Starting phenix.real_space_refine on Thu Mar 5 05:40:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rdf_4816/03_2026/6rdf_4816.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rdf_4816/03_2026/6rdf_4816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rdf_4816/03_2026/6rdf_4816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rdf_4816/03_2026/6rdf_4816.map" model { file = "/net/cci-nas-00/data/ceres_data/6rdf_4816/03_2026/6rdf_4816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rdf_4816/03_2026/6rdf_4816.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 Zn 1 6.06 5 S 33 5.16 5 C 12734 2.51 5 N 3312 2.21 5 O 3775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19855 Number of models: 1 Model: "" Number of chains: 18 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 646 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "T" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 330 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 4.35, per 1000 atoms: 0.22 Number of scatterers: 19855 At special positions: 0 Unit cell: (180.063, 117.936, 252.72, 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) Zn 1 29.99 S 33 16.00 O 3775 8.00 N 3312 7.00 C 12734 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=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 991.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4918 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 6 sheets defined 68.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.689A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 30 removed outlier: 3.522A pdb=" N VAL 0 26 " --> pdb=" O VAL 0 22 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 removed outlier: 3.727A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 70 removed outlier: 3.608A pdb=" N LYS 1 68 " --> pdb=" O LEU 1 64 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 100 removed outlier: 3.620A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 96 through 100' Processing helix chain '1' and resid 106 through 142 removed outlier: 3.581A pdb=" N ALA 1 122 " --> pdb=" O ARG 1 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA 1 139 " --> pdb=" O THR 1 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 3.671A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 199 removed outlier: 4.261A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 208 No H-bonds generated for 'chain '1' and resid 206 through 208' Processing helix chain '1' and resid 209 through 224 removed outlier: 3.739A pdb=" N SER 1 214 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU 1 215 " --> pdb=" O SER 1 211 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 244 through 271 removed outlier: 3.814A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS 1 266 " --> pdb=" O LYS 1 262 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL 1 270 " --> pdb=" O LYS 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.603A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 278 through 286 removed outlier: 3.726A pdb=" N PHE 1 282 " --> pdb=" O LEU 1 279 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP 1 283 " --> pdb=" O ASN 1 280 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA 1 284 " --> pdb=" O GLU 1 281 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 removed outlier: 3.790A pdb=" N ALA 1 303 " --> pdb=" O GLU 1 299 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 317 removed outlier: 3.755A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 318 through 322 Processing helix chain '1' and resid 323 through 327 removed outlier: 3.765A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 removed outlier: 3.530A pdb=" N GLU 1 334 " --> pdb=" O ALA 1 331 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 362 removed outlier: 3.645A pdb=" N LEU 1 358 " --> pdb=" O PRO 1 354 " (cutoff:3.500A) Processing helix chain '1' and resid 363 through 367 removed outlier: 3.870A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.829A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU 1 385 " --> pdb=" O ARG 1 381 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 415 removed outlier: 3.628A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU 1 401 " --> pdb=" O GLU 1 397 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.760A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 444 Processing helix chain '1' and resid 446 through 460 removed outlier: 3.693A pdb=" N LYS 1 451 " --> pdb=" O ALA 1 447 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA 1 460 " --> pdb=" O LYS 1 456 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 removed outlier: 3.744A pdb=" N THR 1 471 " --> pdb=" O ALA 1 467 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN 1 474 " --> pdb=" O VAL 1 470 " (cutoff:3.500A) Processing helix chain '1' and resid 479 through 483 removed outlier: 3.576A pdb=" N ILE 1 483 " --> pdb=" O PRO 1 480 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 495 Processing helix chain '1' and resid 497 through 516 removed outlier: 3.849A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER 1 503 " --> pdb=" O GLU 1 499 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU 1 512 " --> pdb=" O ASP 1 508 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA 1 515 " --> pdb=" O ALA 1 511 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.716A pdb=" N THR 1 526 " --> pdb=" O LEU 1 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS 1 531 " --> pdb=" O GLN 1 527 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 removed outlier: 3.545A pdb=" N VAL 1 545 " --> pdb=" O PRO 1 541 " (cutoff:3.500A) Processing helix chain '1' and resid 549 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 removed outlier: 3.569A pdb=" N ARG 1 600 " --> pdb=" O ILE 1 596 " (cutoff:3.500A) Processing helix chain '2' and resid 7 through 17 removed outlier: 3.651A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS 2 13 " --> pdb=" O PRO 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 39 removed outlier: 