Starting phenix.real_space_refine on Mon Aug 25 23:35:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cat_45403/08_2025/9cat_45403_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cat_45403/08_2025/9cat_45403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cat_45403/08_2025/9cat_45403_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cat_45403/08_2025/9cat_45403_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cat_45403/08_2025/9cat_45403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cat_45403/08_2025/9cat_45403.map" } resolution = 2.9 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= 0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 102 5.16 5 C 19227 2.51 5 N 5275 2.21 5 O 5902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30518 Number of models: 1 Model: "" Number of chains: 16 Chain: "Q" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5275 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 30, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 9, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "R" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3535 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1005 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 9, 'TRANS': 114} Chain breaks: 1 Chain: "T" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3336 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3384 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 422} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "Y" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 248 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.42, per 1000 atoms: 0.18 Number of scatterers: 30518 At special positions: 0 Unit cell: (127.748, 182.615, 194.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 P 12 15.00 O 5902 8.00 N 5275 7.00 C 19227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7272 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 35 sheets defined 44.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'Q' and resid 709 through 724 removed outlier: 3.833A pdb=" N GLY Q 713 " --> pdb=" O TYR Q 709 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY Q 724 " --> pdb=" O LEU Q 720 " (cutoff:3.500A) Processing helix chain 'Q' and resid 736 through 752 Processing helix chain 'Q' and resid 763 through 765 No H-bonds generated for 'chain 'Q' and resid 763 through 765' Processing helix chain 'Q' and resid 766 through 778 removed outlier: 3.636A pdb=" N LEU Q 778 " --> pdb=" O ILE Q 774 " (cutoff:3.500A) Processing helix chain 'Q' and resid 789 through 800 Processing helix chain 'Q' and resid 819 through 826 removed outlier: 3.623A pdb=" N VAL Q 823 " --> pdb=" O SER Q 819 " (cutoff:3.500A) Processing helix chain 'Q' and resid 843 through 847 removed outlier: 3.933A pdb=" N ILE Q 846 " --> pdb=" O ALA Q 843 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS Q 847 " --> pdb=" O GLN Q 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 843 through 847' Processing helix chain 'Q' and resid 851 through 858 Processing helix chain 'Q' and resid 878 through 888 Processing helix chain 'Q' and resid 894 through 901 Processing helix chain 'Q' and resid 921 through 928 removed outlier: 3.697A pdb=" N HIS Q 925 " --> pdb=" O LEU Q 921 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET Q 926 " --> pdb=" O ARG Q 922 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU Q 928 " --> pdb=" O LEU Q 924 " (cutoff:3.500A) Processing helix chain 'Q' and resid 957 through 971 Processing helix chain 'Q' and resid 1004 through 1013 removed outlier: 3.864A pdb=" N HIS Q1013 " --> pdb=" O LYS Q1009 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1014 through 1017 removed outlier: 3.913A pdb=" N PHE Q1017 " --> pdb=" O PRO Q1014 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1014 through 1017' Processing helix chain 'Q' and resid 1086 through 1093 removed outlier: 3.856A pdb=" N TYR Q1090 " --> pdb=" O PRO Q1086 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1101 through 1111 Processing helix chain 'Q' and resid 1121 through 1133 Processing helix chain 'Q' and resid 1138 through 1144 Processing helix chain 'Q' and resid 1147 through 1155 Processing helix chain 'Q' and resid 1169 through 1178 Processing helix chain 'Q' and resid 1185 through 1191 removed outlier: 3.576A pdb=" N LEU Q1191 " --> pdb=" O MET Q1187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1192 through 1201 Processing helix chain 'Q' and resid 1202 through 1206 removed outlier: 3.685A pdb=" N CYS Q1205 " --> pdb=" O TYR Q1202 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE Q1206 " --> pdb=" O LEU Q1203 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1202 through 1206' Processing helix chain 'Q' and resid 1227 through 1238 Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1264 through 1268 Processing helix chain 'Q' and resid 1290 through 1297 Processing helix chain 'Q' and resid 1298 through 1315 removed outlier: 4.483A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1324 through 1339 removed outlier: 3.683A pdb=" N TYR Q1337 " --> pdb=" O GLU Q1333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1353 through 1364 removed outlier: 3.971A pdb=" N VAL Q1358 " --> pdb=" O ARG Q1354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1374 through 1378 Processing helix chain 'Q' and resid 1397 through 1403 removed outlier: 3.552A pdb=" N GLN Q1403 " --> pdb=" O THR Q1399 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1404 through 1408 Processing helix chain 'Q' and resid 1427 through 1446 removed outlier: 4.155A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 34 Processing helix chain 'R' and resid 82 through 87 Processing helix chain 'R' and resid 89 through 95 removed outlier: 3.581A pdb=" N SER R 94 " --> pdb=" O GLN R 90 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 121 Processing helix chain 'R' and resid 143 through 157 Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 215 through 231 Processing helix chain 'R' and resid 239 through 250 removed outlier: 3.542A pdb=" N TYR R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 261 Processing helix chain 'R' and resid 266 through 271 removed outlier: 3.867A pdb=" N ASP R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 589 through 597 Processing helix chain 'R' and resid 607 through 609 No H-bonds generated for 'chain 'R' and resid 607 through 609' Processing helix chain 'R' and resid 616 through 621 removed outlier: 3.720A pdb=" N VAL R 621 " --> pdb=" O GLU R 617 " (cutoff:3.500A) Processing helix chain 'R' and resid 622 through 626 removed outlier: 3.775A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) Processing helix chain 'R' and resid 637 through 647 removed outlier: 3.600A pdb=" N LEU R 646 " --> pdb=" O SER R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 658 through 666 removed outlier: 3.609A pdb=" N VAL R 665 " --> pdb=" O SER R 661 " (cutoff:3.500A) Processing helix chain 'R' and resid 672 through 676 removed outlier: 3.895A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) Processing helix chain 'R' and resid 679 through 692 removed outlier: 3.849A pdb=" N PHE R 691 " --> pdb=" O GLU R 687 " (cutoff:3.500A) Processing helix chain 'R' and resid 708 through 716 removed outlier: 3.792A pdb=" N MET R 714 " --> pdb=" O ALA R 710 " (cutoff:3.500A) Processing helix chain 'R' and resid 721 through 727 removed outlier: 3.620A pdb=" N TYR R 724 " --> pdb=" O GLU R 721 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG R 725 " --> pdb=" O GLU R 722 " (cutoff:3.500A) Processing helix chain 'R' and resid 731 through 738 Processing helix chain 'S' and resid 30 through 38 removed outlier: 3.735A pdb=" N ARG S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 removed outlier: 3.572A pdb=" N LEU S 66 " --> pdb=" O SER S 62 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 150 through 156 removed outlier: 3.648A pdb=" N GLU S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.776A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.505A pdb=" N TYR T 111 " --> pdb=" O SER T 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 108 through 111' Processing helix chain 'T' and resid 116 through 127 Processing helix chain 'T' and resid 182 through 192 removed outlier: 3.634A pdb=" N TYR T 186 " --> pdb=" O ASP T 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 216 through 219 Processing helix chain 'T' and resid 249 through 257 Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.559A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 313 through 316 Processing helix chain 'T' and resid 317 through 328 removed outlier: 3.595A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 365 Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 removed outlier: 3.554A pdb=" N ASP T 401 " --> pdb=" O SER T 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU T 402 " --> pdb=" O SER T 398 " (cutoff:3.500A) Processing helix chain 'T' and resid 411 through 418 Processing helix chain 'T' and resid 418 through 429 removed outlier: 3.720A pdb=" N SER T 429 " --> pdb=" O LEU T 425 