Starting phenix.real_space_refine on Mon Aug 25 13:23:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2i_47453/08_2025/9e2i_47453_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2i_47453/08_2025/9e2i_47453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e2i_47453/08_2025/9e2i_47453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2i_47453/08_2025/9e2i_47453.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2i_47453/08_2025/9e2i_47453_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2i_47453/08_2025/9e2i_47453_neut.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 177 5.16 5 C 18018 2.51 5 N 4878 2.21 5 O 5319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28392 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4611 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 23, 'TRANS': 548} Chain breaks: 7 Chain: "B" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4800 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 24, 'TRANS': 570} Chain breaks: 4 Chain: "C" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4622 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 23, 'TRANS': 549} Chain breaks: 6 Chain: "D" Number of atoms: 4745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4745 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 564} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4753 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 24, 'TRANS': 564} Chain breaks: 5 Chain: "F" Number of atoms: 4861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4861 Classifications: {'peptide': 604} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 6.40, per 1000 atoms: 0.23 Number of scatterers: 28392 At special positions: 0 Unit cell: (139.32, 135, 172.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 177 16.00 O 5319 8.00 N 4878 7.00 C 18018 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: 2.39 Conformation dependent library (CDL) restraints added in 893.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 7 sheets defined 77.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 59 through 76 removed outlier: 3.805A pdb=" N THR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.716A pdb=" N PHE A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 167 removed outlier: 3.556A pdb=" N GLN A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 162 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 188 removed outlier: 4.141A pdb=" N GLU A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 4.297A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 228 through 265 Proline residue: A 237 - end of helix Proline residue: A 241 - end of helix removed outlier: 3.904A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.890A pdb=" N LEU A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 313 removed outlier: 3.719A pdb=" N THR A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 331 through 342 removed outlier: 4.076A pdb=" N ARG A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 350 through 360 removed outlier: 3.840A pdb=" N ALA A 355 " --> pdb=" O CYS A 351 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.871A pdb=" N VAL A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 486 removed outlier: 3.614A pdb=" N GLN A 467 " --> pdb=" O HIS A 463 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 503 through 523 removed outlier: 3.576A pdb=" N SER A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 555 removed outlier: 3.961A pdb=" N ASN A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.520A pdb=" N ASP A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.645A pdb=" N GLN A 584 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 619 removed outlier: 3.614A pdb=" N SER A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 647 removed outlier: 3.534A pdb=" N HIS A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 664 Processing helix chain 'A' and resid 667 through 681 Processing helix chain 'A' and resid 683 through 706 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'B' and resid 60 through 75 removed outlier: 3.814A pdb=" N GLU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'B' and resid 106 through 122 removed outlier: 3.547A pdb=" N PHE B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 3.542A pdb=" N LYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 162 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 189 removed outlier: 3.880A pdb=" N VAL B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.841A pdb=" N VAL B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET B 223 " --> pdb=" O MET B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 239 Proline residue: B 237 - end of helix Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.781A pdb=" N TYR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 273 through 282 Processing helix chain 'B' and resid 285 through 315 removed outlier: 3.559A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 340 removed outlier: 3.686A pdb=" N THR B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 325 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.734A pdb=" N ILE B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 441 " --> pdb=" O TYR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 459 removed outlier: 4.700A pdb=" N VAL B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TRP B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 486 removed outlier: 3.700A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.740A pdb=" N ILE B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 524 removed outlier: 4.286A pdb=" N GLN B 506 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 554 removed outlier: 3.904A pdb=" N MET B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.558A pdb=" N GLN B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 585 removed outlier: 4.307A pdb=" N PHE B 575 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 584 " --> pdb=" O ARG B 580 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 591 Processing helix chain 'B' and resid 593 through 618 removed outlier: 3.644A pdb=" N GLN B 609 " --> pdb=" O GLY B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 633 removed outlier: 3.538A pdb=" N ASP B 632 " --> pdb=" O CYS B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 removed outlier: 3.540A pdb=" N HIS B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 667 through 679 Processing helix chain 'B' and resid 682 through 709 removed outlier: 3.681A pdb=" N GLY B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'C' and resid 60 through 77 removed outlier: 3.535A pdb=" N ARG C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 106 through 120 Processing helix chain 'C' and resid 141 through 167 removed outlier: 3.544A pdb=" N GLU C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 185 Processing helix chain 'C' and resid 206 through 211 removed outlier: 4.194A pdb=" N THR C 210 " --> pdb=" O ARG C 206 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 211' Processing helix chain 'C' and resid 211 through 223 Processing helix chain 'C' and resid 228 through 265 Proline residue: C 237 - end of helix Proline residue: C 241 - end of helix removed outlier: 3.722A pdb=" N ALA C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP C 256 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 282 removed outlier: 4.253A pdb=" N GLN C 280 " --> pdb=" O TRP C 276 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 282 " --> pdb=" O PHE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 312 removed outlier: 3.795A pdb=" N PHE C 311 " --> pdb=" O ASN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 330 Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 344 through 346 No H-bonds generated for 'chain 'C' and resid 344 through 346' Processing helix chain 'C' and resid 347 through 362 removed outlier: 3.685A pdb=" N LYS C 352 " --> pdb=" O PRO C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 456 removed outlier: 4.023A pdb=" N VAL C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.561A pdb=" N ILE C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 503 through 522 removed outlier: 3.748A pdb=" N LEU C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 516 " --> pdb=" O ASN C 512 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 526 removed outlier: 3.676A pdb=" N ASP C 526 " --> pdb=" O ARG C 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 523 through 526' Processing helix chain 'C' and resid 529 through 555 removed outlier: 3.511A pdb=" N ASN C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 571 through 585 removed outlier: 4.299A pdb=" N PHE C 575 " --> pdb=" O THR C 571 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 584 " --> pdb=" O ARG C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 617 removed outlier: 3.507A pdb=" N PHE C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 647 removed outlier: 3.510A pdb=" N HIS C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 664 removed outlier: 3.525A pdb=" N GLN C 658 " --> pdb=" O ARG C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 682 removed outlier: 3.593A pdb=" N GLN C 680 " --> pdb=" O SER C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 710 removed outlier: 3.565A pdb=" N GLU C 708 " --> pdb=" O SER C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 removed outlier: 3.662A pdb=" N ARG C 717 " --> pdb=" O ASN C 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 76 removed outlier: 4.151A pdb=" N ASN D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 102 through 121 removed outlier: 3.682A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE D 117 " --> pdb=" O PHE D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 164 removed outlier: 3.750A pdb=" N LYS D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 162 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 189 removed outlier: 4.068A pdb=" N VAL D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.816A pdb=" N VAL D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE D 208 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 224 removed outlier: 4.151A pdb=" N VAL D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 235 Processing helix chain 'D' and resid 239 through 253 removed outlier: 3.548A pdb=" N ALA D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.521A pdb=" N GLU D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 282 removed outlier: 3.640A pdb=" N GLN D 280 " --> pdb=" O TRP D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 301 Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'D' and resid 319 through 338 removed outlier: 3.751A pdb=" N THR D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) Proline residue: D 334 - end of helix Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 431 through 441 removed outlier: 4.394A pdb=" N ALA D 435 " --> pdb=" O LEU D 431 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 438 " --> pdb=" O PRO D 434 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 441 " --> pdb=" O TYR D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 454 Processing helix chain 'D' and resid 461 through 486 removed outlier: 3.781A pdb=" N ILE D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 502 removed outlier: 3.672A pdb=" N ILE D 501 " --> pdb=" O SER D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 522 removed outlier: 3.637A pdb=" N LEU D 515 " --> pdb=" O ALA D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 555 removed outlier: 4.133A pdb=" N MET D 531 " --> pdb=" O ASP D 527 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP D 532 " --> pdb=" O PRO D 528 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.508A pdb=" N GLN D 569 " --> pdb=" O ASP D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 585 removed outlier: 4.417A pdb=" N PHE D 575 " --> pdb=" O THR D 571 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN D 584 " --> pdb=" O ARG D 580 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 617 removed outlier: 3.766A pdb=" N ASP D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 647 Processing helix chain 'D' and resid 650 through 663 Processing helix chain 'D' and resid 667 through 681 removed outlier: 3.574A pdb=" N THR D 673 " --> pdb=" O PRO D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 710 Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'E' and resid 58 through 76 removed outlier: 3.587A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 105 Processing helix chain 'E' and resid 106 through 120 removed outlier: 3.566A pdb=" N LEU E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 167 removed outlier: 3.887A pdb=" N LEU E 162 " --> pdb=" O GLN E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 188 Processing helix chain 'E' and resid 203 through 211 removed outlier: 4.124A pdb=" N ILE E 208 " --> pdb=" O ASP E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 223 Processing helix chain 'E' and resid 228 through 265 Proline residue: E 237 - end of helix Proline residue: E 241 - end of helix removed outlier: 3.774A pdb=" N PHE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP E 256 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE E 257 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 278 Processing helix chain 'E' and resid 285 through 313 removed outlier: 3.698A pdb=" N THR E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 299 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE E 311 " --> pdb=" O ASN E 307 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 312 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 330 Processing helix chain 'E' and resid 331 through 342 removed outlier: 4.162A pdb=" N ARG E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 350 through 360 Processing helix chain 'E' and resid 431 through 439 removed outlier: 4.327A pdb=" N ALA E 435 " --> pdb=" O LEU E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 3.950A pdb=" N VAL E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 486 removed outlier: 3.627A pdb=" N GLN E 467 " --> pdb=" O HIS E 463 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER E 470 " --> pdb=" O ASN E 466 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE E 485 " --> pdb=" O MET E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 501 Processing helix chain 'E' and resid 503 through 524 removed outlier: 3.503A pdb=" N ILE E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN E 509 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU E 515 " --> pdb=" O ALA E 511 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 516 " --> pdb=" O ASN E 512 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET E 519 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 524 " --> pdb=" O GLU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 555 removed outlier: 3.964A pdb=" N MET E 531 " --> pdb=" O ASP E 527 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP E 532 " --> pdb=" O PRO E 528 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 539 " --> pdb=" O LEU E 535 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN E 540 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN E 545 " --> pdb=" O LEU E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 Processing helix chain 'E' and resid 572 through 585 removed outlier: 3.598A pdb=" N GLN E 584 " --> pdb=" O ARG E 580 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 585 " --> pdb=" O MET E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 617 removed outlier: 3.822A pdb=" N ASP E 602 " --> pdb=" O ALA E 598 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP E 612 " --> pdb=" O PHE E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 633 Processing helix chain 'E' and resid 637 through 647 Processing helix chain 'E' and resid 650 through 664 Processing helix chain 'E' and resid 667 through 681 Processing helix chain 'E' and resid 682 through 708 Processing helix chain 'E' and resid 713 through 723 Processing helix chain 'F' and resid 61 through 76 Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 102 through 121 removed outlier: 3.751A pdb=" N PHE F 117 " --> pdb=" O PHE F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 3.629A pdb=" N LYS F 155 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER F 159 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET F 161 " --> pdb=" O ILE F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 189 removed outlier: 4.179A pdb=" N VAL F 175 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 176 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 188 " --> pdb=" O ILE F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 210 removed outlier: 4.181A pdb=" N TYR F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 203 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR F 205 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE F 208 " --> pdb=" O ASP F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 224 Processing helix chain 'F' and resid 228 through 239 Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 239 through 254 removed outlier: 4.021A pdb=" N TYR F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 removed outlier: 3.685A pdb=" N GLU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 285 through 311 removed outlier: 3.983A pdb=" N GLN F 303 " --> pdb=" O GLN F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 318 removed outlier: 4.082A pdb=" N GLU F 318 " --> pdb=" O GLU F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 329 removed outlier: 3.520A pdb=" N THR F 324 " --> pdb=" O ILE F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 341 removed outlier: 3.921A pdb=" N TRP F 339 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 362 Processing helix chain 'F' and resid 432 through 441 removed outlier: 3.634A pdb=" N ILE F 438 " --> pdb=" O PRO F 434 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER F 440 " --> pdb=" O GLU F 436 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU F 441 " --> pdb=" O TYR F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 456 removed outlier: 4.077A pdb=" N VAL F 456 " --> pdb=" O ASP F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 486 removed outlier: 3.589A pdb=" N SER F 470 " --> pdb=" O ASN F 466 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 485 " --> pdb=" O MET F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 502 removed outlier: 3.670A pdb=" N ILE F 501 " --> pdb=" O SER F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 522 removed outlier: 3.738A pdb=" N THR F 507 " --> pdb=" O GLY F 503 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU F 515 " --> pdb=" O ALA F 511 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 516 " --> pdb=" O ASN F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 555 removed outlier: 3.879A pdb=" N MET F 531 " --> pdb=" O ASP F 527 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP F 532 " --> pdb=" O PRO F 528 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN F 540 " --> pdb=" O GLU F 536 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE F 547 " --> pdb=" O ILE F 543 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 572 through 585 removed outlier: 3.873A pdb=" N GLN F 584 " --> pdb=" O ARG F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 618 Processing helix chain 'F' and resid 628 through 632 Processing helix chain 'F' and resid 637 through 647 Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.672A pdb=" N GLN F 658 " --> pdb=" O ARG F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 681 removed outlier: 3.594A pdb=" N THR F 673 " --> pdb=" O PRO F 669 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 674 " --> pdb=" O LEU F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 709 removed outlier: 3.568A pdb=" N VAL F 703 " --> pdb=" O THR F 699 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 708 " --> pdb=" O SER F 704 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR F 709 " --> pdb=" O LEU F 705 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 724 Processing sheet with id=AA1, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AA5, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AA6, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=AA7, first strand: chain 'F' and resid 86 through 87 1761 hydrogen bonds defined for protein. 5229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4814 1.32 - 1.44: 7679 1.44 - 1.57: 16211 1.57 - 1.70: 0 1.70 - 1.82: 285 Bond restraints: 28989 Sorted by residual: bond pdb=" C PRO B 334 " pdb=" O PRO B 334 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" N VAL A 459 " pdb=" CA VAL A 459 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" N VAL A 296 " pdb=" CA VAL A 296 " ideal model delta sigma weight residual 1.459 1.499 -0.039 1.23e-02 6.61e+03 1.03e+01 bond pdb=" N VAL B 459 " pdb=" CA VAL B 459 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.98e+00 bond pdb=" N ASP D 428 " pdb=" CA ASP D 428 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.49e+00 ... (remaining 28984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 37463 2.04 - 4.09: 1476 4.09 - 6.13: 204 6.13 - 8.18: 35 8.18 - 10.22: 9 Bond angle restraints: 39187 Sorted by residual: angle pdb=" N ILE B 308 " pdb=" CA ILE B 308 " pdb=" C ILE B 308 " ideal model delta sigma weight residual 111.58 104.11 7.47 1.06e+00 8.90e-01 4.97e+01 angle pdb=" N THR F 297 " pdb=" CA THR F 297 " pdb=" C THR F 297 " ideal model delta sigma weight residual 111.28 104.28 7.00 1.09e+00 8.42e-01 4.12e+01 angle pdb=" N PHE F 311 " pdb=" CA PHE F 311 " pdb=" C PHE F 311 " ideal model delta sigma weight residual 111.28 104.33 6.95 1.09e+00 8.42e-01 4.06e+01 angle pdb=" N VAL F 296 " pdb=" CA VAL F 296 " pdb=" C VAL F 296 " ideal model delta sigma weight residual 111.00 104.45 6.55 1.09e+00 8.42e-01 3.62e+01 angle pdb=" C THR D 32 " pdb=" CA THR D 32 " pdb=" CB THR D 32 " ideal model delta sigma weight residual 116.54 109.82 6.72 1.15e+00 7.56e-01 3.42e+01 ... (remaining 39182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14189 17.96 - 35.92: 2233 35.92 - 53.88: 770 53.88 - 71.84: 188 71.84 - 89.80: 56 Dihedral angle restraints: 17436 sinusoidal: 7220 harmonic: 10216 Sorted by residual: dihedral pdb=" CA VAL F 456 " pdb=" C VAL F 456 " pdb=" N TRP F 457 " pdb=" CA TRP F 457 " ideal model delta harmonic sigma weight residual 180.00 154.03 25.97 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA CYS E 48 " pdb=" C CYS E 48 " pdb=" N SER E 49 " pdb=" CA SER E 49 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA PHE D 76 " pdb=" C PHE D 76 " pdb=" N ILE D 77 " pdb=" CA ILE D 77 " ideal model delta harmonic sigma weight residual 180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 17433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3447 0.055 - 0.109: 679 0.109 - 0.164: 108 0.164 - 0.218: 28 0.218 - 0.273: 11 Chirality restraints: 4273 Sorted by residual: chirality pdb=" CA TYR A 304 " pdb=" N TYR A 304 " pdb=" C TYR A 304 " pdb=" CB TYR A 304 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA GLN C 302 " pdb=" N GLN C 302 " pdb=" C GLN C 302 " pdb=" CB GLN C 302 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE E 28 " pdb=" CA ILE E 28 " pdb=" CG1 ILE E 28 " pdb=" CG2 ILE