3.506A pdb=" N VAL 2 29 " --> pdb=" O SER 2 25 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU 2 39 " --> pdb=" O ALA 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 58 removed outlier: 3.692A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY 2 56 " --> pdb=" O LEU 2 52 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA 2 58 " --> pdb=" O LYS 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 removed outlier: 3.871A pdb=" N THR 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 removed outlier: 3.869A pdb=" N SER 2 104 " --> pdb=" O PRO 2 100 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 129 removed outlier: 3.634A pdb=" N ALA 2 126 " --> pdb=" O ASN 2 122 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL 2 128 " --> pdb=" O ALA 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 removed outlier: 3.947A pdb=" N ARG 2 142 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL 2 143 " --> pdb=" O GLU 2 139 " (cutoff:3.500A) Processing helix chain '2' and resid 154 through 168 removed outlier: 3.508A pdb=" N ALA 2 158 " --> pdb=" O ASP 2 154 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 2 160 " --> pdb=" O ALA 2 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY 2 162 " --> pdb=" O ALA 2 158 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS 2 163 " --> pdb=" O LYS 2 159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER 2 167 " --> pdb=" O LYS 2 163 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 removed outlier: 3.512A pdb=" N LYS 2 184 " --> pdb=" O TYR 2 180 " (cutoff:3.500A) Processing helix chain '2' and resid 189 through 198 removed outlier: 3.602A pdb=" N ASP 2 194 " --> pdb=" O LYS 2 190 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 220 Processing helix chain '2' and resid 227 through 232 Processing helix chain '2' and resid 240 through 254 removed outlier: 3.728A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.682A pdb=" N PHE 2 262 " --> pdb=" O ASP 2 258 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA 2 264 " --> pdb=" O GLU 2 260 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 281 through 295 removed outlier: 3.935A pdb=" N GLN 2 287 " --> pdb=" O SER 2 283 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 2 288 " --> pdb=" O SER 2 284 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 3.581A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA 2 314 " --> pdb=" O ALA 2 310 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 341 removed outlier: 3.634A pdb=" N ASP 2 332 " --> pdb=" O ALA 2 328 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE 2 341 " --> pdb=" O THR 2 337 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 354 removed outlier: 3.824A pdb=" N ALA 2 352 " --> pdb=" O GLU 2 348 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA 2 354 " --> pdb=" O ALA 2 350 " (cutoff:3.500A) Processing helix chain '2' and resid 397 through 408 removed outlier: 3.601A pdb=" N ARG 2 406 " --> pdb=" O TYR 2 402 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 442 removed outlier: 3.619A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 91 through 99 removed outlier: 3.620A pdb=" N ASN 3 97 " --> pdb=" O GLU 3 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 removed outlier: 3.551A pdb=" N TRP 3 109 " --> pdb=" O PHE 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 122 Processing helix chain '3' and resid 124 through 129 Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 removed outlier: 3.541A pdb=" N LYS 3 148 " --> pdb=" O THR 3 144 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 168 removed outlier: 4.105A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 172 removed outlier: 3.586A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 169 through 172' Processing helix chain '3' and resid 173 through 181 removed outlier: 3.803A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 Processing helix chain '3' and resid 215 through 229 removed outlier: 3.575A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 removed outlier: 3.563A pdb=" N THR 3 239 " --> pdb=" O ASP 3 235 " (cutoff:3.500A) Processing helix chain '3' and resid 242 through 244 No H-bonds generated for 'chain '3' and resid 242 through 244' Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 271 removed outlier: 3.513A pdb=" N LYS 3 258 " --> pdb=" O ALA 3 254 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP 3 259 " --> pdb=" O ALA 3 255 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 277 No H-bonds generated for 'chain '3' and resid 275 through 277' Processing helix chain '3' and resid 278 through 287 removed outlier: 3.816A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL 3 287 " --> pdb=" O GLY 3 283 " (cutoff:3.500A) Processing helix chain '3' and resid 288 through 292 removed outlier: 4.101A pdb=" N GLU 3 291 " --> pdb=" O SER 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 295 through 309 removed outlier: 3.648A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 3.585A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.617A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 4.059A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.676A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 126 removed outlier: 3.515A pdb=" N VAL 4 122 " --> pdb=" O THR 4 118 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 150 removed outlier: 3.810A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.654A pdb=" N LYS 4 163 " --> pdb=" O THR 4 159 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 removed outlier: 3.735A pdb=" N ALA 4 185 " --> pdb=" O ASP 4 181 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 234 removed outlier: 3.570A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA 4 217 " --> pdb=" O ALA 4 213 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 4.192A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.502A pdb=" N GLU 4 284 " --> pdb=" O ALA 4 280 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 29 removed outlier: 