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 458 Processing helix chain 'U' and resid 47 through 64 removed outlier: 3.539A pdb=" N GLY U 64 " --> pdb=" O MET U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 93 removed outlier: 3.819A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 107 removed outlier: 3.726A pdb=" N PHE U 107 " --> pdb=" O SER U 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 104 through 107' Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.703A pdb=" N LYS U 181 " --> pdb=" O ASP U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 249 Processing helix chain 'U' and resid 253 through 260 Processing helix chain 'U' and resid 266 through 284 removed outlier: 3.632A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 313 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.517A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.790A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.502A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 443 Processing helix chain 'U' and resid 444 through 447 Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.735A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 Processing helix chain 'V' and resid 116 through 127 Processing helix chain 'V' and resid 184 through 193 removed outlier: 4.027A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 217 through 219 No H-bonds generated for 'chain 'V' and resid 217 through 219' Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 273 Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.515A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 316 Processing helix chain 'V' and resid 317 through 328 Processing helix chain 'V' and resid 360 through 365 Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 418 Processing helix chain 'V' and resid 418 through 429 removed outlier: 3.674A pdb=" N SER V 429 " --> pdb=" O LEU V 425 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 459 Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'W' and resid 80 through 93 removed outlier: 3.861A pdb=" N GLY W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 123 Processing helix chain 'W' and resid 172 through 181 Processing helix chain 'W' and resid 241 through 250 removed outlier: 4.029A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.928A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.734A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.879A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.582A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.747A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.782A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 443 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.772A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.505A pdb=" N TYR X 111 " --> pdb=" O SER X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 108 through 111' Processing helix chain 'X' and resid 116 through 128 Processing helix chain 'X' and resid 182 through 192 removed outlier: 3.659A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU X 192 " --> pdb=" O SER X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 273 removed outlier: 3.542A pdb=" N GLN X 271 " --> pdb=" O SER X 267 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU X 272 " --> pdb=" O MET X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 Processing helix chain 'X' and resid 312 through 316 Processing helix chain 'X' and resid 317 through 328 Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 417 removed outlier: 3.675A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 429 removed outlier: 3.574A pdb=" N SER X 429 " --> pdb=" O LEU X 425 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 Processing helix chain 'Y' and resid 47 through 64 removed outlier: 3.503A pdb=" N GLY Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 81 through 93 removed outlier: 3.981A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 107 removed outlier: 3.725A pdb=" N PHE Y 107 " --> pdb=" O SER Y 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 104 through 107' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 255 through 260 Processing helix chain 'Y' and resid 266 through 283 removed outlier: 3.547A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 297 through 301 Processing helix chain 'Y' and resid 302 through 313 Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.503A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.573A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE Y 403 " --> pdb=" O SER Y 399 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE Y 409 " --> pdb=" O VAL Y 405 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.561A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 443 Processing helix chain 'Y' and resid 444 through 447 removed outlier: 3.600A pdb=" N TYR Y 447 " --> pdb=" O GLU Y 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 444 through 447' Processing sheet with id=AA1, first strand: chain 'Q' and resid 728 through 729 removed outlier: 5.890A pdb=" N MET Q 838 " --> pdb=" O LEU Q 866 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU Q 868 " --> pdb=" O MET Q 838 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU Q 840 " --> pdb=" O LEU Q 868 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU Q 759 " --> pdb=" O ILE Q 839 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP Q 841 " --> pdb=" O LEU Q 759 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL Q 761 " --> pdb=" O ASP Q 841 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL Q 760 " --> pdb=" O THR Q 818 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 948 through 954 removed outlier: 6.297A pdb=" N VAL Q1389 " --> pdb=" O TYR Q1420 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU Q1422 " --> pdb=" O VAL Q1389 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE Q1391 " --> pdb=" O LEU Q1422 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL Q1424 " --> pdb=" O PHE Q1391 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU Q1319 " --> pdb=" O ILE Q1390 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL Q1318 " --> pdb=" O PHE Q1370 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU Q1372 " --> pdb=" O VAL Q1318 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE Q1320 " --> pdb=" O LEU Q1372 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE Q1343 " --> pdb=" O LEU Q1371 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N SER Q1373 " --> pdb=" O ILE Q1343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 5.835A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Q' and resid 1071 through 1073 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1073 current: chain 'X' and resid 163 through 172 removed outlier: 3.835A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 209 through 215 removed outlier: 6.089A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 1082 through 1084 Processing sheet with id=AA6, first strand: chain 'R' and resid 14 through 15 removed outlier: 7.203A pdb=" N VAL R 14 " --> pdb=" O GLU R 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 61 through 64 removed outlier: 3.944A pdb=" N THR R 164 " --> pdb=" O ILE R 134 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU R 136 " --> pdb=" O THR R 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 100 through 101 removed outlier: 3.592A pdb=" N PHE R 104 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 184 through 189 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 203 through 204 current: chain 'R' and resid 700 through 701 Processing sheet with id=AB1, first strand: chain 'S' and resid 125 through 126 Processing sheet with id=AB2, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB3, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.201A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU T 308 " --> pdb=" O VAL T 337 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ALA T 339 " --> pdb=" O LEU T 308 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE T 310 " --> pdb=" O ALA T 339 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER T 340 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY T 79 " --> pdb=" O SER T 340 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 129 through 151 removed outlier: 8.370A pdb=" N GLY T 142 " --> pdb=" O SER T 172 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER T 172 " --> pdb=" O GLY T 142 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL T 144 " --> pdb=" O LEU T 170 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU T 170 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU T 146 " --> pdb=" O VAL T 168 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL T 168 " --> pdb=" O GLU T 146 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR T 148 " --> pdb=" O VAL T 166 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL T 166 " --> pdb=" O THR T 148 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU T 150 " --> pdb=" O SER T 164 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY T 175 " --> pdb=" O SER T 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 