E 28 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4270 not shown) Planarity restraints: 5063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 303 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLN A 303 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN A 303 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 304 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 262 " 0.019 2.00e-02 2.50e+03 2.96e-02 1.54e+01 pdb=" CG PHE A 262 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 262 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 262 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 262 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 262 " -0.025 2.00e-02 2.50e+03 pdb=" CZ PHE A 262 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 295 " -0.018 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C GLU A 295 " 0.060 2.00e-02 2.50e+03 pdb=" O GLU A 295 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 296 " -0.020 2.00e-02 2.50e+03 ... (remaining 5060 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 877 2.69 - 3.24: 30060 3.24 - 3.80: 47923 3.80 - 4.35: 65213 4.35 - 4.90: 98277 Nonbonded interactions: 242350 Sorted by model distance: nonbonded pdb=" O HIS A 347 " pdb=" ND1 HIS A 347 " model vdw 2.140 3.120 nonbonded pdb=" NH1 ARG D 55 " pdb=" O HIS D 56 " model vdw 2.172 3.120 nonbonded pdb=" OD1 ASN D 273 " pdb=" N TRP D 276 " model vdw 2.203 3.120 nonbonded pdb=" OG SER A 85 " pdb=" OE1 GLU A 114 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG F 55 " pdb=" O HIS F 56 " model vdw 2.204 3.120 ... (remaining 242345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 185 or resid 205 through 251 or (resid 252 and \ (name N or name CA or name C or name O or name CB )) or resid 253 through 291 or \ (resid 292 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 3 through 360 or resid 427 through 618 or resid 632 through 724)) selection = (chain 'B' and (resid 28 through 34 or resid 43 through 50 or resid 58 through 1 \ 21 or resid 145 through 185 or resid 205 through 251 or (resid 252 and (name N o \ r name CA or name C or name O or name CB )) or resid 253 through 291 or (resid 2 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 293 through \ 317 or resid 322 through 360 or resid 427 through 618 or resid 632 through 724) \ ) selection = (chain 'C' and (resid 28 through 34 or resid 43 through 56 or resid 59 through 1 \ 21 or resid 145 through 251 or (resid 252 and (name N or name CA or name C or na \ me O or name CB )) or resid 253 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 317 or resid 322 through \ 360 or resid 427 through 724)) selection = (chain 'D' and (resid 28 through 34 or resid 43 through 50 or resid 58 through 1 \ 85 or resid 205 through 251 or (resid 252 and (name N or name CA or name C or na \ me O or name CB )) or resid 253 through 317 or resid 322 through 360 or resid 42 \ 7 through 618 or resid 632 through 724)) selection = (chain 'E' and (resid 28 through 34 or resid 43 through 50 or resid 58 through 1 \ 85 or resid 205 through 251 or (resid 252 and (name N or name CA or name C or na \ me O or name CB )) or resid 253 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 317 or resid 322 through \ 618 or resid 632 through 724)) selection = (chain 'F' and (resid 28 through 34 or resid 43 through 50 or resid 58 through 1 \ 85 or resid 205 through 291 or (resid 292 and (name N or name CA or name C or na \ me O or name CB )) or resid 293 through 317 or resid 322 through 360 or resid 42 \ 7 through 618 or resid 632 through 724)) } 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.510 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28989 Z= 0.299 Angle : 0.888 10.221 39187 Z= 0.576 Chirality : 0.047 0.273 4273 Planarity : 0.006 0.117 5063 Dihedral : 20.290 89.804 10824 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.33 % Favored : 92.80 % Rotamer: Outliers : 8.03 % Allowed : 29.06 % Favored : 62.92 % 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 aren not related in a simple way. whole: -2.20 (0.14), residues: 3444 helix: -0.86 (0.10), residues: 2357 sheet: None (None), residues: 0 loop : -2.61 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 220 TYR 0.031 0.002 TYR D 614 PHE 0.056 0.002 PHE A 262 TRP 0.048 0.002 TRP D 180 HIS 0.017 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00467 (28989) covalent geometry : angle 0.88760 (39187) hydrogen bonds : bond 0.31374 ( 1761) hydrogen bonds : angle 8.51747 ( 5229) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 658 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.9026 (t) cc_final: 0.8760 (t) REVERT: A 73 TRP cc_start: 0.7362 (t-100) cc_final: 0.6981 (t-100) REVERT: A 183 MET cc_start: 0.7931 (ttp) cc_final: 0.7440 (ttp) REVERT: A 219 MET cc_start: 0.8626 (mmm) cc_final: 0.7919 (mmm) REVERT: A 256 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7576 (p0) REVERT: A 428 ASP cc_start: 0.7413 (m-30) cc_final: 0.6744 (m-30) REVERT: A 444 LYS cc_start: 0.6766 (pttm) cc_final: 0.6181 (mtmm) REVERT: A 489 SER cc_start: 0.8811 (t) cc_final: 0.8464 (p) REVERT: A 556 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: A 557 CYS cc_start: 0.8336 (t) cc_final: 0.8087 (t) REVERT: A 599 SER cc_start: 0.8742 (m) cc_final: 0.8465 (t) REVERT: A 616 ASN cc_start: 0.8317 (m-40) cc_final: 0.8086 (m-40) REVERT: A 632 ASP cc_start: 0.7751 (t0) cc_final: 0.7139 (t70) REVERT: A 675 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8485 (tt) REVERT: A 679 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7603 (mtm-85) REVERT: B 54 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7295 (mtm110) REVERT: B 118 LEU cc_start: 0.8685 (mt) cc_final: 0.8315 (mt) REVERT: B 258 GLU cc_start: 0.7935 (tp30) cc_final: 0.7709 (tm-30) REVERT: B 487 ASP cc_start: 0.8053 (m-30) cc_final: 0.7767 (m-30) REVERT: B 565 ASP cc_start: 0.8277 (m-30) cc_final: 0.7896 (m-30) REVERT: B 590 GLN cc_start: 0.5020 (OUTLIER) cc_final: 0.4601 (mp10) REVERT: B 680 GLN cc_start: 0.8709 (tm-30) cc_final: 0.7966 (tm-30) REVERT: C 73 TRP cc_start: 0.7663 (t-100) cc_final: 0.7402 (t-100) REVERT: C 164 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6966 (mp0) REVERT: C 183 MET cc_start: 0.6784 (tmm) cc_final: 0.6470 (tmm) REVERT: C 444 LYS cc_start: 0.6665 (pttm) cc_final: 0.6243 (mtmm) REVERT: C 459 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7651 (p) REVERT: C 483 ASP cc_start: 0.8118 (t0) cc_final: 0.7546 (t0) REVERT: C 486 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: C 487 ASP cc_start: 0.7558 (m-30) cc_final: 0.7184 (m-30) REVERT: C 593 LEU cc_start: 0.7540 (mt) cc_final: 0.7161 (mm) REVERT: C 599 SER cc_start: 0.8714 (m) cc_final: 0.8322 (p) REVERT: C 611 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8020 (mtp85) REVERT: C 685 GLU cc_start: 0.7962 (mp0) cc_final: 0.7685 (mm-30) REVERT: D 98 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6554 (pp) REVERT: D 174 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: D 256 ASP cc_start: 0.6417 (OUTLIER) cc_final: 0.6025 (p0) REVERT: D 271 MET cc_start: 0.3280 (ttm) cc_final: 0.1120 (ttm) REVERT: D 279 MET cc_start: 0.5477 (mmp) cc_final: 0.5078 (mmp) REVERT: D 280 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7814 (pp30) REVERT: D 285 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7378 (p0) REVERT: D 295 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: D 315 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5582 (mp0) REVERT: D 447 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8262 (mpt180) REVERT: D 517 ASP cc_start: 0.7808 (t0) cc_final: 0.7547 (t0) REVERT: D 537 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7482 (mm-30) REVERT: D 554 ASN cc_start: 0.8007 (m-40) cc_final: 0.7787 (m110) REVERT: D 595 THR cc_start: 0.8456 (m) cc_final: 0.8217 (p) REVERT: D 614 TYR cc_start: 0.8240 (t80) cc_final: 0.8008 (t80) REVERT: D 672 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: E 58 HIS cc_start: 0.2417 (OUTLIER) cc_final: 0.1302 (m-70) REVERT: E 226 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6117 (ppp) REVERT: E 290 LYS cc_start: 0.8366 (mmtt) cc_final: 0.7962 (mmtt) REVERT: E 301 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7498 (tp30) REVERT: E 447 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7982 (mpt180) REVERT: E 483 ASP cc_start: 0.8383 (t0) cc_final: 0.8036 (t0) REVERT: E 537 GLU cc_start: 0.8054 (tp30) cc_final: 0.7572 (tp30) REVERT: E 560 GLU cc_start: 0.7820 (tt0) cc_final: 0.7224 (tt0) REVERT: E 582 MET cc_start: 0.8854 (mtp) cc_final: 0.8559 (mtp) REVERT: E 594 GLU cc_start: 0.7677 (tp30) cc_final: 0.7451 (tp30) REVERT: E 635 LYS cc_start: 0.7217 (mptm) cc_final: 0.6930 (mptm) REVERT: E 640 LEU cc_start: 0.8718 (tp) cc_final: 0.8505 (tt) REVERT: E 646 SER cc_start: 0.8592 (m) cc_final: 0.8297 (p) REVERT: E 672 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7869 (mm-30) REVERT: E 685 GLU cc_start: 0.7977 (mp0) cc_final: 0.7713 (mm-30) REVERT: E 686 TYR cc_start: 0.8277 (t80) cc_final: 0.7429 (t80) REVERT: E 688 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7968 (mt-10) REVERT: F 75 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: F 90 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.3502 (mp0) REVERT: F 158 GLN cc_start: 0.8068 (tp40) cc_final: 0.7829 (tm-30) REVERT: F 160 LYS cc_start: 0.8181 (tptp) cc_final: 0.7923 (tptp) REVERT: F 219 MET cc_start: 0.8343 (mtm) cc_final: 0.7948 (mtm) REVERT: F 301 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: F 305 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8174 (tt) REVERT: F 308 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7888 (mp) REVERT: F 324 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.7332 (p) REVERT: F 329 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8273 (tm-30) REVERT: F 459 VAL cc_start: 0.8500 (t) cc_final: 0.8269 (m) REVERT: F 484 ASP cc_start: 0.7792 (m-30) cc_final: 0.7565 (m-30) REVERT: F 487 ASP cc_start: 0.7967 (m-30) cc_final: 0.7701 (m-30) REVERT: F 582 MET cc_start: 0.8630 (mtp) cc_final: 0.8283 (mtm) REVERT: F 645 THR cc_start: 0.8684 (m) cc_final: 0.8339 (p) REVERT: F 647 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: F 649 LYS cc_start: 0.8408 (mppt) cc_final: 0.8125 (mppt) REVERT: F 724 LYS cc_start: 0.7749 (mtmp) cc_final: 0.7500 (mttp) outliers start: 249 outliers final: 146 residues processed: 836 average time/residue: 0.1870 time to fit residues: 235.9262 Evaluate side-chains 809 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 637 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 359 HIS Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 601 SER Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 720 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 58 HIS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 342 ARG Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 447 ARG Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 570 LYS Chi-restraints excluded: chain E residue 571 THR Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 625 LYS Chi-restraints excluded: chain E residue 651 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 301 GLU Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 530 CYS Chi-restraints excluded: chain F residue 647 GLN Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 691 MET Chi-restraints excluded: chain F residue 700 ASP Chi-restraints excluded: chain F residue 719 LEU Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 466 ASN B 30 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN D 57 HIS D 280 GLN ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN D 347 HIS D 359 HIS D 506 GLN D 677 HIS ** D 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 677 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.191160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.146262 restraints weight = 48156.433| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.49 r_work: 0.3595 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 28989 Z= 0.211 Angle : 0.730 11.104 39187 Z= 0.384 Chirality : 0.043 0.286 4273 Planarity : 0.006 0.067 5063 Dihedral : 11.261 97.520 4226 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.78 % Favored : 93.79 % Rotamer: Outliers : 8.09 % Allowed : 26.57 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3444 helix: 0.04 (0.10), residues: 2531 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 539 TYR 0.029 0.002 TYR E 300 PHE 0.022 0.002 PHE E 27 TRP 0.029 0.002 TRP E 259 HIS 0.008 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00448 (28989) covalent geometry : angle 0.72955 (39187) hydrogen bonds : bond 0.07545 ( 1761) hydrogen bonds : angle 5.60016 ( 5229) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 673 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.8176 (t) cc_final: 0.7824 (t) REVERT: A 75 GLN cc_start: 0.6631 (tp40) cc_final: 0.6235 (tp40) REVERT: A 76 PHE cc_start: 0.7533 (m-10) cc_final: 0.7190 (m-10) REVERT: A 162 LEU cc_start: 0.8139 (mt) cc_final: 0.7931 (mt) REVERT: A 172 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6854 (ttm170) REVERT: A 219 MET cc_start: 0.8232 (mmm) cc_final: 0.7593 (mmm) REVERT: A 444 LYS cc_start: 0.6489 (pttm) cc_final: 0.6054 (mtmm) REVERT: A 457 TRP cc_start: 0.8082 (m-10) cc_final: 0.6952 (m-10) REVERT: A 489 SER cc_start: 0.8652 (t) cc_final: 0.8367 (p) REVERT: A 532 ASP cc_start: 0.7394 (t0) cc_final: 0.7113 (t0) REVERT: A 557 CYS cc_start: 0.8032 (t) cc_final: 0.7776 (t) REVERT: A 613 ASP cc_start: 0.7990 (m-30) cc_final: 0.7677 (m-30) REVERT: A 616 ASN cc_start: 0.8224 (m-40) cc_final: 0.8008 (m-40) REVERT: A 632 ASP cc_start: 0.7670 (t0) cc_final: 0.7144 (t70) REVERT: A 671 LYS cc_start: 0.8293 (mttt) cc_final: 0.7999 (mptt) REVERT: A 675 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8366 (tt) REVERT: A 721 HIS cc_start: 0.8060 (t70) cc_final: 0.7813 (t70) REVERT: B 118 LEU cc_start: 0.8581 (mt) cc_final: 0.8202 (mt) REVERT: B 146 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6713 (tmm160) REVERT: B 221 PHE cc_start: 0.7909 (t80) cc_final: 0.7386 (t80) REVERT: B 299 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 304 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6844 (p90) REVERT: B 487 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: B 532 ASP cc_start: 0.7530 (m-30) cc_final: 0.7262 (m-30) REVERT: B 565 ASP cc_start: 0.7767 (m-30) cc_final: 0.7352 (m-30) REVERT: B 590 GLN cc_start: 0.5080 (OUTLIER) cc_final: 0.4676 (mp10) REVERT: B 680 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 691 MET cc_start: 0.8218 (ttm) cc_final: 0.8007 (mtp) REVERT: C 73 TRP cc_start: 0.7803 (t-100) cc_final: 0.7495 (t-100) REVERT: C 158 GLN cc_start: 0.8304 (mt0) cc_final: 0.8081 (mt0) REVERT: C 182 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: C 183 MET cc_start: 0.6824 (tmm) cc_final: 0.6413 (tmm) REVERT: C 323 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6078 (mp10) REVERT: C 444 LYS cc_start: 0.6365 (pttm) cc_final: 0.5916 (mtmm) REVERT: C 459 VAL cc_start: 0.7888 (OUTLIER) cc_final: 0.7606 (p) REVERT: C 483 ASP cc_start: 0.8022 (t0) cc_final: 0.7381 (t0) REVERT: C 487 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6888 (m-30) REVERT: C 538 MET cc_start: 0.8112 (mmm) cc_final: 0.7876 (mmp) REVERT: C 570 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7850 (ttmm) REVERT: C 599 SER cc_start: 0.8398 (m) cc_final: 0.8074 (p) REVERT: C 612 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7643 (t0) REVERT: C 672 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7552 (mm-30) REVERT: C 685 GLU cc_start: 0.7254 (mp0) cc_final: 0.7008 (mm-30) REVERT: C 688 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7262 (mt-10) REVERT: D 25 SER cc_start: 0.7064 (OUTLIER) cc_final: 0.6692 (t) REVERT: D 98 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6336 (pp) REVERT: D 105 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7620 (mtm-85) REVERT: D 146 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6881 (tpp-160) REVERT: D 174 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: D 216 ASP cc_start: 0.8222 (t0) cc_final: 0.7782 (t0) REVERT: D 219 MET cc_start: 0.7401 (tmm) cc_final: 0.7159 (tmm) REVERT: D 308 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7091 (mt) REVERT: D 315 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.6005 (mp0) REVERT: D 447 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8025 (mpt180) REVERT: D 538 MET cc_start: 0.7702 (mmm) cc_final: 0.7453 (mmm) REVERT: D 550 TYR cc_start: 0.8300 (t80) cc_final: 0.8004 (t80) REVERT: D 554 ASN cc_start: 0.7930 (m-40) cc_final: 0.7669 (m-40) REVERT: D 568 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.7176 (ttm-80) REVERT: D 633 GLU cc_start: 0.4692 (OUTLIER) cc_final: 0.4425 (mm-30) REVERT: D 649 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7212 (mmtm) REVERT: E 58 HIS cc_start: 0.1717 (OUTLIER) cc_final: 0.0624 (m-70) REVERT: E 70 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6951 (mpt90) REVERT: E 182 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: E 219 MET cc_start: 0.8311 (mtp) cc_final: 0.7462 (mtp) REVERT: E 226 MET cc_start: 0.6598 (ppp) cc_final: 0.6245 (ppp) REVERT: E 271 MET cc_start: 0.0988 (tmm) cc_final: 0.0729 (ttt) REVERT: E 342 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.5419 (mtm180) REVERT: E 475 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8306 (mt) REVERT: E 483 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7880 (t0) REVERT: E 537 GLU cc_start: 0.7830 (tp30) cc_final: 0.7158 (tp30) REVERT: E 566 MET cc_start: 0.8027 (tmm) cc_final: 0.7505 (tmm) REVERT: E 611 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8151 (ttt-90) REVERT: E 615 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8202 (mtpp) REVERT: E 635 LYS cc_start: 0.6974 (mptm) cc_final: 0.6695 (mptm) REVERT: E 646 SER cc_start: 0.8514 (m) cc_final: 0.8202 (p) REVERT: E 672 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7550 (mm-30) REVERT: E 685 GLU cc_start: 0.7438 (mp0) cc_final: 0.7212 (mm-30) REVERT: E 722 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7900 (mtt180) REVERT: F 56 HIS cc_start: 0.5451 (OUTLIER) cc_final: 0.5235 (m90) REVERT: F 64 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5765 (tm-30) REVERT: F 160 LYS cc_start: 0.8074 (tptp) cc_final: 0.7855 (tptp) REVERT: F 166 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8082 (tt) REVERT: F 216 ASP cc_start: 0.8358 (t0) cc_final: 0.8155 (t0) REVERT: F 487 ASP cc_start: 0.7876 (m-30) cc_final: 0.7661 (m-30) REVERT: F 574 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8096 (mp) REVERT: F 616 ASN cc_start: 0.8480 (t0) cc_final: 0.7508 (t0) REVERT: F 649 LYS cc_start: 0.8130 (mppt) cc_final: 0.7925 (mppt) REVERT: F 672 GLU cc_start: 0.7545 (mp0) cc_final: 0.7030 (mp0) outliers start: 251 outliers final: 131 residues processed: 861 average time/residue: 0.1837 time to fit residues: 236.4450 Evaluate side-chains 794 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 631 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 633 GLU Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 58 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 342 ARG Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 611 ARG Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 40 optimal weight: 0.9990 chunk 327 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 303 optimal weight: 8.9990 chunk 266 optimal weight: 0.5980 chunk 162 optimal weight: 0.3980 chunk 24 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 279 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 285 ASN A 336 ASN B 229 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN C 616 ASN C 647 GLN D 463 HIS D 721 HIS E 319 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 554 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.191494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146143 restraints weight = 47826.073| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.44 r_work: 0.3588 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28989 Z= 0.192 Angle : 0.681 12.250 39187 Z= 0.350 Chirality : 0.042 0.244 4273 Planarity : 0.006 0.069 5063 Dihedral : 9.010 72.617 4017 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.97 % Favored : 94.60 % Rotamer: Outliers : 7.32 % Allowed : 26.89 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 3444 helix: 0.54 (0.10), residues: 2537 sheet: None (None), residues: 0 loop : -2.55 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 292 TYR 0.023 0.002 TYR A 300 PHE 0.029 0.002 PHE E 27 TRP 0.023 0.001 TRP F 89 HIS 0.008 0.001 HIS D 463 Details of bonding type rmsd covalent geometry : bond 0.00419 (28989) covalent geometry : angle 0.68091 (39187) hydrogen bonds : bond 0.06448 ( 1761) hydrogen bonds : angle 5.20397 ( 5229) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 651 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7953 (t) cc_final: 0.7410 (t) REVERT: A 73 TRP cc_start: 0.7133 (t-100) cc_final: 0.6899 (t-100) REVERT: A 106 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7102 (tt) REVERT: A 219 MET cc_start: 0.8116 (mmm) cc_final: 0.7530 (mmm) REVERT: A 291 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7140 (ppt170) REVERT: A 426 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6321 (mm) REVERT: A 444 LYS cc_start: 0.6476 (pttm) cc_final: 0.6083 (mtmm) REVERT: A 457 TRP cc_start: 0.8043 (m-10) cc_final: 0.6925 (m-10) REVERT: A 484 ASP cc_start: 0.8121 (m-30) cc_final: 0.7793 (m-30) REVERT: A 489 SER cc_start: 0.8629 (t) cc_final: 0.8317 (p) REVERT: A 532 ASP cc_start: 0.7315 (t0) cc_final: 0.7045 (t0) REVERT: A 557 CYS cc_start: 0.8007 (t) cc_final: 0.7768 (t) REVERT: A 632 ASP cc_start: 0.7708 (t0) cc_final: 0.7149 (t70) REVERT: A 671 LYS cc_start: 0.8312 (mttt) cc_final: 0.8045 (mptt) REVERT: A 688 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7452 (mt-10) REVERT: A 696 GLU cc_start: 0.7999 (tp30) cc_final: 0.7696 (tp30) REVERT: A 721 HIS cc_start: 0.8129 (t70) cc_final: 0.7886 (t70) REVERT: B 54 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.6385 (mtm-85) REVERT: B 72 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7065 (t0) REVERT: B 75 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: B 105 ARG cc_start: 0.7802 (ptp90) cc_final: 0.7268 (ptp90) REVERT: B 118 LEU cc_start: 0.8619 (mt) cc_final: 0.8274 (mt) REVERT: B 146 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6810 (tmm160) REVERT: B 174 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: B 220 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7567 (mmm-85) REVERT: B 221 PHE cc_start: 0.7846 (t80) cc_final: 0.7209 (t80) REVERT: B 258 GLU cc_start: 0.7773 (tp30) cc_final: 0.7552 (tm-30) REVERT: B 487 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: B 565 ASP cc_start: 0.7789 (m-30) cc_final: 0.7409 (m-30) REVERT: B 590 GLN cc_start: 0.5171 (OUTLIER) cc_final: 0.4751 (mp10) REVERT: B 680 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 723 LEU cc_start: 0.8633 (tp) cc_final: 0.8430 (mp) REVERT: C 73 TRP cc_start: 0.7852 (t-100) cc_final: 0.7520 (t-100) REVERT: C 155 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7788 (mtmm) REVERT: C 183 MET cc_start: 0.6949 (tmm) cc_final: 