3.556A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 59 removed outlier: 3.731A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN 5 52 " --> pdb=" O ALA 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 72 through 81 Processing helix chain '5' and resid 88 through 106 removed outlier: 4.201A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS 5 94 " --> pdb=" O GLU 5 90 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 removed outlier: 3.666A pdb=" N LYS 5 119 " --> pdb=" O ILE 5 115 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 50 through 58 Processing helix chain '6' and resid 72 through 95 removed outlier: 3.545A pdb=" N LEU 6 79 " --> pdb=" O ALA 6 75 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 104 through 118 removed outlier: 3.775A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '6' and resid 133 through 138 removed outlier: 3.872A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 105 removed outlier: 3.659A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 114 removed outlier: 3.816A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 123 through 145 removed outlier: 3.577A pdb=" N PHE 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS 7 139 " --> pdb=" O ASP 7 135 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 154 Processing helix chain '7' and resid 157 through 165 removed outlier: 3.651A pdb=" N ARG 7 164 " --> pdb=" O ASN 7 160 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 187 removed outlier: 3.539A pdb=" N ASN 7 184 " --> pdb=" O GLY 7 180 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 removed outlier: 3.929A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 32 through 39 removed outlier: 3.546A pdb=" N LYS 8 38 " --> pdb=" O THR 8 34 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 44 Processing helix chain '8' and resid 44 through 78 removed outlier: 3.835A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 16 removed outlier: 3.631A pdb=" N LYS 9 9 " --> pdb=" O SER 9 5 " (cutoff:3.500A) Processing helix chain '9' and resid 33 through 55 removed outlier: 3.639A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN 9 50 " --> pdb=" O MET 9 46 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 9 53 " --> pdb=" O VAL 9 49 " (cutoff:3.500A) Processing helix chain '9' and resid 76 through 80 removed outlier: 3.550A pdb=" N GLN 9 80 " --> pdb=" O TRP 9 77 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 95 removed outlier: 3.596A pdb=" N ALA 9 86 " --> pdb=" O ASP 9 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 144 Processing helix chain 'M' and resid 147 through 164 removed outlier: 3.605A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 198 removed outlier: 3.703A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 265 removed outlier: 3.903A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix removed outlier: 3.542A pdb=" N LEU M 265 " --> pdb=" O LEU M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 308 removed outlier: 3.720A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.823A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 229 removed outlier: 3.506A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER P 228 " --> pdb=" O LYS P 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 75 removed outlier: 3.535A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 4.182A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU T 74 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 185 removed outlier: 4.423A pdb=" N VAL 1 226 " --> pdb=" O ALA 1 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 369 through 372 removed outlier: 7.237A pdb=" N LYS 2 376 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 Processing sheet with id=AA4, first strand: chain '7' and resid 36 through 41 Processing sheet with id=AA5, first strand: chain 'P' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'P' and resid 188 through 190 1072 hydrogen bonds defined for protein. 3135 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: 3.07 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6225 1.34 - 1.45: 3244 1.45 - 1.57: 10715 1.57 - 1.69: 1 1.69 - 1.81: 54 Bond restraints: 20239 Sorted by residual: bond pdb=" N ILE M 227 " pdb=" CA ILE M 227 " ideal model delta sigma weight residual 1.463 1.494 -0.031 1.14e-02 7.69e+03 7.34e+00 bond pdb=" N ILE 3 101 " pdb=" CA ILE 3 101 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.18e-02 7.18e+03 6.49e+00 bond pdb=" N LYS 3 88 " pdb=" CA LYS 3 88 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.42e-02 4.96e+03 5.97e+00 bond pdb=" N THR M 226 " pdb=" CA THR M 226 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.40e+00 bond pdb=" CB THR M 153 " pdb=" CG2 THR M 153 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.35e+00 ... (remaining 20234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 26922 2.58 - 5.16: 466 5.16 - 7.74: 66 7.74 - 10.33: 12 10.33 - 12.91: 3 Bond angle restraints: 27469 Sorted by residual: angle pdb=" C VAL 7 157 " pdb=" N VAL 7 158 " pdb=" CA VAL 7 158 " ideal model delta sigma weight residual 120.33 126.10 -5.77 8.00e-01 1.56e+00 5.20e+01 angle pdb=" N PRO 3 77 " pdb=" CA PRO 3 77 " pdb=" CB PRO 3 77 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" C PHE 2 222 " pdb=" N LYS 2 223 " pdb=" CA LYS 2 223 " ideal model delta sigma weight residual 121.54 132.70 -11.16 1.91e+00 2.74e-01 3.42e+01 angle pdb=" C GLU 2 225 " pdb=" N LYS 2 226 " pdb=" CA LYS 2 226 " ideal model delta sigma weight residual 121.54 132.48 -10.94 1.91e+00 2.74e-01 3.28e+01 angle pdb=" C VAL P 185 " pdb=" N MET P 186 " pdb=" CA MET P 186 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.34e+01 ... (remaining 27464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 11181 18.11 - 36.21: 830 36.21 - 54.32: 133 54.32 - 72.42: 27 72.42 - 90.53: 11 Dihedral angle restraints: 12182 sinusoidal: 4595 harmonic: 7587 Sorted by residual: dihedral pdb=" CA VAL P 185 " pdb=" C VAL P 185 " pdb=" N MET P 186 " pdb=" CA MET P 186 " ideal model delta harmonic sigma weight residual 180.00 141.76 38.24 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA MET P 186 " pdb=" C MET P 186 " pdb=" N GLN P 187 " pdb=" CA GLN P 187 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LYS 5 119 " pdb=" C LYS 5 119 " pdb=" N PRO 5 120 " pdb=" CA PRO 5 120 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 12179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2751 0.077 - 0.155: 375 0.155 - 0.232: 35 0.232 - 0.309: 1 0.309 - 0.386: 1 Chirality restraints: 3163 Sorted by residual: chirality pdb=" CB ILE 3 90 " pdb=" CA ILE 3 90 " pdb=" CG1 ILE 3 90 " pdb=" CG2 ILE 3 90 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB VAL 1 94 " pdb=" CA VAL 1 94 " pdb=" CG1 VAL 1 94 " pdb=" CG2 VAL 1 94 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA PRO 3 77 " pdb=" N PRO 3 77 " pdb=" C PRO 3 77 " pdb=" CB PRO 3 77 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 3160 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA 3 210 " 0.054 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO 3 211 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO 3 211 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO 3 211 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 261 " 0.049 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO M 262 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO M 262 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 262 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO 1 93 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " 0.038 5.00e-02 4.00e+02 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3216 2.75 - 3.29: 18290 3.29 - 3.82: 32796 3.82 - 4.36: 41062 4.36 - 4.90: 68671 Nonbonded interactions: 164035 Sorted by model distance: nonbonded pdb=" CD2 LEU M 224 " pdb=" O HOH M 709 " model vdw 2.212 3.460 nonbonded pdb=" CG LEU M 224 " pdb=" O HOH M 709 " model vdw 2.218 3.470 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.227 3.040 nonbonded pdb=" O THR 5 83 " pdb=" OH TYR 7 119 " model vdw 2.240 3.040 nonbonded pdb=" O LEU 1 315 " pdb=" OG SER 1 318 " model vdw 2.278 3.040 ... (remaining 164030 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 20241 Z= 0.338 Angle : 0.891 12.907 27469 Z= 0.499 Chirality : 0.054 0.386 3163 Planarity : 0.007 0.080 3505 Dihedral : 13.404 90.526 7264 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.67 % Favored : 95.17 % Rotamer: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.00 (0.10), residues: 2569 helix: -4.55 (0.05), residues: 1682 sheet: -1.91 (0.65), residues: 52 loop : -2.21 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 387 TYR 0.025 0.003 TYR 4 211 PHE 0.022 0.002 PHE 3 115 TRP 0.017 0.002 TRP 9 73 HIS 0.011 0.002 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00791 (20239) covalent geometry : angle 0.89072 (27469) hydrogen bonds : bond 0.30133 ( 1072) hydrogen bonds : angle 10.92869 ( 3135) metal coordination : bond 0.06085 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 376 time to evaluate : 0.742 Fit side-chains REVERT: 1 155 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7268 (tm-30) REVERT: 1 346 GLN cc_start: 0.8224 (pp30) cc_final: 0.7692 (mp10) REVERT: 1 572 ASP cc_start: 0.7846 (m-30) cc_final: 0.7537 (m-30) REVERT: 1 586 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7794 (mm-30) REVERT: 1 613 ASP cc_start: 0.8118 (m-30) cc_final: 0.7825 (m-30) REVERT: 2 154 ASP cc_start: 0.6606 (t70) cc_final: 0.5922 (p0) REVERT: 2 197 LEU cc_start: 0.7848 (mt) cc_final: 0.7504 (mt) REVERT: 4 197 ASP cc_start: 0.8593 (t70) cc_final: 0.8357 (t0) REVERT: 4 255 ARG cc_start: 0.8122 (ttm170) cc_final: 0.7897 (mtp180) REVERT: 5 37 GLU cc_start: 0.8716 (pt0) cc_final: 0.8447 (pt0) REVERT: 6 37 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8437 (ttmt) REVERT: 8 69 LYS cc_start: 0.8543 (mttt) cc_final: 0.6233 (tmtt) REVERT: 9 13 LYS cc_start: 0.6687 (mtmt) cc_final: 0.6138 (tttm) REVERT: 9 56 ASN cc_start: 0.8584 (p0) cc_final: 0.8247 (p0) REVERT: M 97 VAL cc_start: 0.9252 (t) cc_final: 0.9034 (m) REVERT: M 168 MET cc_start: 0.8101 (mmt) cc_final: 0.7818 (mmt) REVERT: M 230 THR cc_start: 0.9168 (t) cc_final: 0.8936 (m) REVERT: P 183 LYS cc_start: 0.8291 (ptmm) cc_final: 0.8005 (ptmt) REVERT: P 205 ARG cc_start: 0.7596 (ptt-90) cc_final: 0.3492 (mmp-170) REVERT: T 49 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.7947 (mtp85) outliers start: 3 outliers final: 2 residues processed: 379 average time/residue: 0.1869 time to fit residues: 100.9402 Evaluate side-chains 244 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 209 ASN 1 257 HIS 1 285 GLN 1 298 GLN 1 316 ASN 1 365 GLN 1 482 ASN 1 531 HIS 1 587 ASN 1 590 HIS 2 243 GLN 2 427 GLN ** 3 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 206 ASN 3 229 ASN 3 256 GLN 4 240 GLN 5 29 GLN 5 107 ASN 5 117 GLN 6 40 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 7 60 GLN 7 86 HIS 7 91 ASN 7 98 ASN 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 8 29 GLN 8 78 HIS M 108 ASN M 163 ASN P 223 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102580 restraints weight = 28691.007| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.87 r_work: 0.2828 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20241 Z= 0.160 Angle : 0.616 14.339 27469 Z= 0.327 Chirality : 0.041 0.180 3163 Planarity : 0.006 0.060 3505 Dihedral : 5.476 31.752 2749 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 1.50 % Allowed : 8.39 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.14), residues: 2569 helix: -2.35 (0.10), residues: 1692 sheet: -0.75 (0.79), residues: 45 loop : -1.47 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 4 176 TYR 0.028 0.002 TYR 4 211 PHE 0.013 0.001 PHE M 180 TRP 0.018 0.002 TRP 9 73 HIS 0.007 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00362 (20239) covalent geometry : angle 0.61566 (27469) hydrogen bonds : bond 0.04540 ( 1072) hydrogen bonds : angle 4.84390 ( 3135) metal coordination : bond 0.00140 