175 through 181 current: chain 'T' and resid 209 through 214 Processing sheet with id=AB5, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AB6, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AB7, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.285A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 125 through 143 removed outlier: 7.345A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 199 through 205 removed outlier: 5.507A pdb=" N VAL U 222 " --> pdb=" O LEU U 202 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG U 204 " --> pdb=" O VAL U 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 329 through 331 Processing sheet with id=AC1, first strand: chain 'V' and resid 44 through 45 Processing sheet with id=AC2, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.501A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA V 339 " --> pdb=" O ILE V 310 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER V 340 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 129 through 151 removed outlier: 6.156A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS V 165 " --> pdb=" O PRO V 149 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP V 151 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE V 163 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY V 175 " --> pdb=" O SER V 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 175 through 181 current: chain 'V' and resid 211 through 215 removed outlier: 5.732A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AC5, first strand: chain 'V' and resid 394 through 395 removed outlier: 7.338A pdb=" N GLN V 394 " --> pdb=" O ILE V 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC7, first strand: chain 'W' and resid 98 through 101 removed outlier: 6.181A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 125 through 147 removed outlier: 6.791A pdb=" N THR W 159 " --> pdb=" O VAL W 141 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE W 143 " --> pdb=" O LYS W 157 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS W 157 " --> pdb=" O ILE W 143 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE W 145 " --> pdb=" O GLN W 155 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN W 155 " --> pdb=" O ILE W 145 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 198 through 204 Processing sheet with id=AC9, first strand: chain 'W' and resid 329 through 331 Processing sheet with id=AD1, first strand: chain 'X' and resid 44 through 45 removed outlier: 3.537A pdb=" N GLU X 45 " --> pdb=" O PHE X 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.273A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA X 339 " --> pdb=" O ILE X 310 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 344 through 346 removed outlier: 3.517A pdb=" N SER X 355 " --> pdb=" O THR X 345 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.247A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'Y' and resid 40 through 41 Processing sheet with id=AD6, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.439A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL Y 71 " --> pdb=" O MET Y 323 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR Y 325 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL Y 73 " --> pdb=" O THR Y 325 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 125 through 146 removed outlier: 6.792A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 170 current: chain 'Y' and resid 199 through 204 Processing sheet with id=AD8, first strand: chain 'Y' and resid 330 through 331 1156 hydrogen bonds defined for protein. 3354 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: 5.60 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10176 1.34 - 1.47: 6317 1.47 - 1.59: 14311 1.59 - 1.71: 18 1.71 - 1.83: 179 Bond restraints: 31001 Sorted by residual: bond pdb=" N VAL Q1177 " pdb=" CA VAL Q1177 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.23e-02 6.61e+03 7.50e+00 bond pdb=" N ARG Q1425 " pdb=" CA ARG Q1425 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.38e+00 bond pdb=" N ILE Q1428 " pdb=" CA ILE Q1428 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.24e-02 6.50e+03 6.63e+00 bond pdb=" N TYR T 462 " pdb=" CA TYR T 462 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.45e-02 4.76e+03 5.86e+00 bond pdb=" N VAL R 616 " pdb=" CA VAL R 616 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.34e-02 5.57e+03 5.84e+00 ... (remaining 30996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 41579 3.62 - 7.25: 302 7.25 - 10.87: 62 10.87 - 14.50: 12 14.50 - 18.12: 4 Bond angle restraints: 41959 Sorted by residual: angle pdb=" C HIS U 23 " pdb=" CA HIS U 23 " pdb=" CB HIS U 23 " ideal model delta sigma weight residual 111.85 98.91 12.94 1.47e+00 4.63e-01 7.75e+01 angle pdb=" CA HIS U 23 " pdb=" CB HIS U 23 " pdb=" CG HIS U 23 " ideal model delta sigma weight residual 113.80 121.32 -7.52 1.00e+00 1.00e+00 5.66e+01 angle pdb=" N LEU T 463 " pdb=" CA LEU T 463 " pdb=" CB LEU T 463 " ideal model delta sigma weight residual 110.50 122.17 -11.67 1.70e+00 3.46e-01 4.71e+01 angle pdb=" CB MET Q1288 " pdb=" CG MET Q1288 " pdb=" SD MET Q1288 " ideal model delta sigma weight residual 112.70 130.82 -18.12 3.00e+00 1.11e-01 3.65e+01 angle pdb=" N GLN Q1172 " pdb=" CA GLN Q1172 " pdb=" C GLN Q1172 " ideal model delta sigma weight residual 111.28 105.30 5.98 1.09e+00 8.42e-01 3.01e+01 ... (remaining 41954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.50: 17252 24.50 - 49.01: 1503 49.01 - 73.51: 207 73.51 - 98.02: 31 98.02 - 122.52: 1 Dihedral angle restraints: 18994 sinusoidal: 7732 harmonic: 11262 Sorted by residual: dihedral pdb=" O2A ADP W1001 " pdb=" O3A ADP W1001 " pdb=" PA ADP W1001 " pdb=" PB ADP W1001 " ideal model delta sinusoidal sigma weight residual 300.00 177.48 122.52 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" CA SER Y 18 " pdb=" C SER Y 18 " pdb=" N LEU Y 19 " pdb=" CA LEU Y 19 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA GLU W 182 " pdb=" C GLU W 182 " pdb=" N LYS W 183 " pdb=" CA LYS W 183 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 18991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4207 0.073 - 0.146: 641 0.146 - 0.219: 45 0.219 - 0.291: 4 0.291 - 0.364: 1 Chirality restraints: 4898 Sorted by residual: chirality pdb=" CB ILE Q 873 " pdb=" CA ILE Q 873 " pdb=" CG1 ILE Q 873 " pdb=" CG2 ILE Q 873 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE Q1343 " pdb=" CA ILE Q1343 " pdb=" CG1 ILE Q1343 " pdb=" CG2 ILE Q1343 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE R 670 " pdb=" CA ILE R 670 " pdb=" CG1 ILE R 670 " pdb=" CG2 ILE R 670 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 4895 not shown) Planarity restraints: 5374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Q1425 " 0.523 9.50e-02 1.11e+02 2.34e-01 3.36e+01 pdb=" NE ARG Q1425 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG Q1425 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG Q1425 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG Q1425 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN T 461 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ASN T 461 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN T 461 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR T 462 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU R 259 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" CD GLU R 259 " 0.050 2.00e-02 2.50e+03 pdb=" OE1 GLU R 259 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU R 259 " -0.017 2.00e-02 2.50e+03 ... (remaining 5371 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8478 2.81 - 3.33: 26847 3.33 - 3.85: 52886 3.85 - 4.38: 59764 4.38 - 4.90: 103551 Nonbonded interactions: 251526 Sorted by model distance: nonbonded pdb=" O GLY Q1185 " pdb=" OG SER Q1189 " model vdw 2.282 3.040 nonbonded pdb=" O ALA V 26 " pdb=" O3' ADP V1001 " model vdw 2.287 3.040 nonbonded pdb=" O ASN Q 772 " pdb=" OG SER Q 775 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR S 134 " pdb=" O GLU Y 166 " model vdw 2.296 3.040 nonbonded pdb=" O SER T 82 " pdb=" OG SER T 82 " model vdw 2.297 3.040 ... (remaining 251521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'T' and (resid 22 through 205 or (resid 206 and (name N or name CA or nam \ e C or name O or name CB )) or resid 207 through 417 or (resid 418 and (name N o \ r name CA or name C or name O or name CB )) or resid 419 through 462 or resid 10 \ 01)) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 366 or (resid 367 a \ nd (name N or name CA or name C or name O or name CB )) or resid 368 through 100 \ 1)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 205 or (resid 206 a \ nd (name N or name CA or name C or name O or name CB )) or resid 207 through 366 \ or (resid 367 and (name N or name CA or name C or name O or name CB )) or resid \ 368 through 417 or (resid 418 and (name N or name CA or name C or name O or nam \ e CB )) or resid 419 through 462 or resid 1001)) } ncs_group { reference = (chain 'U' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 459 or \ resid 1001)) selection = (chain 