Starting phenix.real_space_refine on Mon Aug 25 12:36:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ccd_45441/08_2025/9ccd_45441_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ccd_45441/08_2025/9ccd_45441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ccd_45441/08_2025/9ccd_45441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ccd_45441/08_2025/9ccd_45441.map" model { file = "/net/cci-nas-00/data/ceres_data/9ccd_45441/08_2025/9ccd_45441_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ccd_45441/08_2025/9ccd_45441_neut.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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 85 5.16 5 C 17064 2.51 5 N 4676 2.21 5 O 5286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 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: 27123 Number of models: 1 Model: "" Number of chains: 16 Chain: "Q" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1864 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 18, 'TRANS': 215} Chain breaks: 1 Chain: "R" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3548 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1009 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3335 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "W" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3394 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 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: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3341 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 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: 7.04, per 1000 atoms: 0.26 Number of scatterers: 27123 At special positions: 0 Unit cell: (137.24, 125.96, 193.64, 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 85 16.00 P 12 15.00 O 5286 8.00 N 4676 7.00 C 17064 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: 1.98 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 32 sheets defined 43.0% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 4.082A 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 1145 Processing helix chain 'Q' and resid 1147 through 1154 removed outlier: 3.937A pdb=" N GLU Q1154 " --> pdb=" O LYS Q1150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1169 through 1178 removed outlier: 4.136A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1185 through 1191 Processing helix chain 'Q' and resid 1192 through 1201 Processing helix chain 'Q' and resid 1202 through 1206 removed outlier: 3.538A pdb=" N CYS Q1205 " --> pdb=" O TYR Q1202 " (cutoff:3.500A) removed outlier: 3.586A 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 1280 through 1284 removed outlier: 3.654A pdb=" N SER Q1283 " --> pdb=" O LYS Q1280 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER Q1284 " --> pdb=" O ASN Q1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1280 through 1284' Processing helix chain 'R' and resid 82 through 87 removed outlier: 3.876A pdb=" N ASP R 85 " --> pdb=" O VAL R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 95 removed outlier: 3.797A pdb=" N GLN R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 143 through 158 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: 3.577A pdb=" N TYR R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 263 removed outlier: 3.675A pdb=" N GLU R 262 " --> pdb=" O ASP R 258 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 274 removed outlier: 3.728A pdb=" N ASP R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N THR R 272 " --> pdb=" O GLU R 268 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN R 273 " --> pdb=" O ASN R 269 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 589 through 597 Processing helix chain 'R' and resid 606 through 609 Processing helix chain 'R' and resid 616 through 624 removed outlier: 3.945A pdb=" N VAL R 621 " --> pdb=" O GLU R 617 " (cutoff:3.500A) Proline residue: R 622 - end of helix Processing helix chain 'R' and resid 637 through 649 removed outlier: 3.844A pdb=" N LYS R 649 " --> pdb=" O ILE R 645 " (cutoff:3.500A) Processing helix chain 'R' and resid 658 through 666 Processing helix chain 'R' and resid 672 through 677 removed outlier: 3.988A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL R 677 " --> pdb=" O ASN R 674 " (cutoff:3.500A) Processing helix chain 'R' and resid 679 through 692 removed outlier: 3.621A pdb=" N LEU R 692 " --> pdb=" O PHE R 688 " (cutoff:3.500A) Processing helix chain 'R' and resid 708 through 720 Processing helix chain 'R' and resid 722 through 727 removed outlier: 3.915A pdb=" N ARG R 725 " --> pdb=" O GLU R 722 " (cutoff:3.500A) Processing helix chain 'R' and resid 730 through 738 Processing helix chain 'S' and resid 29 through 38 removed outlier: 4.146A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL S 36 " --> pdb=" O PHE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 removed outlier: 3.594A pdb=" N LEU S 66 " --> pdb=" O SER S 62 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.840A 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 151 through 156 Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.663A pdb=" N ARG T 55 " --> pdb=" O GLN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.582A 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: 3.561A pdb=" N SER T 188 " --> pdb=" O THR T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 257 removed outlier: 3.594A pdb=" N ASN T 256 " --> pdb=" O LEU T 252 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 297 removed outlier: 3.600A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP T 297 " --> pdb=" O ALA T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 Processing helix chain 'T' and resid 317 through 329 removed outlier: 3.598A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU T 329 " --> pdb=" O ASN T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 359 Processing helix chain 'T' and resid 360 through 365 removed outlier: 3.583A pdb=" N ASP T 365 " --> pdb=" O PRO T 361 " (cutoff:3.500A) Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 417 Processing helix chain 'T' and resid 418 through 429 removed outlier: 3.770A pdb=" N SER T 429 " --> pdb=" O LEU T 425 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 removed outlier: 3.650A pdb=" N VAL T 439 " --> pdb=" O VAL T 435 " (cutoff:3.500A) Processing helix chain 'T' and resid 448 through 458 Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 93 removed outlier: 4.008A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.664A pdb=" N LYS U 181 " --> pdb=" O ASP U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 209 No H-bonds generated for 'chain 'U' and resid 207 through 209' Processing helix chain 'U' and resid 241 through 248 Processing helix chain 'U' and resid 253 through 260 Processing helix chain 'U' and resid 267 through 284 Processing helix chain 'U' and resid 302 through 313 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.824A 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: 4.019A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.600A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 443 removed outlier: 3.665A pdb=" N SER U 436 " --> pdb=" O ASP U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 444 through 447 Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.674A 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 108 through 111 removed outlier: 3.641A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 127 removed outlier: 3.512A pdb=" N THR V 120 " --> pdb=" O LYS V 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 192 removed outlier: 3.758A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 216 through 219 removed outlier: 3.616A pdb=" N ALA V 219 " --> pdb=" O ASP V 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 216 through 219' Processing helix chain 'V' and resid 249 through 258 removed outlier: 3.515A pdb=" N ARG V 258 " --> pdb=" O VAL V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 273 removed outlier: 3.608A pdb=" N MET V 268 " --> pdb=" O ASP V 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU V 272 " --> pdb=" O MET V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.756A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 313 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 419 through 429 Processing helix chain 'V' and resid 435 through 446 removed outlier: 3.546A pdb=" N VAL V 439 " --> pdb=" O VAL V 435 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'W' and resid 80 through 93 removed outlier: 3.606A pdb=" N GLY W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 107 removed outlier: 3.577A pdb=" N PHE W 107 " --> pdb=" O SER W 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 104 through 107' 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 248 Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.831A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.706A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.680A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 343 Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.662A 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: 