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: 1 49 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7908 (tt0) REVERT: 1 346 GLN cc_start: 0.8643 (pp30) cc_final: 0.7906 (mp10) REVERT: 1 352 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: 1 414 GLU cc_start: 0.7849 (pt0) cc_final: 0.7612 (pp20) REVERT: 1 442 ASP cc_start: 0.8175 (m-30) cc_final: 0.7946 (m-30) REVERT: 1 572 ASP cc_start: 0.8575 (m-30) cc_final: 0.8353 (m-30) REVERT: 1 613 ASP cc_start: 0.8031 (m-30) cc_final: 0.7554 (m-30) REVERT: 2 74 ASN cc_start: 0.8793 (t0) cc_final: 0.8513 (t0) REVERT: 2 154 ASP cc_start: 0.7036 (t70) cc_final: 0.5680 (p0) REVERT: 4 162 PHE cc_start: 0.6302 (t80) cc_final: 0.6095 (t80) REVERT: 4 255 ARG cc_start: 0.8595 (ttm170) cc_final: 0.8217 (mtp180) REVERT: 6 37 LYS cc_start: 0.8870 (ttpp) cc_final: 0.8474 (ttmt) REVERT: 8 69 LYS cc_start: 0.8550 (mttt) cc_final: 0.6274 (tmtt) REVERT: 9 56 ASN cc_start: 0.8717 (p0) cc_final: 0.8408 (p0) REVERT: M 168 MET cc_start: 0.8790 (mmt) cc_final: 0.8567 (mmt) REVERT: M 230 THR cc_start: 0.9418 (t) cc_final: 0.9125 (m) REVERT: M 270 MET cc_start: 0.7238 (tmm) cc_final: 0.6565 (mmm) REVERT: M 324 LYS cc_start: 0.7567 (tppt) cc_final: 0.6959 (tptp) REVERT: P 183 LYS cc_start: 0.8084 (ptmm) cc_final: 0.7777 (ttpt) REVERT: P 205 ARG cc_start: 0.8051 (ptt-90) cc_final: 0.3830 (mmp-170) REVERT: P 216 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8358 (tt0) REVERT: T 49 ARG cc_start: 0.8785 (mtp-110) cc_final: 0.8288 (mtp85) outliers start: 31 outliers final: 18 residues processed: 301 average time/residue: 0.1576 time to fit residues: 71.3181 Evaluate side-chains 259 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 223 GLU Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 352 GLU Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 46 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 3 189 HIS 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.100107 restraints weight = 28846.086| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.04 r_work: 0.2796 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20241 Z= 0.196 Angle : 0.596 13.924 27469 Z= 0.310 Chirality : 0.042 0.197 3163 Planarity : 0.004 0.056 3505 Dihedral : 5.149 41.712 2749 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 1.79 % Allowed : 10.42 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.16), residues: 2569 helix: -1.05 (0.12), residues: 1699 sheet: -1.07 (0.82), residues: 40 loop : -1.11 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 387 TYR 0.025 0.002 TYR 4 211 PHE 0.017 0.001 PHE M 275 TRP 0.014 0.002 TRP 9 73 HIS 0.007 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00464 (20239) covalent geometry : angle 0.59594 (27469) hydrogen bonds : bond 0.04029 ( 1072) hydrogen bonds : angle 4.26562 ( 3135) metal coordination : bond 0.00085 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 0.727 Fit side-chains REVERT: 1 49 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7960 (tt0) REVERT: 1 346 GLN cc_start: 0.8710 (pp30) cc_final: 0.8045 (mp10) REVERT: 1 352 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: 1 414 GLU cc_start: 0.7893 (pt0) cc_final: 0.7650 (pp20) REVERT: 1 442 ASP cc_start: 0.8255 (m-30) cc_final: 0.8050 (m-30) REVERT: 1 572 ASP cc_start: 0.8556 (m-30) cc_final: 0.8336 (m-30) REVERT: 1 613 ASP cc_start: 0.8094 (m-30) cc_final: 0.7684 (m-30) REVERT: 2 154 ASP cc_start: 0.7144 (t70) cc_final: 0.5820 (p0) REVERT: 2 316 ASP cc_start: 0.7615 (m-30) cc_final: 0.7383 (m-30) REVERT: 5 1 MET cc_start: 0.7018 (mtp) cc_final: 0.6673 (ttm) REVERT: 8 69 LYS cc_start: 0.8598 (mttt) cc_final: 0.6355 (tmtt) REVERT: 9 56 ASN cc_start: 0.8718 (p0) cc_final: 0.8353 (p0) REVERT: M 168 MET cc_start: 0.8902 (mmt) cc_final: 0.8682 (mmt) REVERT: M 324 LYS cc_start: 0.7508 (tppt) cc_final: 0.6953 (tttm) REVERT: P 186 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.4548 (mmm) REVERT: P 205 ARG cc_start: 0.8105 (ptt-90) cc_final: 0.3984 (mmp-170) REVERT: P 216 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8311 (tt0) outliers start: 37 outliers final: 21 residues processed: 280 average time/residue: 0.1502 time to fit residues: 64.2004 Evaluate side-chains 249 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 352 GLU Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 229 ILE Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 111 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 204 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 146 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 0 61 HIS 1 562 ASN 2 177 GLN 5 59 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104368 restraints weight = 28690.323| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.93 r_work: 0.2919 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20241 Z= 0.113 Angle : 0.528 12.013 27469 Z= 0.273 Chirality : 0.040 0.204 3163 Planarity : 0.004 0.052 3505 Dihedral : 4.773 39.184 2749 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.79 % Allowed : 11.59 % Favored : 86.62 % 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 are not related in a simple way. whole: -0.76 (0.16), residues: 2569 helix: -0.20 (0.13), residues: 1692 sheet: -0.79 (0.84), residues: 40 loop : -0.86 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 387 TYR 0.024 0.001 TYR 4 211 PHE 0.014 0.001 PHE M 275 TRP 0.016 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00256 (20239) covalent geometry : angle 0.52753 (27469) hydrogen bonds : bond 0.03326 ( 1072) hydrogen bonds : angle 3.86257 ( 3135) metal coordination : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.678 Fit side-chains REVERT: 1 49 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7911 (tt0) REVERT: 1 223 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7275 (mp0) REVERT: 1 263 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8537 (tp) REVERT: 1 346 GLN cc_start: 0.8722 (pp30) cc_final: 0.8138 (mp10) REVERT: 1 352 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: 