'W' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 1001)) \ selection = (chain 'Y' and (resid 18 through 459 or resid 1001)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.420 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.004 0.063 31002 Z= 0.201 Angle : 0.869 18.122 41959 Z= 0.445 Chirality : 0.051 0.364 4898 Planarity : 0.006 0.234 5374 Dihedral : 17.609 122.523 11722 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.09 % Allowed : 28.05 % Favored : 71.86 % Cbeta Deviations : 0.06 % 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 aren not related in a simple way. whole: -2.08 (0.12), residues: 3862 helix: -1.63 (0.10), residues: 1618 sheet: -0.39 (0.20), residues: 680 loop : -1.35 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG T 191 TYR 0.029 0.002 TYR S 53 PHE 0.037 0.002 PHE S 44 TRP 0.033 0.002 TRP Q1396 HIS 0.007 0.001 HIS U 23 Details of bonding type rmsd covalent geometry : bond 0.00437 (31001) covalent geometry : angle 0.86933 (41959) hydrogen bonds : bond 0.17439 ( 1156) hydrogen bonds : angle 6.58736 ( 3354) Misc. bond : bond 0.00120 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 813 PHE cc_start: 0.2863 (p90) cc_final: 0.2276 (t80) REVERT: Q 833 MET cc_start: 0.3684 (mmt) cc_final: 0.3461 (mmm) REVERT: Q 877 MET cc_start: 0.4988 (ppp) cc_final: 0.3244 (ptt) REVERT: Q 886 PHE cc_start: 0.7978 (t80) cc_final: 0.7749 (t80) REVERT: T 317 ASP cc_start: 0.8392 (t0) cc_final: 0.8132 (t0) REVERT: W 262 THR cc_start: 0.8767 (p) cc_final: 0.8562 (p) REVERT: X 132 ARG cc_start: 0.8600 (ttm170) cc_final: 0.7853 (ttm170) REVERT: X 282 GLU cc_start: 0.8624 (tt0) cc_final: 0.8123 (tm-30) REVERT: Y 271 ASP cc_start: 0.9240 (m-30) cc_final: 0.8816 (m-30) REVERT: Z 303 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8307 (mp0) outliers start: 3 outliers final: 2 residues processed: 217 average time/residue: 0.6448 time to fit residues: 164.1287 Evaluate side-chains 179 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain Z residue 314 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.0570 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1106 ASN Q1359 HIS ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 GLN R 146 GLN R 659 GLN T 245 GLN T 250 HIS W 341 HIS X 190 GLN X 461 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054084 restraints weight = 91358.734| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.17 r_work: 0.2818 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31002 Z= 0.190 Angle : 0.587 7.313 41959 Z= 0.293 Chirality : 0.043 0.158 4898 Planarity : 0.004 0.050 5374 Dihedral : 6.629 156.889 4265 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.93 % Allowed : 24.76 % Favored : 72.31 % 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 aren not related in a simple way. whole: -0.74 (0.13), residues: 3862 helix: 0.08 (0.12), residues: 1639 sheet: -0.36 (0.19), residues: 680 loop : -1.05 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 311 TYR 0.019 0.001 TYR S 53 PHE 0.019 0.001 PHE Q 813 TRP 0.018 0.001 TRP Q 901 HIS 0.006 0.001 HIS U 23 Details of bonding type rmsd covalent geometry : bond 0.00434 (31001) covalent geometry : angle 0.58710 (41959) hydrogen bonds : bond 0.03742 ( 1156) hydrogen bonds : angle 4.35108 ( 3354) Misc. bond : bond 0.00193 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 186 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: Q 886 PHE cc_start: 0.7914 (t80) cc_final: 0.7567 (t80) REVERT: Q 1173 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8135 (mt-10) REVERT: Q 1201 GLU cc_start: 0.8628 (mp0) cc_final: 0.8216 (mp0) REVERT: R 152 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8747 (tp-100) REVERT: R 676 LYS cc_start: 0.3739 (OUTLIER) cc_final: 0.2729 (pttm) REVERT: S 39 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8268 (tpt90) REVERT: S 71 ASN cc_start: 0.9435 (t0) cc_final: 0.9138 (t0) REVERT: S 75 ASN cc_start: 0.9430 (m-40) cc_final: 0.9065 (m-40) REVERT: T 317 ASP cc_start: 0.8569 (t0) cc_final: 0.8368 (t0) REVERT: U 311 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7948 (mmt180) REVERT: V 258 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7733 (ppt170) REVERT: V 355 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8538 (t) REVERT: W 262 THR cc_start: 0.8657 (p) cc_final: 0.8416 (p) REVERT: X 132 ARG cc_start: 0.8708 (ttm170) cc_final: 0.8080 (ttm170) REVERT: X 282 GLU cc_start: 0.8883 (tt0) cc_final: 0.8298 (tm-30) REVERT: Y 281 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9066 (tptp) outliers start: 98 outliers final: 26 residues processed: 272 average time/residue: 0.6166 time to fit residues: 198.3413 Evaluate side-chains 202 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1308 LEU Chi-restraints excluded: chain Q residue 1379 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 GLN Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 676 LYS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 266 ARG Chi-restraints excluded: chain U residue 268 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 311 ARG Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 258 ARG Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 89 SER Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain X residue 234 LYS Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 353 VAL Chi-restraints excluded: chain Y residue 281 LYS Chi-restraints excluded: chain Y residue 330 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 226 optimal weight: 7.9990 chunk 116 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 335 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 112 optimal weight: 0.2980 chunk 118 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 844 GLN Q1204 ASN ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 ASN S 141 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 415 ASN Z 301 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.073050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.053535 restraints weight = 91850.617| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.19 r_work: 0.2805 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31002 Z= 0.176 Angle : 0.572 8.734 41959 Z= 0.280 Chirality : 0.043 0.166 4898 Planarity : 0.003 0.049 5374 Dihedral : 6.112 140.552 4262 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.32 % Allowed : 24.55 % Favored : 72.13 % 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 aren not related in a simple way. whole: -0.25 (0.13), residues: 3862 helix: 0.73 (0.13), residues: 1644 sheet: -0.36 (0.19), residues: 680 loop : -0.96 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 191 TYR 0.016 0.001 TYR V 295 PHE 0.015 0.001 PHE Y 308 TRP 0.015 0.001 TRP Q 901 HIS 0.003 0.001 HIS W 341 Details of bonding type rmsd covalent geometry : bond 0.00404 (31001) covalent geometry : angle 0.57215 (41959) hydrogen bonds : bond 0.03489 ( 1156) hydrogen bonds : angle 4.12100 ( 3354) Misc. bond : bond 0.01044 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 183 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: Q 717 LEU cc_start: 0.8877 (tm) cc_final: 0.8651 (pp) REVERT: Q 886 PHE cc_start: 0.7958 (t80) cc_final: 0.7558 (t80) REVERT: Q 1173 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8177 (mt-10) REVERT: Q 1201 GLU cc_start: 0.8643 (mp0) cc_final: 0.8228 (mp0) REVERT: Q 1427 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8892 (p) REVERT: R 152 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8862 (tm-30) REVERT: R 227 MET cc_start: 0.9424 (tpp) cc_final: 0.8173 (mpp) REVERT: R 676 LYS cc_start: 0.3652 (OUTLIER) cc_final: 0.2934 (pttm) REVERT: S 39 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8429 (tpt90) REVERT: S 75 ASN cc_start: 0.9390 (m-40) cc_final: 0.9112 (m-40) REVERT: T 317 ASP cc_start: 0.8577 (t0) cc_final: 0.8313 (t0) REVERT: U 142 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8389 (OUTLIER) REVERT: U 261 ASP cc_start: 0.8694 (t0) cc_final: 0.8337 (t0) REVERT: V 191 ARG cc_start: 0.8969 (tmm-80) cc_final: 0.8652 (ttp80) REVERT: V 258 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7787 (ppt170) REVERT: V 264 ASP cc_start: 0.8555 (p0) cc_final: 0.8289 (p0) REVERT: V 355 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8541 (t) REVERT: V 396 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8577 (tp30) REVERT: W 220 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7710 (pmt170) REVERT: W 262 THR cc_start: 0.8633 (p) cc_final: 0.8385 (p) REVERT: X 132 ARG cc_start: 0.8679 (ttm170) cc_final: 0.8043 (ttm170) REVERT: X 282 GLU cc_start: 0.8916 (tt0) cc_final: 0.8417 (tm-30) outliers start: 111 outliers final: 27 residues processed: 280 average time/residue: 0.7795 time to fit residues: 256.7242 Evaluate side-chains 207 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1308 LEU Chi-restraints excluded: chain Q residue 1379 LEU Chi-restraints excluded: chain Q residue 1427 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 GLN Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 676 LYS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 258 