4.016A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.761A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 442 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.789A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 97 Processing helix chain 'X' and resid 116 through 127 Processing helix chain 'X' and resid 182 through 191 removed outlier: 3.689A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 273 removed outlier: 3.704A pdb=" N MET X 268 " --> pdb=" O ASP X 264 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU X 273 " --> pdb=" O MET X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.789A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN X 298 " --> pdb=" O LYS X 294 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 316 Processing helix chain 'X' and resid 317 through 328 removed outlier: 3.717A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) 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: 3.687A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 428 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 Processing helix chain 'Y' and resid 81 through 93 removed outlier: 3.701A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) 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: 4.044A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA Y 278 " --> pdb=" O ASN Y 274 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 Processing helix chain 'Y' and resid 302 through 313 removed outlier: 4.061A pdb=" N ARG Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.732A 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: 3.701A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE Y 403 " --> pdb=" O SER Y 399 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN Y 407 " --> pdb=" O ILE Y 403 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 Processing helix chain 'Y' and resid 432 through 443 Processing helix chain 'Y' and resid 444 through 447 Processing sheet with id=AA1, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 5.962A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'Q' and resid 1071 through 1072 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1072 current: chain 'X' and resid 163 through 172 removed outlier: 3.723A 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: 5.739A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.269A pdb=" N TYR Q1083 " --> pdb=" O GLU Q1222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'R' and resid 61 through 64 removed outlier: 3.573A pdb=" N HIS R 61 " --> pdb=" O ALA R 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA R 51 " --> pdb=" O HIS R 61 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE R 63 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE R 134 " --> pdb=" O THR R 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 100 through 101 removed outlier: 3.576A pdb=" N PHE R 104 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, first strand: chain 'R' and resid 275 through 278 Processing sheet with id=AA8, first strand: chain 'S' and resid 125 through 126 Processing sheet with id=AA9, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB1, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.494A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N SER T 340 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU T 77 " --> pdb=" O SER T 340 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 129 through 151 removed outlier: 6.240A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASP T 151 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE T 163 " --> pdb=" O ASP T 151 " (cutoff:3.500A) removed outlier: 3.535A 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 208 through 215 removed outlier: 6.501A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 345 through 346 Processing sheet with id=AB4, first strand: chain 'T' and resid 394 through 395 removed outlier: 7.329A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AB6, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.227A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU U 293 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA U 324 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE U 295 " --> pdb=" O ALA U 324 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 125 through 147 removed outlier: 6.971A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE U 145 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN U 155 " --> pdb=" O ILE U 145 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE U 160 " --> pdb=" O THR U 167 " (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: 5.714A pdb=" N VAL U 222 " --> pdb=" O LEU U 202 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ARG U 204 " --> pdb=" O VAL U 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 329 through 331 Processing sheet with id=AB9, first strand: chain 'V' and resid 44 through 45 removed outlier: 3.563A pdb=" N GLU V 45 " --> pdb=" O PHE V 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 102 through 106 removed outlier: 3.657A pdb=" N SER V 340 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 129 through 151 removed outlier: 6.227A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N HIS V 165 " --> pdb=" O PRO V 149 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP V 151 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE V 163 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) removed outlier: 3.575A 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 207 through 214 Processing sheet with id=AC3, first strand: chain 'V' and resid 344 through 346 removed outlier: 3.526A pdb=" N THR V 345 " --> pdb=" O SER V 355 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC5, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.294A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 125 through 147 removed outlier: 6.666A pdb=" N THR W 159 " --> pdb=" O VAL W 141 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE W 143 " --> pdb=" O LYS W 157 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS W 157 " --> pdb=" O ILE W 143 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE W 145 " --> pdb=" O GLN W 155 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN W 155 " --> pdb=" O ILE W 145 " (cutoff:3.500A) removed outlier: 3.793A 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=AC7, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AC8, first strand: chain 'X' and resid 44 through 45 removed outlier: 3.596A pdb=" N GLU X 45 " --> pdb=" O PHE X 48 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE X 48 " --> pdb=" O GLU X 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.386A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU X 308 " --> pdb=" O VAL X 337 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ALA X 339 " --> pdb=" O LEU X 308 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE X 310 " --> pdb=" O ALA X 339 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 344 through 346 removed outlier: 3.804A pdb=" N THR X 345 " --> pdb=" O SER X 355 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER X 355 " --> pdb=" O THR X 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'Y' and resid 40 through 41 Processing sheet with id=AD3, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.312A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 125 through 146 removed outlier: 7.149A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 171 current: chain 'Y' and resid 199 through 204 Processing sheet with id=AD5, first strand: chain 'Y' and resid 330 through 331 1007 hydrogen bonds defined for protein. 2925 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: 4.53 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8540 1.34 - 1.46: 5376 1.46 - 1.58: 13447 1.58 - 1.71: 19 1.71 - 1.83: 148 Bond restraints: 27530 Sorted by residual: bond pdb=" CG PRO R 131 " pdb=" CD PRO R 131 " ideal model delta sigma weight residual 1.503 1.284 0.219 3.40e-02 8.65e+02 4.14e+01 bond pdb=" N PRO R 131 " pdb=" CD PRO R 131 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" CB PRO R 131 " pdb=" CG PRO R 131 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.18e+01 bond pdb=" C SER Q1287 " pdb=" N MET Q1288 " ideal model delta sigma weight residual 1.329 1.281 0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" CB ASN R 128 " pdb=" CG ASN R 128 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.20e+00 ... (remaining 27525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 36748 3.41 - 6.82: 427 6.82 - 10.23: 63 10.23 - 13.64: 12 13.64 - 17.05: 2 Bond angle restraints: 37252 Sorted by residual: angle pdb=" CA PRO R 131 " pdb=" N PRO R 131 " pdb=" CD PRO R 131 " ideal model delta sigma weight residual 112.00 94.95 17.05 1.40e+00 5.10e-01 1.48e+02 angle pdb=" N PRO R 131 " pdb=" CD PRO R 131 " pdb=" CG PRO R 131 " ideal model delta sigma weight residual 103.20 90.85 12.35 1.50e+00 4.44e-01 6.78e+01 angle pdb=" C LYS W 94 " pdb=" N ASP W 95 " pdb=" CA ASP W 95 " ideal model delta sigma weight residual 122.08 130.36 -8.28 1.47e+00 4.63e-01 3.18e+01 angle pdb=" CA GLN W 223 " pdb=" CB GLN W 223 " pdb=" CG GLN