 MET cc_start: 0.7568 (ppp) cc_final: 0.7218 (ppp) REVERT: E 247 MET cc_start: 0.8791 (mtp) cc_final: 0.8441 (tmm) REVERT: G 243 MET cc_start: 0.9188 (tpp) cc_final: 0.8327 (tpp) REVERT: G 247 MET cc_start: 0.8935 (mtp) cc_final: 0.8694 (tmm) REVERT: H 53 MET cc_start: 0.8327 (tmm) cc_final: 0.7693 (tmm) REVERT: H 88 MET cc_start: 0.8583 (ptp) cc_final: 0.8103 (ptp) REVERT: H 243 MET cc_start: 0.8870 (tpp) cc_final: 0.7726 (tpp) REVERT: H 247 MET cc_start: 0.8591 (mtp) cc_final: 0.7973 (mtm) REVERT: A 324 ARG cc_start: 0.8505 (mtt180) cc_final: 0.7826 (mtm180) REVERT: A 335 MET cc_start: 0.8355 (mmp) cc_final: 0.7992 (mmm) REVERT: A 336 THR cc_start: 0.9280 (t) cc_final: 0.9041 (p) REVERT: A 380 MET cc_start: 0.9115 (mmm) cc_final: 0.8123 (tpp) REVERT: A 743 PHE cc_start: 0.8750 (m-80) cc_final: 0.8461 (t80) REVERT: C 335 MET cc_start: 0.8183 (mmp) cc_final: 0.7683 (mmp) REVERT: C 336 THR cc_start: 0.9272 (t) cc_final: 0.9059 (p) REVERT: C 380 MET cc_start: 0.9116 (mmm) cc_final: 0.8552 (tpp) REVERT: C 406 MET cc_start: 0.8725 (ppp) cc_final: 0.7591 (ppp) REVERT: C 541 TYR cc_start: 0.6963 (m-10) cc_final: 0.6761 (m-10) REVERT: C 613 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8708 (mm) REVERT: C 743 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8564 (t80) REVERT: D 335 MET cc_start: 0.8264 (mmp) cc_final: 0.7806 (mmm) REVERT: D 336 THR cc_start: 0.9334 (t) cc_final: 0.9097 (p) REVERT: D 380 MET cc_start: 0.9093 (mmm) cc_final: 0.8151 (tpp) REVERT: D 406 MET cc_start: 0.8850 (ppp) cc_final: 0.8341 (ppp) REVERT: D 619 MET cc_start: 0.8093 (tmm) cc_final: 0.7743 (tmm) outliers start: 21 outliers final: 13 residues processed: 168 average time/residue: 0.2028 time to fit residues: 58.2603 Evaluate side-chains 160 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 743 PHE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 746 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 245 optimal weight: 4.9990 chunk 350 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 43 optimal weight: 0.0270 chunk 108 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.061100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049658 restraints weight = 190132.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051230 restraints weight = 100666.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052266 restraints weight = 67258.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.052919 restraints weight = 51671.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.053335 restraints weight = 43660.171| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33600 Z= 0.142 Angle : 0.529 11.974 45444 Z= 0.270 Chirality : 0.038 0.150 5088 Planarity : 0.003 0.037 5644 Dihedral : 10.606 172.976 4908 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.73 % Allowed : 10.82 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.14), residues: 3916 helix: 2.41 (0.10), residues: 2628 sheet: -0.48 (0.39), residues: 172 loop : 0.07 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 208 TYR 0.013 0.001 TYR D 524 PHE 0.026 0.001 PHE A 341 TRP 0.023 0.001 TRP A 327 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (33580) covalent geometry : angle 0.52875 / 0.27 (45424) SS BOND : bond 0.00194 / 0.10 ( 4) SS BOND : angle 0.56507 / 0.38 ( 8) hydrogen bonds : bond 0.03812 / 2.55 ( 1916) hydrogen bonds : angle 3.80553 / 2.68 ( 5556) metal coordination : bond 0.00877 / 0.68 ( 16) metal coordination : angle 1.24584 / 0.73 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 MET cc_start: 0.8310 (mmp) cc_final: 0.7794 (mmm) REVERT: B 336 THR cc_start: 0.9299 (t) cc_final: 0.9094 (p) REVERT: B 380 MET cc_start: 0.9168 (mmm) cc_final: 0.8063 (tpp) REVERT: B 619 MET cc_start: 0.8140 (tmm) cc_final: 0.7664 (tmm) REVERT: B 634 