1 414 GLU cc_start: 0.7828 (pt0) cc_final: 0.7592 (pp20) REVERT: 1 442 ASP cc_start: 0.8157 (m-30) cc_final: 0.7934 (m-30) REVERT: 1 572 ASP cc_start: 0.8605 (m-30) cc_final: 0.8393 (m-30) REVERT: 1 586 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8503 (mm-30) REVERT: 1 613 ASP cc_start: 0.7987 (m-30) cc_final: 0.7566 (m-30) REVERT: 2 74 ASN cc_start: 0.8713 (t0) cc_final: 0.8410 (t0) REVERT: 3 269 GLN cc_start: 0.8621 (tt0) cc_final: 0.8374 (tp40) REVERT: 4 255 ARG cc_start: 0.8593 (ttm170) cc_final: 0.8372 (ttm170) REVERT: 5 1 MET cc_start: 0.6924 (mtp) cc_final: 0.6643 (ttm) REVERT: 8 69 LYS cc_start: 0.8515 (mttt) cc_final: 0.6261 (tmtt) REVERT: 9 22 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7403 (mm-30) REVERT: 9 56 ASN cc_start: 0.8666 (p0) cc_final: 0.8033 (p0) REVERT: M 168 MET cc_start: 0.8838 (mmt) cc_final: 0.8620 (mmt) REVERT: M 324 LYS cc_start: 0.7559 (tppt) cc_final: 0.6939 (tttm) REVERT: P 186 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.4361 (mmm) REVERT: P 205 ARG cc_start: 0.8018 (ptt-90) cc_final: 0.3991 (mmp-170) outliers start: 37 outliers final: 20 residues processed: 292 average time/residue: 0.1570 time to fit residues: 69.5303 Evaluate side-chains 255 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 263 LEU Chi-restraints excluded: chain 1 residue 352 GLU Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 132 optimal weight: 0.0670 chunk 202 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 233 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 5 59 ASN 7 24 GLN 7 91 ASN 8 78 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104994 restraints weight = 28390.538| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.88 r_work: 0.2881 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20241 Z= 0.116 Angle : 0.525 12.954 27469 Z= 0.270 Chirality : 0.040 0.215 3163 Planarity : 0.004 0.047 3505 Dihedral : 4.579 38.938 2749 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 2.18 % Allowed : 12.26 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2569 helix: 0.25 (0.13), residues: 1701 sheet: -0.63 (0.85), residues: 41 loop : -0.77 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 387 TYR 0.022 0.001 TYR 4 211 PHE 0.015 0.001 PHE P 182 TRP 0.010 0.001 TRP 4 206 HIS 0.004 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00266 (20239) covalent geometry : angle 0.52531 (27469) hydrogen bonds : bond 0.03249 ( 1072) hydrogen bonds : angle 3.71217 ( 3135) metal coordination : bond 0.00042 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.871 Fit side-chains REVERT: 1 49 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8021 (tt0) REVERT: 1 118 ARG cc_start: 0.8653 (mtp-110) cc_final: 0.8361 (mtp-110) REVERT: 1 346 GLN cc_start: 0.8756 (pp30) cc_final: 0.8191 (mp10) REVERT: 1 352 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: 1 399 MET cc_start: 0.9160 (mmt) cc_final: 0.8952 (mmt) REVERT: 1 586 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8495 (mm-30) REVERT: 1 613 ASP cc_start: 0.8009 (m-30) cc_final: 0.7592 (m-30) REVERT: 2 45 ARG cc_start: 0.8785 (mtp85) cc_final: 0.8556 (mtm180) REVERT: 2 74 ASN cc_start: 0.8723 (t0) cc_final: 0.8400 (t0) REVERT: 8 69 LYS cc_start: 0.8538 (mttt) cc_final: 0.6312 (tmtt) REVERT: 9 22 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7345 (mm-30) REVERT: M 270 MET cc_start: 0.7216 (tmm) cc_final: 0.6265 (mmm) REVERT: M 324 LYS cc_start: 0.7611 (tppt) cc_final: 0.7003 (tttm) REVERT: P 205 ARG cc_start: 0.8074 (ptt-90) cc_final: 0.4053 (mmp-170) outliers start: 45 outliers final: 28 residues processed: 287 average time/residue: 0.1525 time to fit residues: 66.5911 Evaluate side-chains 256 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 352 GLU Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 55 LYS Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 115 ILE Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 231 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 113 optimal weight: 0.0870 chunk 185 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 380 GLN 4 68 HIS 5 59 ASN 5 82 HIS 7 91 ASN 8 78 HIS 9 35 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103034 restraints weight = 28543.242| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.85 r_work: 0.2859 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20241 Z= 0.161 Angle : 0.554 13.827 27469 Z= 0.284 Chirality : 0.042 0.251 3163 Planarity : 0.004 0.047 3505 Dihedral : 4.602 43.220 2748 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 2.18 % Allowed : 12.94 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2569 helix: 0.41 (0.13), residues: 1707 sheet: -0.53 (0.86), residues: 41 loop : -0.74 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 49 TYR 0.022 0.001 TYR 4 211 PHE 0.012 0.001 PHE M 180 TRP 0.017 0.001 TRP 9 73 HIS 0.006 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00382 (20239) covalent geometry : angle 0.55357 (27469) hydrogen bonds : bond 0.03413 ( 1072) hydrogen bonds : angle 3.75414 ( 3135) metal coordination : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: 1 49 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7969 (tt0) REVERT: 1 346 GLN cc_start: 0.8791 (pp30) cc_final: 0.8269 (mp10) REVERT: 1 399 MET cc_start: 0.9147 (mmt) cc_final: 0.8926 (mmt) REVERT: 1 414 GLU cc_start: 0.7947 (pt0) cc_final: 0.7659 (pp20) REVERT: 1 586 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8517 (mm-30) REVERT: 1 613 ASP cc_start: 0.8077 (m-30) cc_final: 0.7673 (m-30) REVERT: 2 74 ASN cc_start: 0.8751 (t0) cc_final: 0.8423 (t0) REVERT: 4 111 GLN cc_start: 0.8541 (tt0) cc_final: 0.8224 (mt0) REVERT: 8 69 LYS cc_start: 0.8528 (mttt) cc_final: 0.6313 (tmtt) REVERT: 9 22 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7298 (mm-30) REVERT: M 324 LYS cc_start: 0.7667 (tppt) cc_final: 0.7037 (tttm) REVERT: P 205 ARG cc_start: 0.8086 (ptt-90) cc_final: 0.4058 (mmp-170) outliers start: 45 outliers final: 33 residues processed: 277 average time/residue: 