W 223 " ideal model delta sigma weight residual 114.10 124.99 -10.89 2.00e+00 2.50e-01 2.96e+01 angle pdb=" CA GLU R 244 " pdb=" CB GLU R 244 " pdb=" CG GLU R 244 " ideal model delta sigma weight residual 114.10 124.12 -10.02 2.00e+00 2.50e-01 2.51e+01 ... (remaining 37247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 14983 22.02 - 44.04: 1620 44.04 - 66.07: 255 66.07 - 88.09: 48 88.09 - 110.11: 12 Dihedral angle restraints: 16918 sinusoidal: 6908 harmonic: 10010 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 -60.00 -170.11 110.11 1 2.00e+01 2.50e-03 3.23e+01 dihedral pdb=" O2A ADP T1001 " pdb=" O3A ADP T1001 " pdb=" PA ADP T1001 " pdb=" PB ADP T1001 " ideal model delta sinusoidal sigma weight residual -60.00 46.51 -106.51 1 2.00e+01 2.50e-03 3.08e+01 dihedral pdb=" O1B ADP X1001 " pdb=" O3A ADP X1001 " pdb=" PB ADP X1001 " pdb=" PA ADP X1001 " ideal model delta sinusoidal sigma weight residual -60.00 -150.74 90.74 1 2.00e+01 2.50e-03 2.43e+01 ... (remaining 16915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3611 0.068 - 0.135: 668 0.135 - 0.203: 82 0.203 - 0.270: 14 0.270 - 0.338: 3 Chirality restraints: 4378 Sorted by residual: chirality pdb=" CB THR R 245 " pdb=" CA THR R 245 " pdb=" OG1 THR R 245 " pdb=" CG2 THR R 245 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA MET X 122 " pdb=" N MET X 122 " pdb=" C MET X 122 " pdb=" CB MET X 122 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE W 125 " pdb=" CA ILE W 125 " pdb=" CG1 ILE W 125 " pdb=" CG2 ILE W 125 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4375 not shown) Planarity restraints: 4770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 130 " -0.070 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO R 131 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO R 131 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 131 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR Y 439 " 0.017 2.00e-02 2.50e+03 2.34e-02 1.10e+01 pdb=" CG TYR Y 439 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR Y 439 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR Y 439 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR Y 439 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR Y 439 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR Y 439 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR Y 439 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU R 112 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" CD GLU R 112 " -0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU R 112 " 0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU R 112 " 0.017 2.00e-02 2.50e+03 ... (remaining 4767 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6204 2.79 - 3.31: 24136 3.31 - 3.84: 46035 3.84 - 4.37: 50876 4.37 - 4.90: 88316 Nonbonded interactions: 215567 Sorted by model distance: nonbonded pdb=" OG SER X 355 " pdb=" O VAL X 359 " model vdw 2.258 3.040 nonbonded pdb=" O LEU U 255 " pdb=" OG1 THR U 259 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR W 82 " pdb=" O2A ADP W1001 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR S 134 " pdb=" O GLU Y 166 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR Y 398 " pdb=" O PHE Y 430 " model vdw 2.289 3.040 ... (remaining 215562 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 1001) 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 440 or (resid 441 t \ hrough 442 and (name N or name CA or name C or name O or name CB )) or resid 443 \ through 1001)) 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 440 or (resid 441 t \ hrough 442 and (name N or name CA or name C or name O or name CB )) or resid 443 \ through 1001)) } ncs_group { reference = (chain 'U' and (resid 18 through 130 or (resid 131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 132 through 181 or (resid 182 through 183 a \ nd (name N or name CA or name C or name O or name CB )) or resid 184 through 210 \ or resid 221 through 236 or (resid 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 through 459 or resid 1001)) selection = (chain 'W' and (resid 18 through 130 or (resid 131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 132 through 181 or (resid 182 through 183 a \ nd (name N or name CA or name C or name O or name CB )) or resid 184 through 210 \ or resid 221 through 236 or (resid 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 through 1001)) selection = (chain 'Y' and (resid 18 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 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: 7.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.200 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.005 0.219 27531 Z= 0.213 Angle : 0.953 17.055 37252 Z= 0.500 Chirality : 0.053 0.338 4378 Planarity : 0.006 0.094 4770 Dihedral : 17.811 110.109 10462 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 28.38 % Favored : 71.62 % 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: -1.93 (0.13), residues: 3442 helix: -1.67 (0.11), residues: 1419 sheet: 0.28 (0.22), residues: 607 loop : -1.41 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG W 220 TYR 0.056 0.002 TYR Y 439 PHE 0.020 0.002 PHE Y 430 TRP 0.013 0.002 TRP R 108 HIS 0.009 0.001 HIS S 135 Details of bonding type rmsd covalent geometry : bond 0.00468 (27530) covalent geometry : angle 0.95255 (37252) hydrogen bonds : bond 0.17479 ( 1007) hydrogen bonds : angle 6.74614 ( 2925) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1101 ASP cc_start: 0.8050 (m-30) cc_final: 0.7470 (p0) REVERT: Q 1187 MET cc_start: 0.8835 (mmt) cc_final: 0.8459 (mmm) REVERT: Q 1195 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7994 (tptp) REVERT: Q 1248 ASP cc_start: 0.8072 (t0) cc_final: 0.7819 (t0) REVERT: R 18 ASP cc_start: 0.8306 (m-30) cc_final: 0.7949 (p0) REVERT: R 705 ASP cc_start: 0.8293 (t0) cc_final: 0.7848 (t0) REVERT: R 708 LEU cc_start: 0.9197 (tp) cc_final: 0.8952 (mp) REVERT: R 712 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8695 (mmmt) REVERT: S 62 SER cc_start: 0.7739 (m) cc_final: 0.7487 (p) REVERT: S 117 ASP cc_start: 0.8243 (m-30) cc_final: 0.8002 (m-30) REVERT: T 146 GLU cc_start: 0.7710 (tt0) cc_final: 0.7485 (pt0) REVERT: T 438 ASP cc_start: 0.8190 (m-30) cc_final: 0.7595 (m-30) REVERT: U 105 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7576 (mt-10) REVERT: V 225 GLU cc_start: 0.5983 (tp30) cc_final: 0.4380 (mp0) REVERT: V 264 ASP cc_start: 0.8526 (p0) cc_final: 0.8269 (p0) REVERT: X 249 LEU cc_start: 0.8025 (mt) cc_final: 0.7625 (mp) REVERT: X 253 ASP cc_start: 0.7970 (m-30) cc_final: 0.7654 (m-30) REVERT: X 276 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8742 (ttmm) REVERT: X 326 LYS cc_start: 0.8932 (tppt) cc_final: 0.8566 (ttpt) REVERT: Y 267 SER cc_start: 0.8419 (p) cc_final: 0.8180 (t) REVERT: Y 389 LYS cc_start: 0.8677 (tmtt) cc_final: 0.8328 (ttpp) REVERT: Z 311 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8399 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.1923 time to fit residues: 145.9266 Evaluate side-chains 250 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.0470 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1244 GLN R 120 HIS R 609 GLN T 256 ASN U 25 HIS V 51 GLN V 205 ASN V 394 GLN X 271 GLN Y 49 GLN Y 119 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.090223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.075747 restraints weight = 88476.828| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.84 r_work: 0.3473 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27531 Z= 0.136 Angle : 0.622 9.940 37252 Z= 0.313 Chirality : 0.044 0.238 4378 Planarity : 0.004 0.050 4770 Dihedral : 6.528 111.226 3803 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.58 % Allowed : 25.67 % Favored : 71.75 % 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: -0.77 (0.14), residues: 3442 helix: -0.18 (0.13), residues: 1415 sheet: 0.39 (0.22), residues: 591 loop : -1.13 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 431 TYR 0.019 0.001 TYR Y 439 PHE 0.014 0.001 PHE W 308 TRP 0.016 0.001 TRP R 586 HIS 0.011 0.001 HIS V 238 Details of bonding type rmsd covalent geometry : bond 0.00307 (27530) covalent geometry : angle 0.62208 (37252) hydrogen bonds : bond 0.03905 ( 1007) hydrogen bonds : angle 4.51092 ( 2925) Misc. bond : bond 0.00226 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 275 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1101 ASP cc_start: 0.7936 (m-30) cc_final: 0.7497 (p0) REVERT: Q 1142 ARG cc_start: 0.8902 (mtm110) cc_final: 0.8676 (mtm110) REVERT: Q 1187 MET cc_start: 0.9104 (mmt) cc_final: 0.8853 (mmm) REVERT: Q 1196 HIS cc_start: 0.8580 (t-90) cc_final: 0.8319 (m170) REVERT: R 18 ASP cc_start: 0.8371 (m-30) cc_final: 0.7891 (p0) REVERT: R 643 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8814 (tm-30) REVERT: R 663 ASP cc_start: 0.8884 (m-30) cc_final: 0.8648 (m-30) REVERT: S 53 TYR cc_start: 0.5058 (t80) cc_final: 0.4684 (t80) REVERT: S 155 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6764 (t80) REVERT: T 438 ASP cc_start: 0.8333 (m-30) cc_final: 0.8105 (m-30) REVERT: V 225 GLU cc_start: 0.4983 (tp30) cc_final: 0.4132 (pp20) REVERT: W 86 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8199 (tmm) REVERT: W 174 LYS cc_start: 0.9208 (mmtm) cc_final: 0.8976 (tptp) REVERT: W 257 LEU cc_start: 0.8613 (tp) cc_final: 0.8266 (mt) REVERT: W 261 ASP cc_start: 0.8889 (t70) cc_final: 0.8648 (t0) REVERT: W 411 MET cc_start: 0.8518 (mpp) cc_final: 0.8268 (mpp) REVERT: X 45 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: X 249 LEU cc_start: 0.8666 (mt) cc_final: 0.8213 (mp) REVERT: X 253 ASP cc_start: 0.8223 (m-30) cc_final: 0.7937 (m-30) REVERT: X 326 LYS cc_start: 0.9161 (tppt) cc_final: 0.8809 (ttpt) REVERT: Y 166 GLU cc_start: 0.7024 (tp30) cc_final: 0.6788 (tp30) REVERT: Y 271 ASP cc_start: 0.8989 (m-30) cc_final: 0.8682 (m-30) REVERT: Y 333 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7871 (mtp180) outliers start: 77 outliers final: 22 residues processed: 339 average time/residue: 0.1679 time to fit residues: 89.1239 Evaluate side-chains 247 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1156 THR Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 61 ILE Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 243 ILE Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 333 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 260 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 253 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN Q1254 GLN S 141 GLN S 162 ASN T 29 HIS ** T 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 341 HIS W 408 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.084597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069831 restraints weight = 88786.689| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.78 r_work: 0.3324 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27531 Z= 0.226 Angle : 0.682 9.206 37252 Z= 0.342 Chirality : 0.047 0.254 4378 Planarity : 0.004 0.050 4770 Dihedral : 6.762 116.806 3803 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.82 % Allowed : 23.99 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.14), residues: 3442 helix: 0.28 (0.14), residues: 1432 sheet: 0.38 (0.21), residues: 581 loop : -1.02 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 210 TYR 0.027 0.002 TYR X 462 PHE 0.020 0.002 PHE W 308 TRP 0.007 0.001 TRP W 280 HIS 0.007 0.001 HIS S 135 Details of bonding type rmsd covalent geometry : bond 0.00536 (27530) covalent geometry : angle 0.68188 (37252) hydrogen bonds : bond 0.04308 ( 1007) hydrogen bonds : angle 4.31283 ( 2925) Misc. bond : bond 0.00157 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 228 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1078 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7450 (mtt90) REVERT: Q 1101 ASP cc_start: 0.8163 (m-30) cc_final: 0.7610 (p0) REVERT: Q 1257 MET cc_start: 0.8467 (mmm) cc_final: 0.8203 (mtm) REVERT: Q 1267 ASP cc_start: 0.8836 (m-30) cc_final: 0.8588 (m-30) REVERT: R 18 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8074 (p0) REVERT: R 114 ILE cc_start: 0.9334 (mt) cc_final: 0.9058 (mm) REVERT: R 192 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8510 (mm-30) REVERT: R 246 MET cc_start: 0.8973 (ptp) cc_final: 0.8584 (ptp) REVERT: R 705 ASP cc_start: 0.8285 (t0) cc_final: 0.7845 (t0) REVERT: R 712 LYS cc_start: 0.9280 (mtmt) cc_final: 0.8909 (mmmt) REVERT: S 47 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8394 (ptp-170) REVERT: T 125 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8625 (t80) REVERT: T 195 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8663 (p) REVERT: T 438 ASP cc_start: 0.8401 (m-30) cc_final: 0.8056 (m-30) REVERT: U 86 MET cc_start: 0.8311 (tpp) cc_final: 0.8015 (ttm) REVERT: V 193 LYS cc_start: 0.8307 (tmtt) cc_final: 0.8089 (tmtt) REVERT: V 225 GLU cc_start: 0.6477 (tp30) cc_final: 0.6038 (tp30) REVERT: W 86 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8144 (tmm) REVERT: W 110 GLU cc_start: 0.8452 (mp0) cc_final: 0.8027 (mp0) REVERT: W 174 LYS cc_start: 0.9288 (mmtm) cc_final: 0.9011 (tptp) REVERT: W 228 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: W 261 ASP cc_start: 0.9024 (t70) cc_final: 0.8772 (t0) REVERT: W 352 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8622 (pt) REVERT: W 411 MET cc_start: 0.8456 (mpp) cc_final: 0.8133 (mpp) REVERT: X 43 ARG cc_start: 0.7649 (tmt170) cc_final: 0.7405 (tpt90) REVERT: X 45 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: X 122 MET cc_start: 0.9045 (tpp) cc_final: 0.8842 (tpp) REVERT: X 253 ASP cc_start: 0.8465 (m-30) cc_final: 0.8230 (m-30) REVERT: X 302 GLU cc_start: 0.7696 (mp0) cc_final: 0.7491 (mp0) REVERT: X 326 LYS cc_start: 0.9100 (tppt) cc_final: 0.8741 (ttpp) REVERT: Y 42 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.9018 (mt-10) REVERT: Y 175 MET cc_start: 0.7451 (ttp) cc_final: 0.7217 (ttp) REVERT: Y 223 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7468 (pp30) REVERT: Y 232 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8077 (mmm160) REVERT: Y 315 ASP cc_start: 0.8328 (m-30) cc_final: 0.7893 (t70) REVERT: Y 333 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7869 (mtp180) REVERT: Y 385 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8518 (m-30) REVERT: Z 311 ARG cc_start: 0.9108 (mmm-85) cc_final: 0.8696 (mmm-85) outliers start: 114 outliers final: 48 residues processed: 329 average time/residue: 0.1763 time to fit residues: 90.0534 Evaluate side-chains 250 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1156 THR Chi-restraints excluded: chain Q residue 1171 THR Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 724 TYR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 440 VAL Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 436 VAL Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 329 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 189 ILE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 294 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 430 ASN Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 333 ARG Chi-restraints excluded: chain Y residue 385 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 123 optimal weight: 2.9990 chunk 342 optimal weight: 0.0980 chunk 305 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 chunk 309 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 HIS S 141 GLN S 162 ASN ** T 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 155 GLN Y 248 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.083837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069172 restraints weight = 89591.888| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.80 r_work: 0.3313 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27531 Z= 0.171 Angle : 0.609 9.096 37252 Z= 0.301 Chirality : 0.045 0.253 4378 Planarity : 0.004 0.042 4770 Dihedral : 6.646 118.962 3803 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.98 % Allowed : 24.26 % Favored : 72.75 % 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: -0.18 (0.14), residues: 3442 helix: 0.58 (0.14), residues: 1440 sheet: 0.42 (0.21), residues: 575 loop : -1.01 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 191 TYR 0.020 0.001 TYR X 462 PHE 0.015 0.001 PHE W 308 TRP 0.008 0.001 TRP R 586 HIS 0.004 0.001 HIS V 250 Details of bonding type rmsd covalent geometry : bond 0.00404 (27530) covalent geometry : angle 0.60926 (37252) hydrogen bonds : bond 0.03579 ( 1007) hydrogen bonds : angle 4.10972 ( 2925) Misc. bond : bond 0.00193 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 204 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1078 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7533 (mtm-85) REVERT: Q 1082 LYS cc_start: 0.8073 (mttm) cc_final: 0.7869 (mmmt) REVERT: Q 1101 ASP cc_start: 0.8183 (m-30) cc_final: 0.7589 (p0) REVERT: Q 1174 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8672 (mp) REVERT: Q 1187 MET cc_start: 0.8968 (mmm) cc_final: 0.8661 (mmm) REVERT: Q 1257 MET cc_start: 0.8309 (mmm) cc_final: 0.8030 (mtm) REVERT: R 18 ASP cc_start: 0.8524 (m-30) cc_final: 0.7996 (p0) REVERT: R 114 ILE cc_start: 0.9336 (mt) cc_final: 0.9064 (mm) REVERT: R 192 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8620 (mm-30) REVERT: S 155 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.6797 (t80) REVERT: T 125 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8631 (t80) REVERT: T 195 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8637 (p) REVERT: T 438 ASP cc_start: 0.8488 (m-30) cc_final: 0.8130 (m-30) REVERT: V 218 TYR cc_start: 0.8951 (m-80) cc_final: 0.8748 (m-80) REVERT: W 29 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8716 (mp) REVERT: W 110 GLU cc_start: 0.8449 (mp0) cc_final: 0.8004 (mp0) REVERT: W 174 LYS cc_start: 0.9287 (mmtm) cc_final: 0.9060 (tptp) REVERT: W 228 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7997 (tp30) REVERT: W 261 ASP cc_start: 0.9014 (t0) cc_final: 0.8751 (t0) REVERT: W 352 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8612 (pt) REVERT: X 45 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: X 150 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6536 (pm20) REVERT: X 253 ASP cc_start: 0.8450 (m-30) cc_final: 0.8193 (m-30) REVERT: X 326 LYS cc_start: 0.9114 (tppt) cc_final: 0.8794 (ttpp) REVERT: Y 155 GLN cc_start: 0.8584 (pm20) cc_final: 0.8227 (tm-30) REVERT: Y 175 MET cc_start: 0.7401 (ttp) cc_final: 0.7185 (ttp) REVERT: Y 315 ASP cc_start: 0.8350 (m-30) cc_final: 0.7934 (t70) REVERT: Y 333 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7938 (mtp180) REVERT: Y 385 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8521 (m-30) REVERT: Z 311 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8757 (tpp80) outliers start: 89 outliers final: 53 residues processed: 280 average time/residue: 0.1738 time to fit residues: 76.1667 Evaluate side-chains 247 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1156 THR Chi-restraints excluded: chain Q residue 1174 LEU Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 724 TYR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 102 SER Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain U residue 257 LEU Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 276 LYS Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 166 GLU Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 329 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 189 ILE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 294 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 333 ARG Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 385 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 83 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 334 optimal weight: 3.9990 chunk 279 optimal weight: 7.9990 chunk 300 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 234 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 141 GLN S 162 ASN T 51 GLN ** T 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.081783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.067380 restraints weight = 90243.029| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.75 r_work: 0.3268 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27531 Z= 0.226 Angle : 0.656 8.536 37252 Z= 0.325 Chirality : 0.046 0.250 4378 Planarity : 0.004 0.050 4770 Dihedral : 6.842 123.423 3803 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.85 % Allowed : 23.69 % Favored : 72.45 % 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: -0.18 (0.14), residues: 3442 helix: 0.66 (0.14), residues: 1436 sheet: 0.28 (0.21), residues: 590 loop : -1.05 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 39 TYR 0.025 0.002 TYR X 462 PHE 0.017 0.002 PHE W 308 TRP 0.007 0.001 TRP R 214 HIS 0.004 0.001 HIS V 250 Details of bonding type rmsd covalent geometry : bond 0.00532 (27530) covalent geometry : angle 0.65564 (37252) hydrogen bonds : bond 0.03959 ( 1007) hydrogen bonds : angle 4.17197 ( 2925) Misc. bond : bond 0.00209 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 193 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1078 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7393 (mtm-85) REVERT: Q 1082 LYS cc_start: 0.8218 (mttm) cc_final: 0.7953 (mmmt) REVERT: Q 1101 ASP cc_start: 0.8257 (m-30) cc_final: 0.7627 (p0) REVERT: Q 1174 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8707 (mp) REVERT: Q 1187 MET cc_start: 0.8991 (mmm) cc_final: 0.8656 (mmm) REVERT: Q 1257 MET cc_start: 0.8310 (mmm) cc_final: 0.8108 (mtm) REVERT: R 18 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.7989 (p0) REVERT: R 114 ILE cc_start: 0.9376 (mt) cc_final: 0.9105 (mm) REVERT: R 238 MET cc_start: 0.7077 (ptm) cc_final: 0.6784 (ptt) REVERT: R 663 ASP cc_start: 0.9089 (m-30) cc_final: 0.8818 (m-30) REVERT: R 714 MET cc_start: 0.8641 (ptm) cc_final: 0.8352 (mtm) REVERT: S 47 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8235 (ptp-170) REVERT: T 125 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8596 (t80) REVERT: T 438 ASP cc_start: 0.8477 (m-30) cc_final: 0.8115 (m-30) REVERT: U 439 TYR cc_start: 0.8922 (m-80) cc_final: 0.8554 (m-80) REVERT: V 227 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: W 29 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8739 (mp) REVERT: W 105 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: W 110 GLU cc_start: 0.8475 (mp0) cc_final: 0.8197 (mp0) REVERT: W 174 LYS cc_start: 0.9322 (mmtm) cc_final: 0.9084 (tptp) REVERT: W 212 TYR cc_start: 0.4257 (OUTLIER) cc_final: 0.2388 (p90) REVERT: W 228 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8071 (tp30) REVERT: W 243 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: W 261 ASP cc_start: 0.9018 (t0) cc_final: 0.8746 (t0) REVERT: W 352 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8629 (pt) REVERT: X 45 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8245 (mt-10) REVERT: X 150 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: X 253 ASP cc_start: 0.8459 (m-30) cc_final: 0.8218 (m-30) REVERT: X 326 LYS cc_start: 0.9138 (tppt) cc_final: 0.8775 (ttpp) REVERT: Y 155 GLN cc_start: 0.8656 (pm20) cc_final: 0.8172 (tm-30) REVERT: Y 173 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6383 (t0) REVERT: Y 252 GLN cc_start: 0.7056 (tp40) cc_final: 0.6627 (mm-40) REVERT: Y 315 ASP cc_start: 0.8397 (m-30) cc_final: 0.7937 (t70) REVERT: Y 333 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7987 (mtp180) REVERT: Z 311 ARG cc_start: 0.9059 (mmm-85) cc_final: 0.8811 (tpp80) outliers start: 115 outliers final: 72 residues processed: 292 average time/residue: 0.1585 time to fit residues: 73.7522 Evaluate side-chains 265 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 178 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1156 THR Chi-restraints excluded: chain Q residue 1171 THR Chi-restraints excluded: chain Q residue 1174 LEU Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 724 TYR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 102 SER Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 257 LEU Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 227 GLU Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 276 LYS Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 166 GLU Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 329 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 189 ILE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 260 GLN Chi-restraints excluded: chain X residue 294 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 333 ARG Chi-restraints excluded: chain Y residue 335 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 55 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 0.1980 chunk 227 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 HIS ** T 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.082342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.068133 restraints weight = 89996.762| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.71 r_work: 0.3287 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27531 Z= 0.167 Angle : 0.607 9.962 37252 Z= 0.299 Chirality : 0.044 0.252 4378 Planarity : 0.003 0.038 4770 Dihedral : 6.675 122.147 3803 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.72 % Allowed : 23.89 % Favored : 72.39 % 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: -0.03 (0.14), residues: 3442 helix: 0.82 (0.14), residues: 1438 sheet: 0.33 (0.21), residues: 588 loop : -1.00 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 258 TYR 0.018 0.001 TYR X 462 PHE 0.016 0.001 PHE W 308 TRP 0.008 0.001 TRP R 711 HIS 0.003 0.001 HIS V 250 Details of bonding type rmsd covalent geometry : bond 0.00394 (27530) covalent geometry : angle 0.60716 (37252) hydrogen bonds : bond 0.03538 ( 1007) hydrogen bonds : angle 4.03967 ( 2925) Misc. bond : bond 0.00184 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 193 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1082 LYS cc_start: 0.8223 (mttm) cc_final: 0.8005 (mmmt) REVERT: Q 1101 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7654 (p0) REVERT: Q 1174 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8698 (mp) REVERT: Q 1187 MET cc_start: 0.8992 (mmm) cc_final: 0.8656 (mmm) REVERT: Q 1257 MET cc_start: 0.8346 (mmm) cc_final: 0.8145 (mtm) REVERT: R 18 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8000 (p0) REVERT: R 114 ILE cc_start: 0.9391 (mt) cc_final: 0.9122 (mm) REVERT: R 192 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8544 (mm-30) REVERT: R 238 MET cc_start: 0.7295 (ptm) cc_final: 0.7076 (ptt) REVERT: R 663 ASP cc_start: 0.9115 (m-30) cc_final: 0.8858 (m-30) REVERT: S 47 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8199 (ptp-170) REVERT: T 125 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8619 (t80) REVERT: T 438 ASP cc_start: 0.8446 (m-30) cc_final: 0.8065 (m-30) REVERT: U 86 MET cc_start: 0.8325 (tpp) cc_final: 0.8014 (ttm) REVERT: U 439 TYR cc_start: 0.8896 (m-80) cc_final: 0.8560 (m-80) REVERT: V 70 MET cc_start: 0.8800 (mmm) cc_final: 0.8598 (mmp) REVERT: V 192 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: W 29 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8798 (mp) REVERT: W 105 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: W 110 GLU cc_start: 0.8491 (mp0) cc_final: 0.8216 (mp0) REVERT: W 174 LYS cc_start: 0.9299 (mmtm) cc_final: 0.9049 (tptp) REVERT: W 182 