0.6561 (tmm) REVERT: C 217 MET cc_start: 0.8410 (mpp) cc_final: 0.8059 (tpp) REVERT: C 444 LYS cc_start: 0.6408 (pttm) cc_final: 0.6098 (mtmm) REVERT: C 459 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7499 (p) REVERT: C 483 ASP cc_start: 0.8020 (t0) cc_final: 0.7674 (t0) REVERT: C 487 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: C 519 MET cc_start: 0.6979 (mtm) cc_final: 0.6391 (mtm) REVERT: C 529 ARG cc_start: 0.7516 (mpt-90) cc_final: 0.7174 (mpt-90) REVERT: C 566 MET cc_start: 0.8249 (tmm) cc_final: 0.7752 (ttp) REVERT: C 570 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7833 (ttmm) REVERT: C 599 SER cc_start: 0.8282 (m) cc_final: 0.7952 (p) REVERT: C 612 ASP cc_start: 0.7956 (m-30) cc_final: 0.7648 (t0) REVERT: C 613 ASP cc_start: 0.7877 (m-30) cc_final: 0.7655 (m-30) REVERT: C 672 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7588 (mm-30) REVERT: C 688 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7235 (mt-10) REVERT: D 89 TRP cc_start: 0.6820 (OUTLIER) cc_final: 0.6224 (m-90) REVERT: D 98 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6423 (pp) REVERT: D 105 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7616 (mtm-85) REVERT: D 146 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6830 (tpp-160) REVERT: D 174 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: D 219 MET cc_start: 0.7616 (tmm) cc_final: 0.7173 (tmm) REVERT: D 279 MET cc_start: 0.4635 (mmp) cc_final: 0.4282 (mmp) REVERT: D 290 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8139 (ptpp) REVERT: D 308 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7176 (mt) REVERT: D 436 GLU cc_start: 0.7366 (pp20) cc_final: 0.7063 (pp20) REVERT: D 447 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8063 (mpt180) REVERT: D 484 ASP cc_start: 0.7791 (m-30) cc_final: 0.7454 (m-30) REVERT: D 517 ASP cc_start: 0.7451 (t0) cc_final: 0.7190 (t0) REVERT: D 554 ASN cc_start: 0.8043 (m-40) cc_final: 0.7719 (m-40) REVERT: D 568 ARG cc_start: 0.7382 (ttm-80) cc_final: 0.7091 (ttm-80) REVERT: D 606 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7326 (mt-10) REVERT: D 633 GLU cc_start: 0.4681 (OUTLIER) cc_final: 0.4428 (mm-30) REVERT: E 58 HIS cc_start: 0.1727 (OUTLIER) cc_final: 0.0870 (m-70) REVERT: E 70 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6936 (mpt90) REVERT: E 114 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6610 (pt0) REVERT: E 182 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: E 226 MET cc_start: 0.6425 (ppp) cc_final: 0.6035 (ppp) REVERT: E 271 MET cc_start: 0.0272 (tmm) cc_final: -0.0081 (ttt) REVERT: E 475 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8432 (mt) REVERT: E 483 ASP cc_start: 0.8265 (t0) cc_final: 0.7850 (t0) REVERT: E 493 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6548 (mpp-170) REVERT: E 537 GLU cc_start: 0.7871 (tp30) cc_final: 0.7554 (tp30) REVERT: E 550 TYR cc_start: 0.8600 (t80) cc_final: 0.7977 (t80) REVERT: E 560 GLU cc_start: 0.7023 (tt0) cc_final: 0.6805 (tt0) REVERT: E 570 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7873 (ttpp) REVERT: E 611 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7972 (ttt-90) REVERT: E 612 ASP cc_start: 0.8123 (m-30) cc_final: 0.7834 (t0) REVERT: E 614 TYR cc_start: 0.8542 (t80) cc_final: 0.8277 (t80) REVERT: E 615 LYS cc_start: 0.8450 (mmmm) cc_final: 0.8196 (mtpp) REVERT: E 635 LYS cc_start: 0.7020 (mptm) cc_final: 0.6683 (mptm) REVERT: E 646 SER cc_start: 0.8527 (m) cc_final: 0.8229 (p) REVERT: E 706 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7187 (mt-10) REVERT: E 722 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7956 (mtt180) REVERT: F 64 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5945 (tm-30) REVERT: F 68 ARG cc_start: 0.7429 (ttp-110) cc_final: 0.7028 (ttp-110) REVERT: F 219 MET cc_start: 0.7786 (mtm) cc_final: 0.7458 (mtm) REVERT: F 251 ASP cc_start: 0.5925 (OUTLIER) cc_final: 0.5181 (t0) REVERT: F 271 MET cc_start: 0.0811 (mmt) cc_final: 0.0397 (mmt) REVERT: F 272 THR cc_start: 0.5669 (OUTLIER) cc_final: 0.5037 (m) REVERT: F 322 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6832 (mt) REVERT: F 428 ASP cc_start: 0.7339 (m-30) cc_final: 0.7015 (m-30) REVERT: F 483 ASP cc_start: 0.7438 (m-30) cc_final: 0.7031 (m-30) REVERT: F 487 ASP cc_start: 0.7886 (m-30) cc_final: 0.7653 (m-30) REVERT: F 574 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8105 (mp) REVERT: F 616 ASN cc_start: 0.8545 (t0) cc_final: 0.8260 (t0) REVERT: F 635 LYS cc_start: 0.7253 (mmpt) cc_final: 0.7017 (mmpt) REVERT: F 649 LYS cc_start: 0.8271 (mppt) cc_final: 0.8056 (mppt) REVERT: F 672 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7094 (mp0) outliers start: 227 outliers final: 123 residues processed: 817 average time/residue: 0.1768 time to fit residues: 217.4954 Evaluate side-chains 777 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 620 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 621 TYR Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 633 GLU Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 699 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 58 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 611 ARG Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 87 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 283 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 219 optimal weight: 0.1980 chunk 91 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 243 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN A 466 ASN ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS C 506 GLN C 616 ASN C 647 GLN D 506 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN F 121 ASN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.192238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147023 restraints weight = 47916.096| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.38 r_work: 0.3612 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28989 Z= 0.164 Angle : 0.653 14.957 39187 Z= 0.331 Chirality : 0.040 0.230 4273 Planarity : 0.005 0.114 5063 Dihedral : 8.051 72.445 3963 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.02 % Favored : 94.57 % Rotamer: Outliers : 7.45 % Allowed : 26.12 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.15), residues: 3444 helix: 0.84 (0.10), residues: 2558 sheet: None (None), residues: 0 loop : -2.53 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 539 TYR 0.029 0.002 TYR B 304 PHE 0.018 0.002 PHE E 27 TRP 0.015 0.001 TRP C 180 HIS 0.012 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00362 (28989) covalent geometry : angle 0.65275 (39187) hydrogen bonds : bond 0.05512 ( 1761) hydrogen bonds : angle 4.89447 ( 5229) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 624 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.8063 (t) cc_final: 0.7535 (t) REVERT: A 73 TRP cc_start: 0.7152 (t-100) cc_final: 0.6824 (t-100) REVERT: A 106 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6963 (tt) REVERT: A 162 LEU cc_start: 0.8178 (mt) cc_final: 0.7959 (mm) REVERT: A 183 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7057 (ttp) REVERT: A 219 MET cc_start: 0.7895 (mmm) cc_final: 0.7354 (mmm) REVERT: A 291 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7091 (ppt170) REVERT: A 426 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6423 (mm) REVERT: A 444 LYS cc_start: 0.6392 (pttm) cc_final: 0.5998 (mtmm) REVERT: A 457 TRP cc_start: 0.8041 (m-10) cc_final: 0.6947 (m-10) REVERT: A 484 ASP cc_start: 0.8101 (m-30) cc_final: 0.7765 (m-30) REVERT: A 489 SER cc_start: 0.8620 (t) cc_final: 0.8286 (p) REVERT: A 532 ASP cc_start: 0.7201 (t0) cc_final: 0.6942 (t0) REVERT: A 671 LYS cc_start: 0.8288 (mttt) cc_final: 0.8052 (mptt) REVERT: A 688 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7173 (mt-10) REVERT: A 721 HIS cc_start: 0.8117 (t70) cc_final: 0.7863 (t70) REVERT: B 66 SER cc_start: 0.7873 (OUTLIER) cc_final: 0.7573 (t) REVERT: B 75 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: B 118 LEU cc_start: 0.8576 (mt) cc_final: 0.8287 (mt) REVERT: B 146 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6800 (tmm160) REVERT: B 158 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7389 (tm-30) REVERT: B 479 SER cc_start: 0.8539 (t) cc_final: 0.8225 (p) REVERT: B 487 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: B 565 ASP cc_start: 0.7719 (m-30) cc_final: 0.7323 (m-30) REVERT: B 590 GLN cc_start: 0.5141 (OUTLIER) cc_final: 0.4744 (mp10) REVERT: B 593 LEU cc_start: 0.7355 (mp) cc_final: 0.7090 (mt) REVERT: B 680 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 723 LEU cc_start: 0.8611 (tp) cc_final: 0.8396 (mp) REVERT: C 114 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.4995 (pt0) REVERT: C 155 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7779 (mtmm) REVERT: C 183 MET cc_start: 0.6840 (tmm) cc_final: 0.6467 (tmm) REVERT: C 217 MET cc_start: 0.8285 (mpp) cc_final: 0.7914 (tpp) REVERT: C 444 LYS cc_start: 0.6414 (pttm) cc_final: 0.6046 (mtmm) REVERT: C 483 ASP cc_start: 0.7988 (t0) cc_final: 0.7341 (t0) REVERT: C 487 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6801 (m-30) REVERT: C 529 ARG cc_start: 0.7495 (mpt-90) cc_final: 0.7127 (mpt-90) REVERT: C 570 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7834 (ttmm) REVERT: C 606 GLU cc_start: 0.7286 (tt0) cc_final: 0.6929 (mt-10) REVERT: C 612 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7665 (t0) REVERT: C 693 GLU cc_start: 0.7293 (tp30) cc_final: 0.7076 (tm-30) REVERT: D 33 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7442 (pp) REVERT: D 89 TRP cc_start: 0.6808 (OUTLIER) cc_final: 0.6183 (m-90) REVERT: D 98 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6438 (pp) REVERT: D 162 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7997 (tt) REVERT: D 219 MET cc_start: 0.7645 (tmm) cc_final: 0.7157 (tmm) REVERT: D 220 ARG cc_start: 0.7500 (ptm160) cc_final: 0.6941 (ttm170) REVERT: D 290 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8418 (ptpp) REVERT: D 308 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7230 (mt) REVERT: D 436 GLU cc_start: 0.7352 (pp20) cc_final: 0.7043 (pp20) REVERT: D 444 LYS cc_start: 0.7676 (mtmt) cc_final: 0.6885 (mtmm) REVERT: D 447 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8053 (mpt180) REVERT: D 484 ASP cc_start: 0.7667 (m-30) cc_final: 0.7432 (m-30) REVERT: D 538 MET cc_start: 0.7792 (mmm) cc_final: 0.7307 (mmm) REVERT: D 554 ASN cc_start: 0.8046 (m-40) cc_final: 0.7775 (m-40) REVERT: D 568 ARG cc_start: 0.7328 (ttm-80) cc_final: 0.7038 (ttm-80) REVERT: D 606 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7298 (mt-10) REVERT: D 633 GLU cc_start: 0.4695 (OUTLIER) cc_final: 0.4460 (mm-30) REVERT: E 58 HIS cc_start: 0.2092 (OUTLIER) cc_final: 0.1298 (m-70) REVERT: E 70 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6932 (mpt90) REVERT: E 114 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6708 (pt0) REVERT: E 226 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5663 (ppp) REVERT: E 227 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.5994 (mm) REVERT: E 475 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8440 (mt) REVERT: E 483 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7772 (t0) REVERT: E 493 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6359 (mpp-170) REVERT: E 537 GLU cc_start: 0.7834 (tp30) cc_final: 0.7522 (tp30) REVERT: E 560 GLU cc_start: 0.6990 (tt0) cc_final: 0.6748 (tt0) REVERT: E 566 MET cc_start: 0.8052 (tmm) cc_final: 0.7518 (tmm) REVERT: E 570 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7817 (ttpp) REVERT: E 611 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7997 (ttt-90) REVERT: E 612 ASP cc_start: 0.8117 (m-30) cc_final: 0.7786 (t0) REVERT: E 614 TYR cc_start: 0.8434 (t80) cc_final: 0.8108 (t80) REVERT: E 615 LYS cc_start: 0.8415 (mmmm) cc_final: 0.8160 (mtpp) REVERT: E 616 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8161 (t0) REVERT: E 635 LYS cc_start: 0.6984 (mptm) cc_final: 0.6667 (mptm) REVERT: E 646 SER cc_start: 0.8504 (m) cc_final: 0.8220 (p) REVERT: E 693 GLU cc_start: 0.7236 (tp30) cc_final: 0.7016 (tp30) REVERT: E 706 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7314 (mt-10) REVERT: E 722 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7927 (mtt180) REVERT: F 64 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5975 (tm-30) REVERT: F 68 ARG cc_start: 0.7512 (ttp-110) cc_final: 0.7139 (ttp-110) REVERT: F 98 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7500 (pp) REVERT: F 219 MET cc_start: 0.7701 (mtm) cc_final: 0.7387 (mtm) REVERT: F 292 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7406 (mtp180) REVERT: F 322 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6717 (mt) REVERT: F 428 ASP cc_start: 0.7251 (m-30) cc_final: 0.6996 (m-30) REVERT: F 483 ASP cc_start: 0.7432 (m-30) cc_final: 0.6955 (m-30) REVERT: F 487 ASP cc_start: 0.7878 (m-30) cc_final: 0.7654 (m-30) REVERT: F 574 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8058 (mp) REVERT: F 616 ASN cc_start: 0.8576 (t0) cc_final: 0.7674 (t0) REVERT: F 672 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: F 724 LYS cc_start: 0.7715 (mtmp) cc_final: 0.7494 (mttp) outliers start: 231 outliers final: 133 residues processed: 795 average time/residue: 0.1809 time to fit residues: 214.2016 Evaluate side-chains 787 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 616 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain C residue 582 MET Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 633 GLU Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 699 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 58 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 611 ARG Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 647 GLN Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 719 LEU Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 246 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 121 optimal weight: 0.0970 chunk 197 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 238 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 316 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN A 590 GLN B 232 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 616 ASN D 336 ASN D 545 GLN D 658 GLN E 58 HIS F 329 GLN ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.192625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147291 restraints weight = 47696.517| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.55 r_work: 0.3603 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28989 Z= 0.146 Angle : 0.635 15.368 39187 Z= 0.319 Chirality : 0.039 0.175 4273 Planarity : 0.005 0.062 5063 Dihedral : 7.796 71.001 3947 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.97 % Favored : 94.69 % Rotamer: Outliers : 6.35 % Allowed : 27.57 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.15), residues: 3444 helix: 1.04 (0.11), residues: 2579 sheet: None (None), residues: 0 loop : -2.43 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 539 TYR 0.034 0.001 TYR A 300 PHE 0.033 0.001 PHE E 27 TRP 0.041 0.001 TRP E 180 HIS 0.015 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00321 (28989) covalent geometry : angle 0.63505 (39187) hydrogen bonds : bond 0.05030 ( 1761) hydrogen bonds : angle 4.68671 ( 5229) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 624 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7990 (t) cc_final: 0.7527 (t) REVERT: A 73 TRP cc_start: 0.7239 (t-100) cc_final: 0.6975 (t-100) REVERT: A 183 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7291 (ttp) REVERT: A 219 MET cc_start: 0.7970 (mmm) cc_final: 0.7390 (mmm) REVERT: A 291 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6988 (ppt170) REVERT: A 426 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6481 (mm) REVERT: A 444 LYS cc_start: 0.6287 (pttm) cc_final: 0.5973 (mtmm) REVERT: A 484 ASP cc_start: 0.8140 (m-30) cc_final: 0.7816 (m-30) REVERT: A 489 SER cc_start: 0.8626 (t) cc_final: 0.8292 (p) REVERT: A 532 ASP cc_start: 0.7159 (t0) cc_final: 0.6908 (t0) REVERT: A 632 ASP cc_start: 0.7487 (t0) cc_final: 0.7000 (t70) REVERT: A 688 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 696 GLU cc_start: 0.7989 (tp30) cc_final: 0.7732 (tp30) REVERT: A 721 HIS cc_start: 0.8091 (t70) cc_final: 0.7862 (t70) REVERT: B 66 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7615 (t) REVERT: B 75 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: B 118 LEU cc_start: 0.8511 (mt) cc_final: 0.8226 (mt) REVERT: B 146 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6800 (tmm160) REVERT: B 220 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7584 (mmm-85) REVERT: B 230 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: B 299 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 487 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: B 565 ASP cc_start: 0.7732 (m-30) cc_final: 0.7352 (m-30) REVERT: B 590 GLN cc_start: 0.5146 (OUTLIER) cc_final: 0.4764 (mp10) REVERT: B 680 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7962 (tm-30) REVERT: C 114 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.5070 (pt0) REVERT: C 183 MET cc_start: 0.6864 (tmm) cc_final: 0.6490 (tmm) REVERT: C 217 MET cc_start: 0.8266 (mpp) cc_final: 0.7905 (tpp) REVERT: C 323 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.5875 (mp10) REVERT: C 429 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7329 (pt0) REVERT: C 444 LYS cc_start: 0.6499 (pttm) cc_final: 0.6098 (mtmm) REVERT: C 483 ASP cc_start: 0.8024 (t0) cc_final: 0.7616 (t0) REVERT: C 487 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: C 529 ARG cc_start: 0.7549 (mpt-90) cc_final: 0.7196 (mpt-90) REVERT: C 606 GLU cc_start: 0.7266 (tt0) cc_final: 0.6889 (mt-10) REVERT: C 612 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7673 (t0) REVERT: C 613 ASP cc_start: 0.7887 (m-30) cc_final: 0.7481 (m-30) REVERT: C 693 GLU cc_start: 0.7345 (tp30) cc_final: 0.7103 (tp30) REVERT: D 89 TRP cc_start: 0.6800 (OUTLIER) cc_final: 0.6168 (m-90) REVERT: D 98 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6470 (pp) REVERT: D 156 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7466 (mm-40) REVERT: D 162 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8082 (tt) REVERT: D 220 ARG cc_start: 0.7394 (ptm160) cc_final: 0.6974 (ttm170) REVERT: D 308 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7233 (mt) REVERT: D 428 ASP cc_start: 0.7186 (m-30) cc_final: 0.6955 (m-30) REVERT: D 436 GLU cc_start: 0.7376 (pp20) cc_final: 0.6997 (pp20) REVERT: D 447 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8090 (mpt180) REVERT: D 517 ASP cc_start: 0.7393 (t0) cc_final: 0.7072 (t0) REVERT: D 538 MET cc_start: 0.7736 (mmm) cc_final: 0.7185 (mmm) REVERT: D 565 ASP cc_start: 0.7969 (t0) cc_final: 0.7682 (t0) REVERT: D 568 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.7085 (ttm-80) REVERT: D 606 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7463 (mt-10) REVERT: D 615 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8041 (ttmm) REVERT: D 633 GLU cc_start: 0.4667 (OUTLIER) cc_final: 0.4466 (mm-30) REVERT: E 58 HIS cc_start: 0.1680 (OUTLIER) cc_final: 0.0880 (m170) REVERT: E 70 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6888 (mpt90) REVERT: E 217 MET cc_start: 0.8161 (mmt) cc_final: 0.7869 (mmt) REVERT: E 226 MET cc_start: 0.6038 (ppp) cc_final: 0.5618 (ppp) REVERT: E 227 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.5785 (mm) REVERT: E 282 GLU cc_start: 0.0004 (OUTLIER) cc_final: -0.0208 (mt-10) REVERT: E 483 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7872 (t0) REVERT: E 493 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6368 (mpp-170) REVERT: E 550 TYR cc_start: 0.8579 (t80) cc_final: 0.7934 (t80) REVERT: E 566 MET cc_start: 0.8108 (tmm) cc_final: 0.7510 (tmm) REVERT: E 611 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8022 (ttt-90) REVERT: E 612 ASP cc_start: 0.8146 (m-30) cc_final: 0.7847 (t0) REVERT: E 614 TYR cc_start: 0.8495 (t80) cc_final: 0.8162 (t80) REVERT: E 635 LYS cc_start: 0.7007 (mptm) cc_final: 0.6687 (mptm) REVERT: E 646 SER cc_start: 0.8501 (m) cc_final: 0.8248 (p) REVERT: E 649 LYS cc_start: 0.8390 (mttp) cc_final: 0.8064 (mtpp) REVERT: E 693 GLU cc_start: 0.7246 (tp30) cc_final: 0.6982 (tp30) REVERT: E 722 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7905 (mtt180) REVERT: E 724 LYS cc_start: 0.7123 (tptt) cc_final: 0.6496 (ttmm) REVERT: F 64 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5934 (tm-30) REVERT: F 68 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7195 (ttp-110) REVERT: F 98 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7476 (pt) REVERT: F 233 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8504 (mptp) REVERT: F 251 ASP cc_start: 0.5701 (OUTLIER) cc_final: 0.5282 (t0) REVERT: F 272 THR cc_start: 0.5876 (OUTLIER) cc_final: 0.4975 (m) REVERT: F 292 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7376 (mtp180) REVERT: F 322 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6501 (mt) REVERT: F 483 ASP cc_start: 0.7502 (m-30) cc_final: 0.7040 (m-30) REVERT: F 487 ASP cc_start: 0.7877 (m-30) cc_final: 0.7648 (m-30) REVERT: F 574 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8036 (mp) REVERT: F 616 ASN cc_start: 0.8581 (t0) cc_final: 0.7687 (t0) REVERT: F 635 LYS cc_start: 0.7287 (mmpt) cc_final: 0.7042 (mmpt) REVERT: F 672 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: F 724 LYS cc_start: 0.7704 (mtmp) cc_final: 0.7498 (mttp) outliers start: 197 outliers final: 121 residues processed: 776 average time/residue: 0.1857 time to fit residues: 215.9356 Evaluate side-chains 763 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 606 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 633 GLU Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 58 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 611 ARG Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 252 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 190 optimal weight: 0.0670 chunk 279 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 GLN D 336 ASN ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 GLN E 650 ASN F 336 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.192818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148627 restraints weight = 47503.112| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.52 r_work: 0.3598 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28989 Z= 0.173 Angle : 0.653 16.243 39187 Z= 0.330 Chirality : 0.041 0.229 4273 Planarity : 0.005 0.065 5063 Dihedral : 7.520 70.010 3937 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.05 % Favored : 94.66 % Rotamer: Outliers : 6.97 % Allowed : 27.15 % Favored : 65.88 % 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 aren not related in a simple way. whole: 0.31 (0.15), residues: 3444 helix: 1.07 (0.10), residues: 2580 sheet: None (None), residues: 0 loop : -2.46 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 661 TYR 0.022 0.001 TYR F 304 PHE 0.029 0.002 PHE C 262 TRP 0.036 0.001 TRP E 180 HIS 0.018 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00391 (28989) covalent geometry : angle 0.65323 (39187) hydrogen bonds : bond 0.05248 ( 1761) hydrogen bonds : angle 4.63382 ( 