0.1531 time to fit residues: 65.1483 Evaluate side-chains 265 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 352 GLU Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 493 LEU Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 33 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 59 ASN 7 24 GLN 7 98 ASN 8 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104682 restraints weight = 28663.952| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.81 r_work: 0.2875 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20241 Z= 0.117 Angle : 0.529 12.905 27469 Z= 0.271 Chirality : 0.040 0.277 3163 Planarity : 0.004 0.045 3505 Dihedral : 4.500 40.783 2748 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 1.84 % Allowed : 13.23 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2569 helix: 0.66 (0.13), residues: 1706 sheet: -0.58 (0.83), residues: 41 loop : -0.68 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 49 TYR 0.022 0.001 TYR 4 211 PHE 0.017 0.001 PHE M 275 TRP 0.016 0.001 TRP 9 73 HIS 0.004 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00272 (20239) covalent geometry : angle 0.52924 (27469) hydrogen bonds : bond 0.03191 ( 1072) hydrogen bonds : angle 3.64221 ( 3135) metal coordination : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: 1 49 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8028 (tt0) REVERT: 1 346 GLN cc_start: 0.8735 (pp30) cc_final: 0.8286 (mp10) REVERT: 1 399 MET cc_start: 0.9159 (mmt) cc_final: 0.8942 (mmt) REVERT: 1 549 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8553 (m-30) REVERT: 1 586 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8491 (mm-30) REVERT: 1 613 ASP cc_start: 0.8028 (m-30) cc_final: 0.7649 (m-30) REVERT: 2 74 ASN cc_start: 0.8703 (t0) cc_final: 0.8357 (t0) REVERT: 4 111 GLN cc_start: 0.8610 (tt0) cc_final: 0.8329 (mt0) REVERT: 7 91 ASN cc_start: 0.9015 (t0) cc_final: 0.8755 (t0) REVERT: 8 69 LYS cc_start: 0.8496 (mttt) cc_final: 0.6301 (tmtt) REVERT: 9 22 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7335 (mm-30) REVERT: M 270 MET cc_start: 0.6945 (tmm) cc_final: 0.6042 (mmm) REVERT: M 324 LYS cc_start: 0.7593 (tppt) cc_final: 0.6987 (tttm) REVERT: P 205 ARG cc_start: 0.8063 (ptt-90) cc_final: 0.4046 (mmp-170) outliers start: 38 outliers final: 30 residues processed: 270 average time/residue: 0.1421 time to fit residues: 58.2896 Evaluate side-chains 262 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 352 GLU Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 493 LEU Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 99 GLU Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 260 LYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 71 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 235 optimal weight: 0.5980 chunk 226 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 59 ASN 7 24 GLN 7 91 ASN 8 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104516 restraints weight = 28601.172| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.87 r_work: 0.2865 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20241 Z= 0.131 Angle : 0.542 12.946 27469 Z= 0.277 Chirality : 0.041 0.309 3163 Planarity : 0.004 0.045 3505 Dihedral : 4.467 41.844 2748 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 1.94 % Allowed : 13.48 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2569 helix: 0.80 (0.13), residues: 1709 sheet: -0.87 (0.80), residues: 41 loop : -0.60 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 49 TYR 0.021 0.001 TYR 4 211 PHE 0.010 0.001 PHE 3 115 TRP 0.015 0.001 TRP 9 73 HIS 0.004 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00306 (20239) covalent geometry : angle 0.54152 (27469) hydrogen bonds : bond 0.03221 ( 1072) hydrogen bonds : angle 3.62854 ( 3135) metal coordination : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: 0 80 HIS cc_start: 0.6284 (m-70) cc_final: 0.6029 (p-80) REVERT: 1 49 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8040 (tt0) REVERT: 1 346 GLN cc_start: 0.8747 (pp30) cc_final: 0.8298 (mp10) REVERT: 1 399 MET cc_start: 0.9168 (mmt) cc_final: 0.8944 (mmt) REVERT: 1 549 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8562 (m-30) REVERT: 1 586 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8519 (mm-30) REVERT: 1 613 ASP cc_start: 0.8093 (m-30) cc_final: 0.7691 (m-30) REVERT: 4 111 GLN cc_start: 0.8588 (tt0) cc_final: 0.8315 (mt0) REVERT: 7 91 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8666 (t0) REVERT: 8 69 LYS cc_start: 0.8481 (mttt) cc_final: 0.6457 (tmtt) REVERT: 9 1 MET cc_start: 0.2479 (ptt) cc_final: -0.0962 (mpp) REVERT: 9 22 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7353 (mm-30) REVERT: M 270 MET cc_start: 0.7030 (tmm) cc_final: 0.6124 (mmm) REVERT: M 324 LYS cc_start: 0.7601 (tppt) cc_final: 0.6981 (tttm) REVERT: P 205 ARG cc_start: 0.8062 (ptt-90) cc_final: 0.4034 (mmp-170) outliers start: 40 outliers final: 34 residues processed: 272 average time/residue: 0.1520 time to fit residues: 62.5682 Evaluate side-chains 263 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 352 GLU Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 493 LEU Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 371 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 99 GLU Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 260 LYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 91 ASN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 239 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 247 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 42 optimal weight: 0.0970 chunk 159 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 59 ASN 7 24 GLN ** 7 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105616 restraints weight = 28424.451| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.89 r_work: 0.2873 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20241 Z= 0.111 Angle : 0.529 12.606 27469 Z= 0.271 Chirality : 0.040 0.311 3163 Planarity : 0.004 0.055 3505 Dihedral : 4.405 