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7802 (pp20) REVERT: W 228 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: W 243 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: W 261 ASP cc_start: 0.8980 (t0) cc_final: 0.8710 (t0) REVERT: W 352 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8623 (pt) REVERT: X 45 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8286 (mt-10) REVERT: X 150 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: X 253 ASP cc_start: 0.8433 (m-30) cc_final: 0.8184 (m-30) REVERT: X 326 LYS cc_start: 0.9096 (tppt) cc_final: 0.8803 (ttpp) REVERT: Y 155 GLN cc_start: 0.8695 (pm20) cc_final: 0.8208 (tm-30) REVERT: Y 166 GLU cc_start: 0.6744 (tp30) cc_final: 0.6117 (tp30) REVERT: Y 173 ASN cc_start: 0.6975 (p0) cc_final: 0.6235 (t0) REVERT: Y 315 ASP cc_start: 0.8391 (m-30) cc_final: 0.7996 (t70) REVERT: Y 333 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7950 (mtp180) REVERT: Z 311 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8782 (tpp80) outliers start: 111 outliers final: 74 residues processed: 287 average time/residue: 0.1632 time to fit residues: 74.2906 Evaluate side-chains 269 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 180 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1129 SER Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1156 THR Chi-restraints excluded: chain Q residue 1174 LEU Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 171 PHE Chi-restraints excluded: chain R residue 639 CYS Chi-restraints excluded: chain R residue 724 TYR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 102 SER Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 372 THR Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 257 LEU Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 192 GLU Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 215 SER Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 276 LYS Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 166 GLU Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 329 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain X residue 189 ILE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 333 ARG Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Z residue 312 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 224 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN ** T 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 HIS X 165 HIS Y 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.080684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066547 restraints weight = 91092.159| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.67 r_work: 0.3251 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 27531 Z= 0.242 Angle : 0.668 8.988 37252 Z= 0.331 Chirality : 0.046 0.255 4378 Planarity : 0.004 0.038 4770 Dihedral : 6.911 125.499 3803 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.12 % Allowed : 23.86 % Favored : 72.02 % 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: 3442 helix: 0.79 (0.14), residues: 1426 sheet: 0.15 (0.20), residues: 590 loop : -1.04 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 258 TYR 0.023 0.002 TYR X 462 PHE 0.027 0.002 PHE W 206 TRP 0.009 0.001 TRP R 711 HIS 0.004 0.001 HIS X 27 Details of bonding type rmsd covalent geometry : bond 0.00572 (27530) covalent geometry : angle 0.66799 (37252) hydrogen bonds : bond 0.04050 ( 1007) hydrogen bonds : angle 4.21003 ( 2925) Misc. bond : bond 0.00237 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 187 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1082 LYS cc_start: 0.8341 (mttm) cc_final: 0.8126 (mmmt) REVERT: Q 1101 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7681 (p0) REVERT: Q 1174 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8750 (mp) REVERT: Q 1187 MET cc_start: 0.8994 (mmm) cc_final: 0.8721 (mmm) REVERT: Q 1257 MET cc_start: 0.8252 (mmm) cc_final: 0.8023 (mtm) REVERT: R 18 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8120 (p0) REVERT: R 114 ILE cc_start: 0.9408 (mt) cc_final: 0.9142 (mm) REVERT: R 189 CYS cc_start: 0.9394 (m) cc_final: 0.8643 (p) REVERT: R 192 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8631 (mm-30) REVERT: R 663 ASP cc_start: 0.9110 (m-30) cc_final: 0.8847 (m-30) REVERT: R 664 MET cc_start: 0.8660 (mtm) cc_final: 0.8323 (ttm) REVERT: R 692 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8205 (mp) REVERT: R 740 GLU cc_start: 0.8642 (tp30) cc_final: 0.8058 (pm20) REVERT: S 47 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8164 (ptp-170) REVERT: T 125 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8598 (t80) REVERT: T 438 ASP cc_start: 0.8486 (m-30) cc_final: 0.8108 (m-30) REVERT: U 86 MET cc_start: 0.8318 (tpp) cc_final: 0.7990 (ttm) REVERT: U 439 TYR cc_start: 0.8919 (m-80) cc_final: 0.8622 (m-80) REVERT: V 192 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: V 227 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7769 (pt0) REVERT: V 425 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8565 (mm) REVERT: W 29 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8823 (mp) REVERT: W 105 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: W 174 LYS cc_start: 0.9329 (mmtm) cc_final: 0.9090 (tptp) REVERT: W 182 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7825 (pp20) REVERT: W 212 TYR cc_start: 0.4527 (OUTLIER) cc_final: 0.2969 (p90) REVERT: W 228 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: W 243 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: W 261 ASP cc_start: 0.9020 (t0) cc_final: 0.8739 (t0) REVERT: W 361 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8231 (tp30) REVERT: X 45 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: X 150 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6586 (pm20) REVERT: X 253 ASP cc_start: 0.8457 (m-30) cc_final: 0.8216 (m-30) REVERT: X 326 LYS cc_start: 0.9129 (tppt) cc_final: 0.8715 (ttpp) REVERT: Y 155 GLN cc_start: 0.8664 (pm20) cc_final: 0.8124 (tm-30) REVERT: Y 166 GLU cc_start: 0.6866 (tp30) cc_final: 0.6226 (tp30) REVERT: Y 173 ASN cc_start: 0.7196 (OUTLIER) cc_final: 0.6532 (t0) REVERT: Y 252 GLN cc_start: 0.7092 (tp40) cc_final: 0.6531 (mm-40) REVERT: Y 264 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7536 (mt-10) REVERT: Y 315 ASP cc_start: 0.8466 (m-30) cc_final: 0.8069 (t70) REVERT: Y 333 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7948 (mtp180) outliers start: 123 outliers final: 88 residues processed: 293 average time/residue: 0.1687 time to fit residues: 78.3364 Evaluate side-chains 285 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 177 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1129 SER Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1156 THR Chi-restraints excluded: chain Q residue 1174 LEU Chi-restraints excluded: chain Q residue 1204 ASN Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 171 PHE Chi-restraints excluded: chain R residue 639 CYS Chi-restraints excluded: chain R residue 692 LEU Chi-restraints excluded: chain R residue 724 TYR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 102 SER Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 372 THR Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 257 LEU Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 192 GLU Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 215 SER Chi-restraints excluded: chain V residue 227 GLU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 276 LYS Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 425 LEU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 140 VAL Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 166 GLU Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 329 VAL Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 361 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain X residue 189 ILE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 260 GLN Chi-restraints excluded: chain X residue 294 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 333 ARG Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 370 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 53 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 325 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 330 optimal weight: 0.7980 chunk 273 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 102 optimal weight: 0.0870 chunk 236 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 HIS S 162 ASN ** T 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.081631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.067482 restraints weight = 90730.580| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.68 r_work: 0.3273 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27531 Z= 0.169 Angle : 0.617 8.959 37252 Z= 0.304 Chirality : 0.044 0.258 4378 Planarity : 0.003 0.037 4770 Dihedral : 6.737 123.341 3803 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.49 % Allowed : 24.83 % Favored : 71.68 % 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: -0.03 (0.14), residues: 3442 helix: 0.89 (0.14), residues: 1431 sheet: 0.15 (0.21), residues: 590 loop : -0.97 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 