ARG Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 396 GLU Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 89 SER Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain X residue 234 LYS Chi-restraints excluded: chain X residue 353 VAL Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain Y residue 330 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 39 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 323 optimal weight: 0.8980 chunk 363 optimal weight: 7.9990 chunk 287 optimal weight: 0.9990 chunk 369 optimal weight: 2.9990 chunk 314 optimal weight: 0.0270 chunk 156 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN Z 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.074181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.054739 restraints weight = 90526.516| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.18 r_work: 0.2836 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31002 Z= 0.103 Angle : 0.535 8.975 41959 Z= 0.260 Chirality : 0.042 0.155 4898 Planarity : 0.003 0.040 5374 Dihedral : 5.885 135.154 4262 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.22 % Allowed : 25.78 % Favored : 72.01 % 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 aren not related in a simple way. whole: -0.01 (0.13), residues: 3862 helix: 0.98 (0.13), residues: 1648 sheet: -0.31 (0.19), residues: 684 loop : -0.88 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q1421 TYR 0.020 0.001 TYR S 53 PHE 0.026 0.001 PHE W 206 TRP 0.013 0.001 TRP Q 901 HIS 0.002 0.001 HIS X 165 Details of bonding type rmsd covalent geometry : bond 0.00236 (31001) covalent geometry : angle 0.53487 (41959) hydrogen bonds : bond 0.02960 ( 1156) hydrogen bonds : angle 3.96083 ( 3354) Misc. bond : bond 0.00306 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 199 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 717 LEU cc_start: 0.8869 (tm) cc_final: 0.8666 (pp) REVERT: Q 886 PHE cc_start: 0.7973 (t80) cc_final: 0.7528 (t80) REVERT: Q 1173 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8176 (mt-10) REVERT: Q 1201 GLU cc_start: 0.8658 (mp0) cc_final: 0.8200 (mp0) REVERT: Q 1316 HIS cc_start: 0.5679 (OUTLIER) cc_final: 0.5387 (t70) REVERT: Q 1427 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8862 (p) REVERT: R 152 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8860 (tm-30) REVERT: R 676 LYS cc_start: 0.3685 (OUTLIER) cc_final: 0.3030 (pttm) REVERT: R 749 ASN cc_start: 0.9381 (OUTLIER) cc_final: 0.9149 (m-40) REVERT: S 39 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8471 (tpt90) REVERT: S 41 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8473 (mm-30) REVERT: S 64 ARG cc_start: 0.5356 (ptt180) cc_final: 0.5097 (ptt90) REVERT: S 70 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8754 (tm-30) REVERT: S 71 ASN cc_start: 0.9431 (t0) cc_final: 0.9221 (t0) REVERT: S 75 ASN cc_start: 0.9414 (m-40) cc_final: 0.9045 (m110) REVERT: S 154 GLU cc_start: 0.8939 (pp20) cc_final: 0.8723 (pp20) REVERT: T 317 ASP cc_start: 0.8599 (t0) cc_final: 0.8342 (t0) REVERT: U 261 ASP cc_start: 0.8660 (t0) cc_final: 0.8017 (t0) REVERT: U 311 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7781 (mmt180) REVERT: V 258 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7859 (ppt170) REVERT: V 264 ASP cc_start: 0.8416 (p0) cc_final: 0.8203 (p0) REVERT: V 355 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8542 (t) REVERT: V 396 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8590 (tp30) REVERT: W 177 ASP cc_start: 0.8898 (m-30) cc_final: 0.8662 (m-30) REVERT: W 220 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7712 (pmt170) REVERT: W 262 THR cc_start: 0.8563 (p) cc_final: 0.8309 (p) REVERT: X 282 GLU cc_start: 0.8882 (tt0) cc_final: 0.8383 (tm-30) REVERT: Y 142 GLU cc_start: 0.9164 (tt0) cc_final: 0.8630 (tm-30) REVERT: Y 282 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: Z 295 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8764 (mmtp) outliers start: 74 outliers final: 23 residues processed: 262 average time/residue: 0.7456 time to fit residues: 231.1351 Evaluate side-chains 210 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 1308 LEU Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1427 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 GLN Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 676 LYS Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 70 GLU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 311 ARG Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 402 LEU Chi-restraints excluded: chain V residue 258 ARG Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 396 GLU Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 89 SER Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 234 LYS Chi-restraints excluded: chain X residue 353 VAL Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain Y residue 282 GLU Chi-restraints excluded: chain Z residue 295 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 113 optimal weight: 0.6980 chunk 351 optimal weight: 2.9990 chunk 56 optimal weight: 0.0060 chunk 316 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 844 GLN ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 153 GLN ** U 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 455 GLN Y 49 GLN Z 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053598 restraints weight = 91696.176| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.17 r_work: 0.2801 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31002 Z= 0.169 Angle : 0.564 9.821 41959 Z= 0.275 Chirality : 0.043 0.211 4898 Planarity : 0.003 0.053 5374 Dihedral : 5.910 129.156 4262 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.81 % Allowed : 25.63 % Favored : 71.56 % 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 aren not related in a simple way. whole: 0.13 (0.14), residues: 3862 helix: 1.10 (0.13), residues: 1660 sheet: -0.32 (0.19), residues: 692 loop : -0.77 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 191 TYR 0.016 0.001 TYR V 295 PHE 0.014 0.001 PHE Y 308 TRP 0.012 0.001 TRP Q 800 HIS 0.003 0.001 HIS X 29 Details of bonding type rmsd covalent geometry : bond 0.00395 (31001) covalent geometry : angle 0.56408 (41959) hydrogen bonds : bond 0.03188 ( 1156) hydrogen bonds : angle 3.95417 ( 3354) Misc. bond : bond 0.00263 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 178 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 1173 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8100 (mt-10) REVERT: Q 1201 GLU cc_start: 0.8705 (mp0) cc_final: 0.8229 (mp0) REVERT: Q 1316 HIS cc_start: 0.5902 (OUTLIER) cc_final: 0.5633 (t70) REVERT: Q 1427 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8777 (p) REVERT: R 152 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8844 (tm-30) REVERT: R 676 LYS cc_start: 0.3691 (OUTLIER) cc_final: 0.3029 (pttm) REVERT: S 39 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8493 (tpt90) REVERT: S 41 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8591 (mm-30) REVERT: S 64 ARG cc_start: 0.5342 (ptt180) cc_final: 0.5066 (ptt90) REVERT: S 70 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.8735 (tm-30) REVERT: S 75 ASN cc_start: 0.9385 (m-40) cc_final: 0.9020 (m-40) REVERT: S 152 ASP cc_start: 0.8998 (p0) cc_final: 0.8792 (p0) REVERT: S 154 GLU cc_start: 0.9033 (pp20) cc_final: 0.8820 (pp20) REVERT: T 317 ASP cc_start: 0.8624 (t0) cc_final: 0.8350 (t0) REVERT: U 89 SER cc_start: 0.9286 (OUTLIER) cc_final: 0.9043 (p) REVERT: U 142 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8394 (OUTLIER) REVERT: U 261 ASP cc_start: 0.8679 (t0) cc_final: 0.8040 (t0) REVERT: V 191 ARG cc_start: 0.8973 (ttp80) cc_final: 0.8570 (ttp80) REVERT: V 258 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7927 (ppt170) REVERT: V 264 ASP cc_start: 0.8566 (p0) cc_final: 0.8279 (p0) REVERT: V 355 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8532 (t) REVERT: V 396 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8593 (tp30) REVERT: W 177 ASP cc_start: 0.8897 (m-30) cc_final: 0.8682 (m-30) REVERT: W 220 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7689 (pmt170) REVERT: W 262 THR cc_start: 0.8614 (p) cc_final: 0.8352 (p) REVERT: W 301 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8930 (mp) REVERT: X 282 GLU cc_start: 0.8916 (tt0) cc_final: 0.8425 (tm-30) REVERT: Y 110 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8712 (pm20) REVERT: Y 142 GLU cc_start: 0.9173 (tt0) cc_final: 0.8626 (tm-30) REVERT: Y 282 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8572 (mp0) REVERT: Y 316 GLU cc_start: 0.8450 (tp30) cc_final: 0.8243 (tp30) REVERT: Z 295 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8771 (mmtp) outliers start: 94 outliers final: 30 residues processed: 256 average time/residue: 0.6947 time to fit residues: 211.7307 Evaluate side-chains 213 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1291 MET Chi-restraints excluded: chain Q residue 1308 LEU Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1427 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 GLN Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 643 