40.842 2748 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 1.60 % Allowed : 14.20 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.17), residues: 2569 helix: 0.96 (0.13), residues: 1712 sheet: -0.95 (0.80), residues: 41 loop : -0.54 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 45 TYR 0.021 0.001 TYR 4 211 PHE 0.018 0.001 PHE M 275 TRP 0.016 0.001 TRP 9 73 HIS 0.004 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00253 (20239) covalent geometry : angle 0.52856 (27469) hydrogen bonds : bond 0.03116 ( 1072) hydrogen bonds : angle 3.57817 ( 3135) metal coordination : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 80 HIS cc_start: 0.6264 (m-70) cc_final: 0.6035 (p-80) REVERT: 1 346 GLN cc_start: 0.8722 (pp30) cc_final: 0.8279 (mp10) REVERT: 1 399 MET cc_start: 0.9175 (mmt) cc_final: 0.8955 (mmt) REVERT: 1 549 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8564 (m-30) REVERT: 1 586 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8546 (mm-30) REVERT: 1 613 ASP cc_start: 0.8053 (m-30) cc_final: 0.7641 (m-30) REVERT: 8 69 LYS cc_start: 0.8473 (mttt) cc_final: 0.6457 (tmtt) REVERT: 9 1 MET cc_start: 0.2174 (ptt) cc_final: -0.1083 (mpp) REVERT: 9 22 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7344 (mm-30) REVERT: 9 50 ASN cc_start: 0.8305 (m-40) cc_final: 0.8103 (m110) REVERT: M 270 MET cc_start: 0.7003 (tmm) cc_final: 0.6127 (mmm) REVERT: M 324 LYS cc_start: 0.7647 (tppt) cc_final: 0.7052 (tttm) REVERT: P 205 ARG cc_start: 0.8066 (ptt-90) cc_final: 0.4018 (mmp-170) REVERT: T 49 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8148 (mtp85) outliers start: 33 outliers final: 32 residues processed: 265 average time/residue: 0.1539 time to fit residues: 61.7277 Evaluate side-chains 261 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 352 GLU Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 371 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 99 GLU Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain T residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 198 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 114 optimal weight: 0.1980 chunk 131 optimal weight: 2.9990 chunk 67 optimal weight: 0.0270 chunk 216 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 380 GLN 5 59 ASN 7 24 GLN 8 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105665 restraints weight = 28591.994| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.76 r_work: 0.2921 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20241 Z= 0.112 Angle : 0.526 11.620 27469 Z= 0.270 Chirality : 0.040 0.320 3163 Planarity : 0.004 0.051 3505 Dihedral : 4.367 40.585 2748 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 1.79 % Allowed : 14.06 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2569 helix: 1.07 (0.13), residues: 1706 sheet: -0.83 (0.81), residues: 41 loop : -0.52 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 45 TYR 0.023 0.001 TYR 6 71 PHE 0.012 0.001 PHE 3 115 TRP 0.015 0.001 TRP 9 73 HIS 0.004 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00255 (20239) covalent geometry : angle 0.52642 (27469) hydrogen bonds : bond 0.03080 ( 1072) hydrogen bonds : angle 3.56605 ( 3135) metal coordination : bond 0.00045 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 80 HIS cc_start: 0.6246 (m-70) cc_final: 0.6042 (p-80) REVERT: 1 195 LYS cc_start: 0.7684 (pttt) cc_final: 0.7407 (ttpp) REVERT: 1 346 GLN cc_start: 0.8692 (pp30) cc_final: 0.8320 (mp10) REVERT: 1 399 MET cc_start: 0.9152 (mmt) cc_final: 0.8927 (mmt) REVERT: 1 549 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8551 (m-30) REVERT: 1 586 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8558 (mm-30) REVERT: 1 613 ASP cc_start: 0.8047 (m-30) cc_final: 0.7636 (m-30) REVERT: 6 76 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7318 (mttt) REVERT: 7 60 GLN cc_start: 0.7465 (tt0) cc_final: 0.7168 (tt0) REVERT: 8 69 LYS cc_start: 0.8464 (mttt) cc_final: 0.6462 (tmtt) REVERT: 9 1 MET cc_start: 0.1838 (ptt) cc_final: -0.0342 (mpp) REVERT: 9 22 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7262 (mm-30) REVERT: M 270 MET cc_start: 0.7041 (tmm) cc_final: 0.6271 (mmm) REVERT: M 324 LYS cc_start: 0.7669 (tppt) cc_final: 0.7071 (tttm) REVERT: P 205 ARG cc_start: 0.8029 (ptt-90) cc_final: 0.4004 (mmp-170) REVERT: T 49 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8121 (mtp85) outliers start: 37 outliers final: 33 residues processed: 275 average time/residue: 0.1508 time to fit residues: 62.9496 Evaluate side-chains 266 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 352 GLU Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 493 LEU Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 371 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 99 GLU Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain T residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 79 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 59 ASN 7 24 GLN 8 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104274 restraints weight = 28701.679| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.88 r_work: 0.2865 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20241 Z= 0.146 Angle : 0.552 12.221 27469 Z= 0.283 Chirality : 0.042 0.297 3163 Planarity : 0.004 0.048 3505 Dihedral : 4.426 42.491 2748 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 1.60 % Allowed : 14.44 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2569 helix: 1.00 (0.13), residues: 1715 sheet: -0.72 (0.82), residues: 41 loop : -0.54 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 45 TYR 0.022 0.001 TYR 4 211 PHE 0.021 0.001 PHE M 275 TRP 0.015 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00347 (20239) covalent geometry : angle 0.55215 (27469) hydrogen bonds : bond 0.03245 ( 1072) hydrogen bonds : angle 3.63993 ( 3135) metal coordination : bond 0.00091 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6781.59 seconds wall clock time: 116 minutes 36.20 seconds (6996.20 seconds total)