270 TYR 0.017 0.001 TYR X 462 PHE 0.019 0.001 PHE W 206 TRP 0.012 0.001 TRP R 711 HIS 0.003 0.001 HIS V 250 Details of bonding type rmsd covalent geometry : bond 0.00402 (27530) covalent geometry : angle 0.61715 (37252) hydrogen bonds : bond 0.03557 ( 1007) hydrogen bonds : angle 4.06363 ( 2925) Misc. bond : bond 0.00193 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 190 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1101 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7655 (p0) REVERT: Q 1174 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8698 (mp) REVERT: Q 1187 MET cc_start: 0.9002 (mmm) cc_final: 0.8725 (mmm) REVERT: Q 1257 MET cc_start: 0.8358 (mmm) cc_final: 0.8155 (mtm) REVERT: R 18 ASP cc_start: 0.8609 (m-30) cc_final: 0.8076 (p0) REVERT: R 114 ILE cc_start: 0.9412 (mt) cc_final: 0.9146 (mm) REVERT: R 189 CYS cc_start: 0.9381 (m) cc_final: 0.8662 (p) REVERT: R 192 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8646 (mm-30) REVERT: R 591 LEU cc_start: 0.8750 (mm) cc_final: 0.8174 (tt) REVERT: R 663 ASP cc_start: 0.9110 (m-30) cc_final: 0.8858 (m-30) REVERT: R 664 MET cc_start: 0.8633 (mtm) cc_final: 0.8279 (ttm) REVERT: R 740 GLU cc_start: 0.8664 (tp30) cc_final: 0.8109 (pm20) REVERT: S 47 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8239 (ptp-170) REVERT: S 139 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8482 (pt) REVERT: T 125 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8621 (t80) REVERT: T 438 ASP cc_start: 0.8433 (m-30) cc_final: 0.8036 (m-30) REVERT: U 86 MET cc_start: 0.8301 (tpp) cc_final: 0.8003 (ttm) REVERT: U 183 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7742 (pptt) REVERT: U 439 TYR cc_start: 0.8911 (m-80) cc_final: 0.8621 (m-80) REVERT: V 70 MET cc_start: 0.8852 (mmm) cc_final: 0.8583 (mmp) REVERT: V 192 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8577 (tt0) REVERT: W 29 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8838 (mp) REVERT: W 105 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: W 110 GLU cc_start: 0.8529 (mp0) cc_final: 0.8265 (mp0) REVERT: W 174 LYS cc_start: 0.9299 (mmtm) cc_final: 0.9065 (tptp) REVERT: W 182 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7822 (pp20) REVERT: W 212 TYR cc_start: 0.4631 (OUTLIER) cc_final: 0.3071 (p90) REVERT: W 243 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7514 (pm20) REVERT: W 261 ASP cc_start: 0.9003 (t0) cc_final: 0.8720 (t0) REVERT: W 361 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: X 45 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: X 150 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6639 (pm20) REVERT: X 188 SER cc_start: 0.9248 (OUTLIER) cc_final: 0.8796 (p) REVERT: X 246 ASP cc_start: 0.8628 (p0) cc_final: 0.8377 (m-30) REVERT: X 253 ASP cc_start: 0.8418 (m-30) cc_final: 0.8165 (m-30) REVERT: X 326 LYS cc_start: 0.9112 (tppt) cc_final: 0.8773 (ttpp) REVERT: Y 155 GLN cc_start: 0.8735 (pm20) cc_final: 0.8196 (tm-30) REVERT: Y 166 GLU cc_start: 0.6806 (tp30) cc_final: 0.6347 (tp30) REVERT: Y 173 ASN cc_start: 0.7095 (p0) cc_final: 0.6352 (t0) REVERT: Y 252 GLN cc_start: 0.7077 (tp40) cc_final: 0.6818 (mm-40) REVERT: Y 315 ASP cc_start: 0.8440 (m-30) cc_final: 0.8071 (t70) REVERT: Y 333 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7944 (mtp180) outliers start: 104 outliers final: 76 residues processed: 280 average time/residue: 0.1591 time to fit residues: 70.9333 Evaluate side-chains 273 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 180 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1129 SER Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1156 THR Chi-restraints excluded: chain Q residue 1174 LEU Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 171 PHE Chi-restraints excluded: chain R residue 639 CYS Chi-restraints excluded: chain R residue 724 TYR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 372 THR Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain U residue 183 LYS Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 257 LEU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 192 GLU Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 215 SER Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 276 LYS Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 140 VAL Chi-restraints excluded: chain W residue 166 GLU Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 329 VAL Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 361 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain X residue 189 ILE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 294 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 333 ARG Chi-restraints excluded: chain Y residue 335 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 142 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 183 optimal weight: 0.2980 chunk 327 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN ** T 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066843 restraints weight = 91074.129| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.69 r_work: 0.3260 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27531 Z= 0.202 Angle : 0.642 8.767 37252 Z= 0.316 Chirality : 0.045 0.254 4378 Planarity : 0.004 0.038 4770 Dihedral : 6.786 124.225 3803 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.85 % Allowed : 24.60 % Favored : 71.55 % 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: -0.06 (0.14), residues: 3442 helix: 0.87 (0.14), residues: 1428 sheet: 0.12 (0.21), residues: 587 loop : -1.00 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 270 TYR 0.019 0.001 TYR X 462 PHE 0.020 0.001 PHE W 206 TRP 0.012 0.001 TRP R 711 HIS 0.004 0.001 HIS V 250 Details of bonding type rmsd covalent geometry : bond 0.00480 (27530) covalent geometry : angle 0.64151 (37252) hydrogen bonds : bond 0.03744 ( 1007) hydrogen bonds : angle 4.11072 ( 2925) Misc. bond : bond 0.00215 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 183 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1101 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7702 (p0) REVERT: Q 1174 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8704 (mp) REVERT: Q 1187 MET cc_start: 0.9004 (mmm) cc_final: 0.8726 (mmm) REVERT: R 18 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8135 (p0) REVERT: R 114 ILE cc_start: 0.9422 (mt) cc_final: 0.9155 (mm) REVERT: R 189 CYS cc_start: 0.9392 (m) cc_final: 0.8681 (p) REVERT: R 192 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8667 (mm-30) REVERT: R 238 MET cc_start: 0.7604 (ptt) cc_final: 0.6918 (ppp) REVERT: R 591 LEU cc_start: 0.8751 (mm) cc_final: 0.8185 (tt) REVERT: R 659 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8616 (tp-100) REVERT: R 663 ASP cc_start: 0.9106 (m-30) cc_final: 0.8465 (m-30) REVERT: R 664 MET cc_start: 0.8641 (mtm) cc_final: 0.8298 (ttm) REVERT: R 692 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8113 (mp) REVERT: R 740 GLU cc_start: 0.8684 (tp30) cc_final: 0.8221 (pm20) REVERT: S 47 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8191 (ptp-170) REVERT: S 139 ILE cc_start: 0.8714 (pt) cc_final: 0.8488 (pt) REVERT: T 125 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8621 (t80) REVERT: T 438 ASP cc_start: 0.8457 (m-30) cc_final: 0.8067 (m-30) REVERT: U 86 MET cc_start: 0.8302 (tpp) cc_final: 0.8006 (ttm) REVERT: U 183 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7894 (pptt) REVERT: U 439 TYR cc_start: 0.8929 (m-80) cc_final: 0.8664 (m-80) REVERT: V 70 MET cc_start: 0.8888 (mmm) cc_final: 0.8616 (mmp) REVERT: V 192 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: W 29 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8843 (mp) REVERT: W 105 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: W 110 GLU cc_start: 0.8519 (mp0) cc_final: 0.8246 (mp0) REVERT: W 174 LYS cc_start: 0.9300 (mmtm) cc_final: 0.9054 (tptp) REVERT: W 182 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7848 (pp20) REVERT: W 204 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7285 (ttm-80) REVERT: W 212 TYR cc_start: 0.4616 (OUTLIER) cc_final: 0.3239 (p90) REVERT: W 243 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: W 261 ASP cc_start: 0.9000 (t0) cc_final: 0.8706 (t0) REVERT: W 352 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8644 (pt) REVERT: W 361 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8142 (tp30) REVERT: X 45 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8287 (mt-10) REVERT: X 150 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6689 (pm20) REVERT: X 188 SER cc_start: 0.9378 (OUTLIER) cc_final: 0.9042 (p) REVERT: X 246 ASP cc_start: 0.8687 (p0) cc_final: 0.8450 (m-30) REVERT: X 253 ASP cc_start: 0.8436 (m-30) cc_final: 0.8199 (m-30) REVERT: X 326 LYS cc_start: 0.9125 (tppt) cc_final: 0.8755 (ttpp) REVERT: Y 173 ASN cc_start: 0.7287 (p0) cc_final: 0.6585 (t0) REVERT: Y 252 GLN cc_start: 0.7109 (tp40) cc_final: 0.6850 (mm-40) REVERT: Y 315 ASP cc_start: 0.8462 (m-30) cc_final: 0.8080 (t70) REVERT: Y 333 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7971 (mtp180) outliers start: 115 outliers final: 85 residues processed: 283 