GLU Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 676 LYS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 70 GLU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 258 ARG Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 396 GLU Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 89 SER Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 301 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 234 LYS Chi-restraints excluded: chain X residue 353 VAL Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 208 ARG Chi-restraints excluded: chain Y residue 282 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Z residue 295 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 195 optimal weight: 4.9990 chunk 202 optimal weight: 0.3980 chunk 295 optimal weight: 2.9990 chunk 255 optimal weight: 0.4980 chunk 321 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 HIS ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.054819 restraints weight = 90787.137| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.15 r_work: 0.2832 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31002 Z= 0.103 Angle : 0.539 12.091 41959 Z= 0.260 Chirality : 0.042 0.179 4898 Planarity : 0.003 0.040 5374 Dihedral : 5.736 127.953 4262 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.40 % Allowed : 26.23 % Favored : 71.38 % 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 aren not related in a simple way. whole: 0.23 (0.14), residues: 3862 helix: 1.20 (0.13), residues: 1662 sheet: -0.29 (0.19), residues: 691 loop : -0.73 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 191 TYR 0.024 0.001 TYR S 53 PHE 0.026 0.001 PHE W 206 TRP 0.012 0.001 TRP Q 901 HIS 0.002 0.000 HIS X 165 Details of bonding type rmsd covalent geometry : bond 0.00236 (31001) covalent geometry : angle 0.53878 (41959) hydrogen bonds : bond 0.02818 ( 1156) hydrogen bonds : angle 3.84788 ( 3354) Misc. bond : bond 0.00173 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 188 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: Q 1173 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8107 (mt-10) REVERT: Q 1201 GLU cc_start: 0.8689 (mp0) cc_final: 0.8192 (mp0) REVERT: Q 1316 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.5455 (t70) REVERT: Q 1427 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8740 (p) REVERT: R 152 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8850 (tm-30) REVERT: R 676 LYS cc_start: 0.3583 (OUTLIER) cc_final: 0.2676 (pttm) REVERT: S 39 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8434 (tpt90) REVERT: S 41 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8526 (mm-30) REVERT: S 64 ARG cc_start: 0.5333 (ptt180) cc_final: 0.5043 (ptt90) REVERT: S 70 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.8693 (tm-30) REVERT: S 75 ASN cc_start: 0.9383 (m-40) cc_final: 0.9023 (m110) REVERT: S 152 ASP cc_start: 0.8997 (p0) cc_final: 0.8795 (p0) REVERT: S 154 GLU cc_start: 0.9009 (pp20) cc_final: 0.8797 (pp20) REVERT: T 317 ASP cc_start: 0.8608 (t0) cc_final: 0.8333 (t0) REVERT: U 89 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.9035 (p) REVERT: U 142 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8385 (OUTLIER) REVERT: U 243 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.9094 (mp0) REVERT: U 261 ASP cc_start: 0.8651 (t0) cc_final: 0.8021 (t0) REVERT: V 191 ARG cc_start: 0.8946 (ttp80) cc_final: 0.8501 (ttp80) REVERT: V 258 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7933 (ppt170) REVERT: V 264 ASP cc_start: 0.8524 (p0) cc_final: 0.8165 (p0) REVERT: V 355 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8522 (t) REVERT: V 396 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8543 (tp30) REVERT: W 177 ASP cc_start: 0.8902 (m-30) cc_final: 0.8682 (m-30) REVERT: W 220 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7716 (pmt170) REVERT: W 262 THR cc_start: 0.8543 (p) cc_final: 0.8272 (p) REVERT: W 301 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8883 (mp) REVERT: X 132 ARG cc_start: 0.8765 (ttm170) cc_final: 0.8210 (ttm170) REVERT: Y 110 GLU cc_start: 0.9019 (pt0) cc_final: 0.8691 (pm20) REVERT: Y 142 GLU cc_start: 0.9156 (tt0) cc_final: 0.8606 (tm-30) REVERT: Y 157 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8470 (tppp) REVERT: Y 229 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8886 (tt) REVERT: Y 282 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: Z 295 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8736 (mmtp) outliers start: 80 outliers final: 28 residues processed: 259 average time/residue: 0.6471 time to fit residues: 199.6678 Evaluate side-chains 219 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 1177 VAL Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1427 THR Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 GLN Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 643 GLU Chi-restraints excluded: chain R residue 676 LYS Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 70 GLU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 402 LEU Chi-restraints excluded: chain V residue 258 ARG Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 396 GLU Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 89 SER Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 301 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 234 LYS Chi-restraints excluded: chain X residue 353 VAL Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 282 GLU Chi-restraints excluded: chain Z residue 295 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 290 optimal weight: 2.9990 chunk 378 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 297 optimal weight: 0.8980 chunk 318 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 336 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 358 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 752 HIS ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.053261 restraints weight = 91529.336| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.17 r_work: 0.2798 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31002 Z= 0.169 Angle : 0.580 12.929 41959 Z= 0.281 Chirality : 0.043 0.172 4898 Planarity : 0.003 0.041 5374 Dihedral : 5.799 123.378 4262 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.51 % Allowed : 26.11 % Favored : 71.38 % 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 aren not related in a simple way. whole: 0.26 (0.14), residues: 3862 helix: 1.23 (0.13), residues: 1655 sheet: -0.28 (0.19), residues: 691 loop : -0.71 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 191 TYR 0.014 0.001 TYR V 295 PHE 0.014 0.001 PHE Y 308 TRP 0.013 0.001 TRP Q 770 HIS 0.003 0.001 HIS X 27 Details of bonding type rmsd covalent geometry : bond 0.00394 (31001) covalent geometry : angle 0.57966 (41959) hydrogen bonds : bond 0.03106 ( 1156) hydrogen bonds : angle 3.89157 ( 3354) Misc. bond : bond 0.00227 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 178 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 1109 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8808 (mtpt) REVERT: Q 1173 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8164 (mt-10) REVERT: Q 1201 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: Q 1316 HIS cc_start: 0.5872 (OUTLIER) cc_final: 0.5577 (t70) REVERT: Q 1427 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8793 (p) REVERT: R 152 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8862 (tm-30) REVERT: R 643 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.8901 (tm-30) REVERT: R 676 LYS cc_start: 0.3698 (OUTLIER) cc_final: 0.2757 (pttm) REVERT: R 702 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8237 (ttp) REVERT: R 749 ASN cc_start: 0.9405 (OUTLIER) cc_final: 0.9193 (m-40) REVERT: S 39 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8451 (tpt90) REVERT: S 41 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8507 (mm-30) REVERT: S 64 ARG cc_start: 0.5323 (ptt180) cc_final: 0.5014 (ptt90) REVERT: S 70 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.8704 (tm-30) REVERT: S 75 ASN cc_start: 0.9416 (m-40) cc_final: 0.9050 (m110) REVERT: S 154 GLU cc_start: 0.9030 (pp20) cc_final: 0.8798 (pp20) REVERT: T 271 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: T 317 ASP cc_start: 0.8665 (t0) cc_final: 0.8425 (t0) REVERT: U 89 SER cc_start: 0.9309 (OUTLIER) cc_final: 0.9059 (p) REVERT: U 142 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8403 (pp20) REVERT: U 243 GLU cc_start: 0.9344 (OUTLIER) cc_final: 0.9123 (mp0) REVERT: U 261 ASP cc_start: 0.8701 (t0) cc_final: 0.8085 (t0) REVERT: V 258 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7965 (ppt170) REVERT: V 264 ASP cc_start: 0.8556 (p0) cc_final: 0.8210 (p0) REVERT: V 355 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8555 (t) REVERT: V 396 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8561 (tp30) REVERT: W 177 ASP cc_start: 0.8911 (m-30) cc_final: 0.8705 (m-30) REVERT: W 220 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7691 (pmt170) REVERT: W 262 THR cc_start: 0.8609 (p) cc_final: 0.8338 (p) REVERT: W 301 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8961 (mp) REVERT: Y 110 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8657 (pm20) REVERT: Y 142 GLU cc_start: 0.9177 (tt0) cc_final: 0.8662 (tm-30) REVERT: Y 157 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8655 (tppp) REVERT: Y 282 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: Y 315 ASP cc_start: 0.8828 (t0) cc_final: 0.8579 (t0) REVERT: Z 295 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8778 (mmtp) outliers start: 84 outliers final: 31 residues processed: 250 average time/residue: 0.6382 time to fit residues: 189.3030 Evaluate side-chains 223 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 823 VAL Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 1072 ASP Chi-restraints excluded: chain Q residue 1109 LYS Chi-restraints excluded: chain Q residue 1177 VAL Chi-restraints excluded: chain Q residue 1201 GLU Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1427 THR Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 GLN Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 643 GLU Chi-restraints excluded: chain R residue 676 LYS Chi-restraints excluded: chain R residue 702 MET Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 70 GLU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 258 ARG Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 396 GLU Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 89 SER Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 301 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 234 LYS Chi-restraints excluded: chain X residue 353 VAL Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 282 GLU Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Z residue 295 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 229 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 283 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 285 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN Z 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.071600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.052360 restraints weight = 92215.240| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.14 r_work: 0.2768 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 31002 Z= 0.238 Angle : 0.630 14.893 41959 Z= 0.306 Chirality : 0.044 0.175 4898 Planarity : 0.003 0.047 5374 Dihedral : 6.042 119.794 4262 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.31 % Allowed : 26.41 % Favored : 71.29 % 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 aren not related in a simple way. whole: 0.16 (0.14), residues: 3862 helix: 1.17 (0.13), residues: 1653 sheet: -0.35 (0.19), residues: 691 loop : -0.76 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 311 TYR 0.020 0.001 TYR S 53 PHE 0.029 0.001 PHE W 206 TRP 0.015 0.001 TRP Q 770 HIS 0.003 0.001 HIS U 25 Details of bonding type rmsd covalent geometry : bond 0.00552 (31001) covalent geometry : angle 0.63033 (41959) hydrogen bonds : bond 0.03433 ( 1156) hydrogen bonds : angle 4.02014 ( 3354) Misc. bond : bond 0.00309 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 179 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 833 MET cc_start: 0.4703 (mmt) cc_final: 0.4490 (mmm) REVERT: Q 860 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6483 (m-10) REVERT: Q 1109 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8856 (mtpt) REVERT: Q 1201 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: Q 1427 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8771 (p) REVERT: R 152 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8885 (tm-30) REVERT: R 643 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.8930 (tm-30) REVERT: R 676 LYS cc_start: 0.3785 (OUTLIER) cc_final: 0.3006 (pttm) REVERT: R 749 ASN cc_start: 0.9380 (OUTLIER) cc_final: 0.9150 (m110) REVERT: S 39 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8361 (tpt90) REVERT: S 41 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8485 (mm-30) REVERT: S 64 ARG cc_start: 0.5366 (ptt180) cc_final: 0.5060 (ptt90) REVERT: S 75 ASN cc_start: 0.9443 (m-40) cc_final: 0.9092 (m110) REVERT: S 154 GLU cc_start: 0.9031 (pp20) cc_final: 0.8808 (pp20) REVERT: T 317 ASP cc_start: 0.8639 (t0) cc_final: 0.8392 (t0) REVERT: U 110 GLU cc_start: 0.8428 (mp0) cc_final: 0.8088 (mp0) REVERT: U 142 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8429 (pp20) REVERT: U 243 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.9107 (mp0) REVERT: U 261 ASP cc_start: 0.8723 (t0) cc_final: 0.8067 (t0) REVERT: V 109 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: V 258 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7972 (ppt170) REVERT: V 264 ASP cc_start: 0.8638 (p0) cc_final: 0.8279 (p0) REVERT: V 315 MET cc_start: 0.9246 (tpp) cc_final: 0.8467 (mpp) REVERT: V 355 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8571 (t) REVERT: W 177 ASP cc_start: 0.8913 (m-30) cc_final: 0.8699 (m-30) REVERT: W 220 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7698 (pmt170) REVERT: W 262 THR cc_start: 0.8657 (p) cc_final: 0.8404 (p) REVERT: X 132 ARG cc_start: 0.8790 (ttm170) cc_final: 0.8218 (ttm170) REVERT: Y 110 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: Y 142 GLU cc_start: 0.9182 (tt0) cc_final: 0.8673 (tm-30) REVERT: Y 147 ARG cc_start: 0.7836 (ppt170) cc_final: 0.7414 (ppt-90) REVERT: Y 157 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8639 (tppp) REVERT: Y 282 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8605 (mp0) REVERT: Y 315 ASP cc_start: 0.8837 (t0) cc_final: 0.8602 (t0) REVERT: Z 295 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8781 (mmtp) outliers start: 77 outliers final: 32 residues processed: 243 average time/residue: 0.6337 time to fit residues: 182.7135 Evaluate side-chains 220 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 823 VAL Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 860 PHE Chi-restraints excluded: chain Q residue 1109 LYS Chi-restraints excluded: chain Q residue 1177 VAL Chi-restraints excluded: chain Q residue 1201 GLU Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1379 LEU Chi-restraints excluded: chain Q residue 1427 THR Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 GLN Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 643 GLU Chi-restraints excluded: chain R residue 676 LYS Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 378 ASP Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 258 ARG Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 89 SER Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 234 LYS Chi-restraints excluded: chain X residue 353 VAL Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 282 GLU Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Z residue 295 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 304 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 288 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 344 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 364 optimal weight: 0.9990 chunk 262 optimal weight: 0.0970 chunk 120 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.054135 restraints weight = 91324.228| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.19 r_work: 0.2822 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31002 Z= 0.110 Angle : 0.582 13.848 41959 Z= 0.280 Chirality : 0.042 0.167 4898 Planarity : 0.003 0.041 5374 Dihedral : 5.743 118.714 4262 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.86 % Allowed : 26.98 % Favored : 71.17 % 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 aren not related in a simple way. whole: 0.31 (0.14), residues: 3862 helix: 1.28 (0.13), residues: 1653 sheet: -0.30 (0.19), residues: 688 loop : -0.68 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 191 TYR 0.014 0.001 TYR X 186 PHE 0.012 0.001 PHE Q1017 TRP 0.019 0.001 TRP Q 770 HIS 0.003 0.001 HIS X 165 Details of bonding type rmsd covalent geometry : bond 0.00258 (31001) covalent geometry : angle 0.58208 (41959) hydrogen bonds : bond 0.02854 ( 1156) hydrogen bonds : angle 3.87261 ( 3354) Misc. bond : bond 0.00202 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 833 MET cc_start: 0.4835 (mmt) cc_final: 0.4577 (mmm) REVERT: Q 860 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6403 (m-10) REVERT: Q 1201 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: Q 1427 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8786 (p) REVERT: R 152 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8855 (tm-30) REVERT: R 676 LYS cc_start: 0.3581 (OUTLIER) cc_final: 0.2830 (pttm) REVERT: R 702 MET cc_start: 0.8765 (ttp) cc_final: 0.8489 (tmm) REVERT: R 749 ASN cc_start: 0.9393 (OUTLIER) cc_final: 0.9163 (m-40) REVERT: S 39 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8378 (tpt90) REVERT: S 41 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8510 (mm-30) REVERT: S 64 ARG cc_start: 0.5241 (ptt180) cc_final: 0.4937 (ptt90) REVERT: S 75 ASN cc_start: 0.9441 (m-40) cc_final: 0.9086 (m110) REVERT: S 154 GLU cc_start: 0.8987 (pp20) cc_final: 0.8753 (pp20) REVERT: T 317 ASP cc_start: 0.8609 (t0) cc_final: 0.8360 (t0) REVERT: U 89 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.9031 (p) REVERT: U 110 GLU cc_start: 0.8406 (mp0) cc_final: 0.8104 (mp0) REVERT: U 142 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8430 (pp20) REVERT: U 165 MET cc_start: 0.8323 (ptp) cc_final: 0.7862 (pmm) REVERT: U 243 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.9094 (mp0) REVERT: U 261 ASP cc_start: 0.8653 (t0) cc_final: 0.8010 (t0) REVERT: V 109 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: V 258 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7992 (ppt170) REVERT: V 264 ASP cc_start: 0.8586 (p0) cc_final: 0.8230 (p0) REVERT: V 355 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8496 (t) REVERT: W 177 ASP cc_start: 0.8909 (m-30) cc_final: 0.8685 (m-30) REVERT: W 220 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7713 (pmt170) REVERT: W 262 THR cc_start: 0.8563 (p) cc_final: 0.8290 (p) REVERT: W 301 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8865 (mp) REVERT: X 132 ARG cc_start: 0.8752 (ttm170) cc_final: 0.8098 (ttm170) REVERT: Y 110 GLU cc_start: 0.8956 (pt0) cc_final: 0.8606 (pm20) REVERT: Y 142 GLU cc_start: 0.9155 (tt0) cc_final: 0.8631 (tm-30) REVERT: Y 147 ARG cc_start: 0.7836 (ppt170) cc_final: 0.7419 (ppt-90) REVERT: Y 157 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8649 (tppp) REVERT: Y 282 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8574 (mp0) REVERT: Y 315 ASP cc_start: 0.8804 (t0) cc_final: 0.8541 (t0) REVERT: Z 295 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8730 (mmtp) outliers start: 62 outliers final: 25 residues processed: 236 average time/residue: 0.6348 time to fit residues: 178.4844 Evaluate side-chains 213 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 823 VAL Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 860 PHE Chi-restraints excluded: chain Q residue 1177 VAL Chi-restraints excluded: chain Q residue 1201 GLU Chi-restraints excluded: chain Q residue 1427 THR Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 GLN Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 676 LYS Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 258 ARG Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 301 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 234 LYS Chi-restraints excluded: chain X residue 353 VAL Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 282 GLU Chi-restraints excluded: chain Z residue 295 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 228 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 376 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 385 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 293 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 344 optimal weight: 0.0570 chunk 244 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 141 GLN T 245 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.074033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054675 restraints weight = 90406.029| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.17 r_work: 0.2835 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31002 Z= 0.103 Angle : 0.573 13.258 41959 Z= 0.276 Chirality : 0.042 0.196 4898 Planarity : 0.003 0.064 5374 Dihedral : 5.577 113.960 4262 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.35 % Allowed : 27.28 % Favored : 71.38 % 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 aren not related in a simple way. whole: 0.37 (0.14), residues: 3862 helix: 1.33 (0.13), residues: 1651 sheet: -0.26 (0.19), residues: 690 loop : -0.65 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 191 TYR 0.013 0.001 TYR T 201 PHE 0.014 0.001 PHE Q 886 TRP 0.015 0.001 TRP Q 770 HIS 0.003 0.000 HIS X 165 Details of bonding type rmsd covalent geometry : bond 0.00241 (31001) covalent geometry : angle 0.57294 (41959) hydrogen bonds : bond 0.02772 ( 1156) hydrogen bonds : angle 3.82052 ( 3354) Misc. bond : bond 0.00176 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7724 Ramachandran restraints generated. 3862 Oldfield, 0 Emsley, 3862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: Q 833 MET cc_start: 0.4719 (mmt) cc_final: 0.4505 (mmm) REVERT: Q 860 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6475 (m-10) REVERT: Q 1201 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: R 152 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8844 (tm-30) REVERT: R 676 LYS cc_start: 0.3568 (OUTLIER) cc_final: 0.2670 (pttm) REVERT: R 702 MET cc_start: 0.8757 (ttp) cc_final: 0.8340 (tmm) REVERT: R 749 ASN cc_start: 0.9389 (OUTLIER) cc_final: 0.9162 (m-40) REVERT: S 39 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8352 (tpt90) REVERT: S 41 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8464 (mm-30) REVERT: S 64 ARG cc_start: 0.5230 (ptt180) cc_final: 0.4922 (ptt90) REVERT: S 75 ASN cc_start: 0.9436 (m-40) cc_final: 0.9142 (m-40) REVERT: S 154 GLU cc_start: 0.8985 (pp20) cc_final: 0.8746 (pp20) REVERT: T 317 ASP cc_start: 0.8663 (t0) cc_final: 0.8389 (t0) REVERT: U 110 GLU cc_start: 0.8392 (mp0) cc_final: 0.8091 (mp0) REVERT: U 142 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8406 (pp20) REVERT: U 165 MET cc_start: 0.8242 (ptp) cc_final: 0.7863 (pmm) REVERT: U 243 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.9124 (mp0) REVERT: U 261 ASP cc_start: 0.8636 (t0) cc_final: 0.8021 (t0) REVERT: V 109 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: V 258 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8015 (ppt170) REVERT: V 264 ASP cc_start: 0.8559 (p0) cc_final: 0.8218 (p0) REVERT: V 355 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8507 (t) REVERT: V 396 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8315 (mm-30) REVERT: W 177 ASP cc_start: 0.8906 (m-30) cc_final: 0.8681 (m-30) REVERT: W 220 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7767 (pmt170) REVERT: W 262 THR cc_start: 0.8563 (p) cc_final: 0.8279 (p) REVERT: W 301 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8894 (mp) REVERT: X 132 ARG cc_start: 0.8728 (ttm170) cc_final: 0.8069 (ttm170) REVERT: Y 110 GLU cc_start: 0.8964 (pt0) cc_final: 0.8629 (pm20) REVERT: Y 142 GLU cc_start: 0.9164 (tt0) cc_final: 0.8625 (tm-30) REVERT: Y 147 ARG cc_start: 0.7839 (ppt170) cc_final: 0.7409 (ppt-90) REVERT: Y 157 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8531 (tppp) REVERT: Y 282 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8540 (mp0) REVERT: Y 315 ASP cc_start: 0.8754 (t0) cc_final: 0.8519 (t0) REVERT: Z 295 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8747 (mmtp) outliers start: 45 outliers final: 21 residues processed: 217 average time/residue: 0.7179 time to fit residues: 184.3000 Evaluate side-chains 207 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 823 VAL Chi-restraints excluded: chain Q residue 830 LEU Chi-restraints excluded: chain Q residue 860 PHE Chi-restraints excluded: chain Q residue 1072 ASP Chi-restraints excluded: chain Q residue 1177 VAL Chi-restraints excluded: chain Q residue 1201 GLU Chi-restraints excluded: chain Q residue 1427 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 GLN Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 676 LYS Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 39 ARG Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 258 ARG Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 396 GLU Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 301 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 234 LYS Chi-restraints excluded: chain X residue 353 VAL Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 282 GLU Chi-restraints excluded: chain Z residue 295 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 147 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 242 optimal weight: 0.0270 chunk 111 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 362 optimal weight: 8.9990 chunk 317 optimal weight: 0.3980 chunk 268 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 overall best weight: 1.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 245 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053672 restraints weight = 91554.799| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.17 r_work: 0.2808 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31002 Z= 0.153 Angle : 0.595 12.991 41959 Z= 0.287 Chirality : 0.043 0.176 4898 Planarity : 0.003 0.038 5374 Dihedral : 5.653 111.169 4262 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.35 % Allowed : 27.37 % Favored : 71.29 % 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 aren not related in a simple way. whole: 0.39 (0.14), residues: 3862 helix: 1.35 (0.13), residues: 1648 sheet: -0.22 (0.19), residues: 686 loop : -0.65 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 191 TYR 0.034 0.001 TYR S 53 PHE 0.013 0.001 PHE Y 308 TRP 0.015 0.001 TRP Q 770 HIS 0.003 0.001 HIS X 165 Details of bonding type rmsd covalent geometry : bond 0.00359 (31001) covalent geometry : angle 0.59495 (41959) hydrogen bonds : bond 0.03026 ( 1156) hydrogen bonds : angle 3.87085 ( 3354) Misc. bond : bond 0.00251 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8488.62 seconds wall clock time: 146 minutes 6.38 seconds (8766.38 seconds total)