5229) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 615 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.8089 (t) cc_final: 0.7610 (t) REVERT: A 73 TRP cc_start: 0.7306 (t-100) cc_final: 0.6948 (t-100) REVERT: A 183 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7206 (ttp) REVERT: A 219 MET cc_start: 0.7886 (mmm) cc_final: 0.7349 (mmm) REVERT: A 291 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6969 (ppt170) REVERT: A 426 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6700 (mm) REVERT: A 444 LYS cc_start: 0.6321 (pttm) cc_final: 0.5977 (mtmm) REVERT: A 484 ASP cc_start: 0.8131 (m-30) cc_final: 0.7830 (m-30) REVERT: A 487 ASP cc_start: 0.7217 (m-30) cc_final: 0.6915 (m-30) REVERT: A 489 SER cc_start: 0.8592 (t) cc_final: 0.8236 (p) REVERT: A 499 HIS cc_start: 0.8573 (p-80) cc_final: 0.8349 (p90) REVERT: A 532 ASP cc_start: 0.7164 (t0) cc_final: 0.6929 (t0) REVERT: A 632 ASP cc_start: 0.7540 (t0) cc_final: 0.7050 (t70) REVERT: A 671 LYS cc_start: 0.8309 (mttt) cc_final: 0.8073 (mptt) REVERT: A 721 HIS cc_start: 0.8097 (t70) cc_final: 0.7845 (t70) REVERT: B 66 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7617 (t) REVERT: B 105 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7396 (ttm110) REVERT: B 118 LEU cc_start: 0.8504 (mt) cc_final: 0.8206 (mt) REVERT: B 230 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: B 487 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: B 565 ASP cc_start: 0.7700 (m-30) cc_final: 0.7244 (m-30) REVERT: B 590 GLN cc_start: 0.5131 (OUTLIER) cc_final: 0.4766 (mp10) REVERT: B 593 LEU cc_start: 0.7382 (mp) cc_final: 0.7122 (mt) REVERT: B 615 LYS cc_start: 0.8444 (mtpp) cc_final: 0.7997 (mtpp) REVERT: B 680 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8189 (tt0) REVERT: C 114 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.5037 (pt0) REVERT: C 183 MET cc_start: 0.6974 (tmm) cc_final: 0.6599 (tmm) REVERT: C 217 MET cc_start: 0.8158 (mpp) cc_final: 0.7785 (tpp) REVERT: C 323 GLN cc_start: 0.6414 (OUTLIER) cc_final: 0.5808 (mp10) REVERT: C 429 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7326 (pt0) REVERT: C 483 ASP cc_start: 0.8010 (t0) cc_final: 0.7409 (t0) REVERT: C 487 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: C 521 LYS cc_start: 0.8369 (mttm) cc_final: 0.8115 (mtmm) REVERT: C 529 ARG cc_start: 0.7507 (mpt-90) cc_final: 0.7132 (mpt-90) REVERT: C 531 MET cc_start: 0.7689 (mmt) cc_final: 0.7409 (mmt) REVERT: C 606 GLU cc_start: 0.7238 (tt0) cc_final: 0.6945 (mt-10) REVERT: C 612 ASP cc_start: 0.8005 (m-30) cc_final: 0.7675 (t0) REVERT: C 693 GLU cc_start: 0.7348 (tp30) cc_final: 0.7083 (tp30) REVERT: D 33 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7380 (pp) REVERT: D 89 TRP cc_start: 0.6743 (OUTLIER) cc_final: 0.6280 (m-90) REVERT: D 98 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6423 (pp) REVERT: D 162 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8091 (tt) REVERT: D 219 MET cc_start: 0.7696 (tmm) cc_final: 0.7363 (tmm) REVERT: D 279 MET cc_start: 0.4429 (mmp) cc_final: 0.3786 (mmp) REVERT: D 308 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7252 (mt) REVERT: D 428 ASP cc_start: 0.7172 (m-30) cc_final: 0.6971 (m-30) REVERT: D 436 GLU cc_start: 0.7378 (pp20) cc_final: 0.7049 (pp20) REVERT: D 444 LYS cc_start: 0.7721 (mtmt) cc_final: 0.6929 (mtmm) REVERT: D 517 ASP cc_start: 0.7440 (t0) cc_final: 0.7108 (t0) REVERT: D 538 MET cc_start: 0.7896 (mmm) cc_final: 0.7341 (mmm) REVERT: D 565 ASP cc_start: 0.7887 (t0) cc_final: 0.7606 (t0) REVERT: D 568 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.7059 (ttm-80) REVERT: D 606 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7374 (mt-10) REVERT: D 612 ASP cc_start: 0.7964 (t0) cc_final: 0.7691 (t0) REVERT: E 58 HIS cc_start: 0.1843 (OUTLIER) cc_final: 0.1634 (m90) REVERT: E 70 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6902 (mpt90) REVERT: E 114 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.5728 (pt0) REVERT: E 217 MET cc_start: 0.8112 (mmt) cc_final: 0.7811 (mmt) REVERT: E 226 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5664 (ppp) REVERT: E 227 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6166 (mm) REVERT: E 271 MET cc_start: -0.1642 (ttt) cc_final: -0.1991 (ttp) REVERT: E 282 GLU cc_start: -0.0088 (OUTLIER) cc_final: -0.0372 (mt-10) REVERT: E 300 TYR cc_start: 0.7120 (m-80) cc_final: 0.6805 (m-80) REVERT: E 327 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7664 (mtpt) REVERT: E 483 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7815 (t0) REVERT: E 493 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6358 (mpp-170) REVERT: E 539 ARG cc_start: 0.7956 (ttt90) cc_final: 0.7713 (ttt90) REVERT: E 550 TYR cc_start: 0.8565 (t80) cc_final: 0.7958 (t80) REVERT: E 612 ASP cc_start: 0.8099 (m-30) cc_final: 0.7764 (t0) REVERT: E 614 TYR cc_start: 0.8481 (t80) cc_final: 0.8067 (t80) REVERT: E 635 LYS cc_start: 0.7066 (mptm) cc_final: 0.6753 (mptm) REVERT: E 646 SER cc_start: 0.8505 (m) cc_final: 0.8230 (p) REVERT: E 693 GLU cc_start: 0.7217 (tp30) cc_final: 0.6982 (tp30) REVERT: E 722 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7904 (mtt180) REVERT: F 64 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5880 (tm-30) REVERT: F 68 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7034 (ttp-110) REVERT: F 98 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7451 (pt) REVERT: F 251 ASP cc_start: 0.5564 (OUTLIER) cc_final: 0.4885 (t70) REVERT: F 272 THR cc_start: 0.5209 (OUTLIER) cc_final: 0.4785 (m) REVERT: F 292 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7324 (mtp180) REVERT: F 299 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7863 (pt0) REVERT: F 336 ASN cc_start: 0.6059 (OUTLIER) cc_final: 0.5580 (p0) REVERT: F 345 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.5970 (mtp-110) REVERT: F 483 ASP cc_start: 0.7463 (m-30) cc_final: 0.7004 (m-30) REVERT: F 486 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7385 (mt-10) REVERT: F 487 ASP cc_start: 0.7901 (m-30) cc_final: 0.7648 (m-30) REVERT: F 519 MET cc_start: 0.7534 (mtm) cc_final: 0.7095 (mtt) REVERT: F 561 GLU cc_start: 0.7645 (tp30) cc_final: 0.7368 (tp30) REVERT: F 574 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8085 (mp) REVERT: F 612 ASP cc_start: 0.7851 (t70) cc_final: 0.7570 (t0) REVERT: F 616 ASN cc_start: 0.8611 (t0) cc_final: 0.7722 (t0) REVERT: F 671 LYS cc_start: 0.8417 (mttp) cc_final: 0.8046 (mttp) REVERT: F 672 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: F 724 LYS cc_start: 0.7690 (mtmp) cc_final: 0.7489 (mttp) outliers start: 216 outliers final: 122 residues processed: 777 average time/residue: 0.1923 time to fit residues: 222.9897 Evaluate side-chains 769 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 613 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 58 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 647 GLN Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 697 LYS Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 299 GLN Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 345 ARG Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 719 LEU Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 148 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 339 optimal weight: 7.9990 chunk 311 optimal weight: 0.9980 chunk 287 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 338 optimal weight: 0.7980 chunk 306 optimal weight: 0.0060 chunk 201 optimal weight: 0.1980 chunk 256 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN D 156 GLN D 263 GLN D 347 HIS D 658 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 ASN F 506 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.193664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148629 restraints weight = 47660.813| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.46 r_work: 0.3618 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28989 Z= 0.142 Angle : 0.650 16.386 39187 Z= 0.323 Chirality : 0.040 0.248 4273 Planarity : 0.005 0.068 5063 Dihedral : 7.175 69.656 3923 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.05 % Favored : 94.66 % Rotamer: Outliers : 6.16 % Allowed : 28.09 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.15), residues: 3444 helix: 1.21 (0.11), residues: 2584 sheet: None (None), residues: 0 loop : -2.47 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 539 TYR 0.024 0.001 TYR F 304 PHE 0.022 0.001 PHE E 27 TRP 0.036 0.001 TRP E 180 HIS 0.013 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00316 (28989) covalent geometry : angle 0.64968 (39187) hydrogen bonds : bond 0.04815 ( 1761) hydrogen bonds : angle 4.53112 ( 5229) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 607 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.3946 (OUTLIER) cc_final: 0.3666 (pp) REVERT: A 69 CYS cc_start: 0.8131 (t) cc_final: 0.7656 (t) REVERT: A 73 TRP cc_start: 0.7328 (t-100) cc_final: 0.7026 (t-100) REVERT: A 183 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7221 (ttp) REVERT: A 219 MET cc_start: 0.7923 (mmm) cc_final: 0.7343 (mmm) REVERT: A 291 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6931 (ppt170) REVERT: A 426 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6738 (mm) REVERT: A 444 LYS cc_start: 0.6359 (pttm) cc_final: 0.6007 (mtmm) REVERT: A 484 ASP cc_start: 0.8128 (m-30) cc_final: 0.7825 (m-30) REVERT: A 487 ASP cc_start: 0.7060 (m-30) cc_final: 0.6771 (m-30) REVERT: A 489 SER cc_start: 0.8601 (t) cc_final: 0.8253 (p) REVERT: A 499 HIS cc_start: 0.8562 (p-80) cc_final: 0.8320 (p90) REVERT: A 532 ASP cc_start: 0.7046 (t0) cc_final: 0.6814 (t0) REVERT: A 632 ASP cc_start: 0.7471 (t0) cc_final: 0.6951 (t70) REVERT: A 671 LYS cc_start: 0.8278 (mttt) cc_final: 0.8050 (mptt) REVERT: A 721 HIS cc_start: 0.8072 (t70) cc_final: 0.7843 (t70) REVERT: B 66 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7595 (t) REVERT: B 105 ARG cc_start: 0.7835 (ptp90) cc_final: 0.7455 (ttm110) REVERT: B 118 LEU cc_start: 0.8482 (mt) cc_final: 0.8189 (mt) REVERT: B 146 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6933 (tmm160) REVERT: B 304 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6983 (p90) REVERT: B 487 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: B 565 ASP cc_start: 0.7689 (m-30) cc_final: 0.7327 (m-30) REVERT: B 590 GLN cc_start: 0.5111 (OUTLIER) cc_final: 0.4773 (mp10) REVERT: B 615 LYS cc_start: 0.8420 (mtpp) cc_final: 0.7939 (mtpp) REVERT: B 680 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8205 (tt0) REVERT: C 73 TRP cc_start: 0.8038 (t-100) cc_final: 0.7775 (t-100) REVERT: C 114 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.5046 (pt0) REVERT: C 180 TRP cc_start: 0.7039 (OUTLIER) cc_final: 0.6732 (t-100) REVERT: C 183 MET cc_start: 0.6927 (tmm) cc_final: 0.6554 (tmm) REVERT: C 217 MET cc_start: 0.8205 (mpp) cc_final: 0.7825 (tpp) REVERT: C 323 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.5622 (mp10) REVERT: C 429 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7304 (pt0) REVERT: C 483 ASP cc_start: 0.8008 (t0) cc_final: 0.7572 (t0) REVERT: C 487 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6846 (m-30) REVERT: C 529 ARG cc_start: 0.7480 (mpt-90) cc_final: 0.7121 (mpt-90) REVERT: C 606 GLU cc_start: 0.7219 (tt0) cc_final: 0.6857 (mt-10) REVERT: C 612 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7760 (t0) REVERT: C 613 ASP cc_start: 0.7840 (m-30) cc_final: 0.7458 (m-30) REVERT: C 693 GLU cc_start: 0.7332 (tp30) cc_final: 0.7062 (tp30) REVERT: D 33 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7356 (pp) REVERT: D 89 TRP cc_start: 0.6655 (OUTLIER) cc_final: 0.6222 (m-90) REVERT: D 98 