average time/residue: 0.1672 time to fit residues: 74.9463 Evaluate side-chains 280 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 174 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1129 SER Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1156 THR Chi-restraints excluded: chain Q residue 1171 THR Chi-restraints excluded: chain Q residue 1174 LEU Chi-restraints excluded: chain Q residue 1204 ASN Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 171 PHE Chi-restraints excluded: chain R residue 639 CYS Chi-restraints excluded: chain R residue 659 GLN Chi-restraints excluded: chain R residue 692 LEU Chi-restraints excluded: chain R residue 724 TYR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 102 SER Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 372 THR Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain U residue 183 LYS Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 257 LEU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 192 GLU Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 215 SER Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 276 LYS Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 140 VAL Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 166 GLU Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 204 ARG Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 329 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 361 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain X residue 189 ILE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 294 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 376 ASP Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 333 ARG Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 370 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 302 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN ** T 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 23 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.081751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.067738 restraints weight = 90210.129| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.66 r_work: 0.3281 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27531 Z= 0.154 Angle : 0.611 8.537 37252 Z= 0.300 Chirality : 0.044 0.254 4378 Planarity : 0.003 0.038 4770 Dihedral : 6.662 121.931 3803 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.32 % Allowed : 25.27 % Favored : 71.41 % 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: 0.05 (0.14), residues: 3442 helix: 0.95 (0.14), residues: 1429 sheet: 0.15 (0.21), residues: 593 loop : -0.91 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 270 TYR 0.015 0.001 TYR X 462 PHE 0.019 0.001 PHE W 206 TRP 0.014 0.001 TRP R 711 HIS 0.003 0.001 HIS V 250 Details of bonding type rmsd covalent geometry : bond 0.00367 (27530) covalent geometry : angle 0.61108 (37252) hydrogen bonds : bond 0.03434 ( 1007) hydrogen bonds : angle 4.01273 ( 2925) Misc. bond : bond 0.00180 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6884 Ramachandran restraints generated. 3442 Oldfield, 0 Emsley, 3442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 186 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1101 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7666 (p0) REVERT: Q 1174 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8671 (mp) REVERT: Q 1187 MET cc_start: 0.9005 (mmm) cc_final: 0.8723 (mmm) REVERT: R 18 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8142 (p0) REVERT: R 114 ILE cc_start: 0.9420 (mt) cc_final: 0.9148 (mm) REVERT: R 189 CYS cc_start: 0.9372 (m) cc_final: 0.8668 (p) REVERT: R 192 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8716 (mm-30) REVERT: R 238 MET cc_start: 0.7584 (ptt) cc_final: 0.6960 (ppp) REVERT: R 591 LEU cc_start: 0.8725 (mm) cc_final: 0.8175 (tt) REVERT: R 659 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8796 (tp-100) REVERT: R 663 ASP cc_start: 0.9111 (m-30) cc_final: 0.8687 (m-30) REVERT: R 664 MET cc_start: 0.8613 (mtm) cc_final: 0.8261 (ttm) REVERT: R 712 LYS cc_start: 0.9155 (mtmt) cc_final: 0.8911 (mmmt) REVERT: R 740 GLU cc_start: 0.8649 (tp30) cc_final: 0.8217 (pm20) REVERT: S 47 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8207 (ptp-170) REVERT: S 139 ILE cc_start: 0.8690 (pt) cc_final: 0.8475 (pt) REVERT: T 125 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8635 (t80) REVERT: T 438 ASP cc_start: 0.8453 (m-30) cc_final: 0.8054 (m-30) REVERT: U 86 MET cc_start: 0.8317 (tpp) cc_final: 0.8043 (ttm) REVERT: U 183 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7903 (pptt) REVERT: U 439 TYR cc_start: 0.8902 (m-80) cc_final: 0.8615 (m-80) REVERT: V 70 MET cc_start: 0.8864 (mmm) cc_final: 0.8588 (mmp) REVERT: V 192 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: W 29 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8848 (mp) REVERT: W 105 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: W 110 GLU cc_start: 0.8500 (mp0) cc_final: 0.8246 (mp0) REVERT: W 174 LYS cc_start: 0.9305 (mmtm) cc_final: 0.9067 (tptp) REVERT: W 182 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7835 (pp20) REVERT: W 212 TYR cc_start: 0.4532 (OUTLIER) cc_final: 0.3290 (p90) REVERT: W 243 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: W 261 ASP cc_start: 0.8993 (t0) cc_final: 0.8708 (t0) REVERT: W 352 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8612 (pt) REVERT: W 361 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: X 150 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6625 (pm20) REVERT: X 188 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9009 (p) REVERT: X 246 ASP cc_start: 0.8666 (p0) cc_final: 0.8433 (m-30) REVERT: X 253 ASP cc_start: 0.8391 (m-30) cc_final: 0.8139 (m-30) REVERT: X 276 LYS cc_start: 0.9167 (ttmm) cc_final: 0.8828 (ttmm) REVERT: X 326 LYS cc_start: 0.9122 (tppt) cc_final: 0.8753 (ttpp) REVERT: Y 155 GLN cc_start: 0.8601 (mp10) cc_final: 0.8159 (tm-30) REVERT: Y 173 ASN cc_start: 0.7351 (p0) cc_final: 0.6666 (t0) REVERT: Y 252 GLN cc_start: 0.7081 (tp40) cc_final: 0.6834 (mm-40) REVERT: Y 315 ASP cc_start: 0.8379 (m-30) cc_final: 0.8012 (t70) REVERT: Y 333 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7949 (mtp180) outliers start: 99 outliers final: 77 residues processed: 271 average time/residue: 0.1575 time to fit residues: 67.6365 Evaluate side-chains 276 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 181 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1129 SER Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1156 THR Chi-restraints excluded: chain Q residue 1174 LEU Chi-restraints excluded: chain Q residue 1204 ASN Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 171 PHE Chi-restraints excluded: chain R residue 639 CYS Chi-restraints excluded: chain R residue 659 GLN Chi-restraints excluded: chain R residue 724 TYR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 102 SER Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 372 THR Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain U residue 183 LYS Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 257 LEU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 192 GLU Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 276 LYS Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 140 VAL Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 166 GLU Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 329 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 361 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 188 SER Chi-restraints excluded: chain X residue 189 ILE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 294 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 376 ASP Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 333 ARG Chi-restraints excluded: chain Y residue 335 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 269 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 338 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN ** T 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.082244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068171 restraints weight = 89399.086| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.66 r_work: 0.3291 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27531 Z= 0.139 Angle : 0.597 8.624 37252 Z= 0.293 Chirality : 0.044 0.252 4378 Planarity : 0.003 0.038 4770 Dihedral : 6.530 120.103 3803 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.12 % Allowed : 25.47 % Favored : 71.41 % 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: 0.12 (0.14), residues: 3442 helix: 1.01 (0.14), residues: 1429 sheet: 0.22 (0.21), residues: 582 loop : -0.87 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 270 TYR 0.013 0.001 TYR V 295 PHE 0.018 0.001 PHE W 206 TRP 0.015 0.001 TRP R 711 HIS 0.003 0.001 HIS V 250 Details of bonding type rmsd covalent geometry : bond 0.00330 (27530) covalent geometry : angle 0.59655 (37252) hydrogen bonds : bond 0.03307 ( 1007) hydrogen bonds : angle 3.94998 ( 2925) Misc. bond : bond 0.00159 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5367.69 seconds wall clock time: 93 minutes 8.87 seconds (5588.87 seconds total)