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8211 (m90) REVERT: F 53 MET cc_start: 0.8330 (tmm) cc_final: 0.8006 (tmm) REVERT: F 188 HIS cc_start: 0.7532 (m90) cc_final: 0.7232 (m90) REVERT: F 243 MET cc_start: 0.9093 (tpp) cc_final: 0.8284 (tpp) REVERT: F 247 MET cc_start: 0.9091 (mtp) cc_final: 0.8717 (tmm) REVERT: E 53 MET cc_start: 0.8438 (tmm) cc_final: 0.8062 (tmm) REVERT: E 198 MET cc_start: 0.7618 (ppp) cc_final: 0.7253 (ppp) REVERT: E 247 MET cc_start: 0.8956 (mtp) cc_final: 0.8463 (tmm) REVERT: G 243 MET cc_start: 0.9283 (tpp) cc_final: 0.8404 (tpp) REVERT: G 247 MET cc_start: 0.9085 (mtp) cc_final: 0.8735 (tmm) REVERT: H 238 GLU cc_start: 0.8704 (pm20) cc_final: 0.8412 (pm20) REVERT: H 243 MET cc_start: 0.8888 (tpp) cc_final: 0.7979 (tpp) REVERT: H 247 MET cc_start: 0.8522 (mtp) cc_final: 0.8106 (mtm) REVERT: A 335 MET cc_start: 0.8456 (mmp) cc_final: 0.8075 (mmm) REVERT: A 336 THR cc_start: 0.9267 (t) cc_final: 0.9031 (p) REVERT: A 380 MET cc_start: 0.9151 (mmm) cc_final: 0.8155 (tpp) REVERT: A 743 PHE cc_start: 0.8812 (m-80) cc_final: 0.8426 (t80) REVERT: C 335 MET cc_start: 0.8256 (mmp) cc_final: 0.7759 (mmp) REVERT: C 336 THR cc_start: 0.9274 (t) cc_final: 0.9070 (p) REVERT: C 380 MET cc_start: 0.9155 (mmm) cc_final: 0.8616 (tpp) REVERT: C 406 MET cc_start: 0.8736 (ppp) cc_final: 0.7513 (ppp) REVERT: C 541 TYR cc_start: 0.6976 (m-10) cc_final: 0.6752 (m-10) REVERT: C 613 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8594 (mm) REVERT: C 743 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8611 (t80) REVERT: D 335 MET cc_start: 0.8310 (mmp) cc_final: 0.7853 (mmm) REVERT: D 336 THR cc_start: 0.9333 (t) cc_final: 0.9110 (p) REVERT: D 380 MET cc_start: 0.9115 (mmm) cc_final: 0.8141 (tpp) REVERT: D 406 MET cc_start: 0.8855 (ppp) cc_final: 0.8375 (ppp) REVERT: D 619 MET cc_start: 0.8154 (tmm) cc_final: 0.7799 (tmm) outliers start: 26 outliers final: 19 residues processed: 166 average time/residue: 0.2094 time to fit residues: 59.4247 Evaluate side-chains 169 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 743 PHE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 746 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 340 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 318 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.061111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049667 restraints weight = 189709.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051244 restraints weight = 100200.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052274 restraints weight = 67003.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.052917 restraints weight = 51551.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.053302 restraints weight = 43641.464| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33600 Z= 0.143 Angle : 0.531 11.547 45444 Z= 0.271 Chirality : 0.038 0.166 5088 Planarity : 0.003 0.037 5644 Dihedral : 10.520 173.531 4908 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.68 % Allowed : 11.05 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.14), residues: 3916 helix: 2.43 (0.10), residues: 2628 sheet: -0.45 (0.39), residues: 172 loop : 0.08 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 208 TYR 0.013 0.001 TYR D 524 PHE 0.024 0.001 PHE A 341 TRP 0.023 0.001 TRP B 327 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (33580) covalent geometry : angle 0.53094 / 0.27 (45424) SS BOND : bond 0.00191 / 0.10 ( 4) SS BOND : angle 0.55397 / 0.38 ( 8) hydrogen bonds : bond 0.03803 / 2.54 ( 1916) hydrogen bonds : angle 3.79115 / 2.67 ( 5556) metal coordination : bond 0.00935 / 0.72 ( 16) metal coordination : angle 1.26936 / 0.78 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4641.78 seconds wall clock time: 81 minutes 55.30 seconds (4915.30 seconds total)