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6505 (pp) REVERT: D 219 MET cc_start: 0.7789 (tmm) cc_final: 0.7498 (tmm) REVERT: D 220 ARG cc_start: 0.7447 (ptm160) cc_final: 0.6828 (ttm170) REVERT: D 236 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7533 (mm-30) REVERT: D 279 MET cc_start: 0.4495 (mmp) cc_final: 0.4260 (mmp) REVERT: D 304 TYR cc_start: 0.6623 (t80) cc_final: 0.5672 (t80) REVERT: D 329 GLN cc_start: 0.8056 (pt0) cc_final: 0.7412 (tt0) REVERT: D 336 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6740 (t0) REVERT: D 428 ASP cc_start: 0.7193 (m-30) cc_final: 0.6966 (m-30) REVERT: D 436 GLU cc_start: 0.7359 (pp20) cc_final: 0.7021 (pp20) REVERT: D 444 LYS cc_start: 0.7733 (mtmt) cc_final: 0.7022 (mtmt) REVERT: D 517 ASP cc_start: 0.7401 (t0) cc_final: 0.7091 (t0) REVERT: D 538 MET cc_start: 0.7775 (mmm) cc_final: 0.7170 (mmm) REVERT: D 565 ASP cc_start: 0.7901 (t0) cc_final: 0.7616 (t0) REVERT: D 568 ARG cc_start: 0.7287 (ttm-80) cc_final: 0.7024 (ttm-80) REVERT: D 606 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7363 (mt-10) REVERT: D 612 ASP cc_start: 0.8006 (t0) cc_final: 0.7747 (t0) REVERT: E 70 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6831 (mpt90) REVERT: E 114 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.5773 (mt-10) REVERT: E 217 MET cc_start: 0.8168 (mmt) cc_final: 0.7882 (mmt) REVERT: E 226 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5755 (ppp) REVERT: E 227 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6288 (mm) REVERT: E 271 MET cc_start: -0.1722 (ttt) cc_final: -0.1927 (ttp) REVERT: E 300 TYR cc_start: 0.7120 (m-80) cc_final: 0.6883 (m-80) REVERT: E 327 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7684 (mtpt) REVERT: E 483 ASP cc_start: 0.8259 (t0) cc_final: 0.7830 (t0) REVERT: E 493 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6352 (mpp-170) REVERT: E 550 TYR cc_start: 0.8572 (t80) cc_final: 0.7959 (t80) REVERT: E 566 MET cc_start: 0.8212 (tmm) cc_final: 0.7420 (tmm) REVERT: E 612 ASP cc_start: 0.8090 (m-30) cc_final: 0.7783 (t0) REVERT: E 614 TYR cc_start: 0.8460 (t80) cc_final: 0.8105 (t80) REVERT: E 635 LYS cc_start: 0.7029 (mptm) cc_final: 0.6717 (mptm) REVERT: E 646 SER cc_start: 0.8472 (m) cc_final: 0.8174 (p) REVERT: E 693 GLU cc_start: 0.7201 (tp30) cc_final: 0.6945 (tp30) REVERT: E 722 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7902 (mtt180) REVERT: F 64 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5909 (tm-30) REVERT: F 68 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.6983 (ttp-110) REVERT: F 98 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7448 (pt) REVERT: F 251 ASP cc_start: 0.5352 (OUTLIER) cc_final: 0.5019 (t0) REVERT: F 272 THR cc_start: 0.5165 (OUTLIER) cc_final: 0.4805 (m) REVERT: F 292 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7087 (mtp180) REVERT: F 295 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7448 (pp20) REVERT: F 336 ASN cc_start: 0.5919 (OUTLIER) cc_final: 0.5383 (p0) REVERT: F 483 ASP cc_start: 0.7502 (m-30) cc_final: 0.6974 (m-30) REVERT: F 487 ASP cc_start: 0.7867 (m-30) cc_final: 0.7625 (m-30) REVERT: F 519 MET cc_start: 0.7374 (mtm) cc_final: 0.7051 (mtt) REVERT: F 561 GLU cc_start: 0.7617 (tp30) cc_final: 0.7320 (tp30) REVERT: F 616 ASN cc_start: 0.8584 (t0) cc_final: 0.7699 (t0) REVERT: F 635 LYS cc_start: 0.7371 (mmpt) cc_final: 0.7055 (mmpt) REVERT: F 671 LYS cc_start: 0.8370 (mttp) cc_final: 0.8107 (mttp) REVERT: F 672 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: F 724 LYS cc_start: 0.7675 (mtmp) cc_final: 0.7473 (mttp) outliers start: 191 outliers final: 122 residues processed: 752 average time/residue: 0.1897 time to fit residues: 212.7025 Evaluate side-chains 747 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 593 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 359 HIS Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 524 GLN Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 697 LYS Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 10 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 108 optimal weight: 0.2980 chunk 99 optimal weight: 0.5980 chunk 308 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 270 optimal weight: 0.5980 chunk 292 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 GLN D 307 ASN D 658 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN F 307 ASN F 336 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.193148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147617 restraints weight = 47668.242| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.46 r_work: 0.3606 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28989 Z= 0.161 Angle : 0.665 17.421 39187 Z= 0.327 Chirality : 0.040 0.208 4273 Planarity : 0.005 0.069 5063 Dihedral : 6.899 69.285 3912 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.34 % Favored : 94.40 % Rotamer: Outliers : 5.93 % Allowed : 27.86 % Favored : 66.20 % 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 aren not related in a simple way. whole: 0.48 (0.15), residues: 3444 helix: 1.20 (0.10), residues: 2589 sheet: None (None), residues: 0 loop : -2.45 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 661 TYR 0.022 0.001 TYR F 304 PHE 0.019 0.001 PHE E 27 TRP 0.031 0.001 TRP E 180 HIS 0.010 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00367 (28989) covalent geometry : angle 0.66461 (39187) hydrogen bonds : bond 0.04910 ( 1761) hydrogen bonds : angle 4.49718 ( 5229) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 604 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.3875 (OUTLIER) cc_final: 0.3618 (pp) REVERT: A 69 CYS cc_start: 0.8114 (t) cc_final: 0.7629 (t) REVERT: A 73 TRP cc_start: 0.7382 (t-100) cc_final: 0.7062 (t-100) REVERT: A 180 TRP cc_start: 0.6837 (OUTLIER) cc_final: 0.6534 (t-100) REVERT: A 183 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7439 (ttp) REVERT: A 219 MET cc_start: 0.7990 (mmm) cc_final: 0.7375 (mmm) REVERT: A 291 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6919 (ppt170) REVERT: A 426 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6953 (mm) REVERT: A 444 LYS cc_start: 0.6386 (pttm) cc_final: 0.6002 (mtmm) REVERT: A 484 ASP cc_start: 0.8092 (m-30) cc_final: 0.7816 (m-30) REVERT: A 487 ASP cc_start: 0.7110 (m-30) cc_final: 0.6823 (m-30) REVERT: A 489 SER cc_start: 0.8609 (t) cc_final: 0.8233 (p) REVERT: A 532 ASP cc_start: 0.7087 (t0) cc_final: 0.6838 (t0) REVERT: A 632 ASP cc_start: 0.7490 (t0) cc_final: 0.6979 (t70) REVERT: A 671 LYS cc_start: 0.8274 (mttt) cc_final: 0.8039 (mptt) REVERT: A 696 GLU cc_start: 0.7965 (tp30) cc_final: 0.7600 (tm-30) REVERT: A 721 HIS cc_start: 0.8093 (t70) cc_final: 0.7857 (t70) REVERT: B 58 HIS cc_start: 0.6832 (m90) cc_final: 0.6562 (m90) REVERT: B 66 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.7594 (t) REVERT: B 118 LEU cc_start: 0.8500 (mt) cc_final: 0.8206 (mt) REVERT: B 146 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6929 (tmm160) REVERT: B 158 GLN cc_start: 0.7731 (tp40) cc_final: 0.7346 (tp40) REVERT: B 230 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: B 299 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 487 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: B 531 MET cc_start: 0.7232 (tpt) cc_final: 0.6854 (tpt) REVERT: B 565 ASP cc_start: 0.7658 (m-30) cc_final: 0.7292 (m-30) REVERT: B 590 GLN cc_start: 0.5129 (OUTLIER) cc_final: 0.4819 (mp10) REVERT: B 593 LEU cc_start: 0.7338 (mp) cc_final: 0.7096 (mt) REVERT: B 615 LYS cc_start: 0.8420 (mtpp) cc_final: 0.7979 (mtpp) REVERT: B 680 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8207 (tt0) REVERT: C 73 TRP cc_start: 0.7988 (t-100) cc_final: 0.7714 (t-100) REVERT: C 114 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.5047 (pt0) REVERT: C 180 TRP cc_start: 0.7044 (OUTLIER) cc_final: 0.6733 (t-100) REVERT: C 183 MET cc_start: 0.7034 (tmm) cc_final: 0.6650 (tmm) REVERT: C 217 MET cc_start: 0.8250 (mpp) cc_final: 0.7875 (tpp) REVERT: C 323 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.5735 (mp10) REVERT: C 429 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7273 (pt0) REVERT: C 483 ASP cc_start: 0.8027 (t0) cc_final: 0.7592 (t0) REVERT: C 487 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6805 (m-30) REVERT: C 529 ARG cc_start: 0.7445 (mpt-90) cc_final: 0.7107 (mpt-90) REVERT: C 606 GLU cc_start: 0.7205 (tt0) cc_final: 0.6873 (mt-10) REVERT: C 612 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7707 (t0) REVERT: C 613 ASP cc_start: 0.7853 (m-30) cc_final: 0.7444 (m-30) REVERT: C 693 GLU cc_start: 0.7332 (tp30) cc_final: 0.7063 (tp30) REVERT: D 33 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7297 (pp) REVERT: D 34 SER cc_start: 0.4492 (OUTLIER) cc_final: 0.4261 (p) REVERT: D 89 TRP cc_start: 0.6831 (OUTLIER) cc_final: 0.6418 (m-90) REVERT: D 98 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6552 (pp) REVERT: D 220 ARG cc_start: 0.7487 (ptm160) cc_final: 0.6825 (ttm170) REVERT: D 279 MET cc_start: 0.4362 (mmp) cc_final: 0.3700 (mmp) REVERT: D 304 TYR cc_start: 0.6795 (t80) cc_final: 0.5615 (t80) REVERT: D 329 GLN cc_start: 0.8130 (pt0) cc_final: 0.7401 (tt0) REVERT: D 428 ASP cc_start: 0.7131 (m-30) cc_final: 0.6923 (m-30) REVERT: D 436 GLU cc_start: 0.7284 (pp20) cc_final: 0.6972 (pp20) REVERT: D 444 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7004 (mtmt) REVERT: D 517 ASP cc_start: 0.7374 (t0) cc_final: 0.7041 (t0) REVERT: D 538 MET cc_start: 0.7840 (mmm) cc_final: 0.7213 (mmm) REVERT: D 565 ASP cc_start: 0.7988 (t0) cc_final: 0.7697 (t0) REVERT: D 568 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.7116 (ttm-80) REVERT: D 606 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7377 (mt-10) REVERT: D 612 ASP cc_start: 0.7960 (t0) cc_final: 0.7709 (t0) REVERT: E 70 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6845 (mpt90) REVERT: E 114 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.5692 (mt-10) REVERT: E 226 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5830 (ppp) REVERT: E 227 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6381 (mm) REVERT: E 271 MET cc_start: -0.1658 (ttt) cc_final: -0.1859 (ttp) REVERT: E 326 LEU cc_start: 0.2419 (OUTLIER) cc_final: 0.2151 (mp) REVERT: E 327 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7716 (mtpt) REVERT: E 332 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6379 (mm-40) REVERT: E 429 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7296 (mt-10) REVERT: E 483 ASP cc_start: 0.8288 (t0) cc_final: 0.7814 (t0) REVERT: E 493 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6301 (mpp-170) REVERT: E 550 TYR cc_start: 0.8550 (t80) cc_final: 0.7958 (t80) REVERT: E 566 MET cc_start: 0.8194 (tmm) cc_final: 0.7300 (tmm) REVERT: E 612 ASP cc_start: 0.8071 (m-30) cc_final: 0.7739 (t0) REVERT: E 614 TYR cc_start: 0.8436 (t80) cc_final: 0.7986 (t80) REVERT: E 632 ASP cc_start: 0.7342 (t0) cc_final: 0.7068 (t0) REVERT: E 635 LYS cc_start: 0.7076 (mptm) cc_final: 0.6739 (mptm) REVERT: E 646 SER cc_start: 0.8488 (m) cc_final: 0.8192 (p) REVERT: E 656 ILE cc_start: 0.8597 (mt) cc_final: 0.8285 (mp) REVERT: E 693 GLU cc_start: 0.7170 (tp30) cc_final: 0.6922 (tp30) REVERT: E 722 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7887 (mtt180) REVERT: F 64 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6079 (tm-30) REVERT: F 68 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.6925 (ttp-110) REVERT: F 98 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7495 (pt) REVERT: F 251 ASP cc_start: 0.5397 (OUTLIER) cc_final: 0.5098 (t0) REVERT: F 295 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7484 (pp20) REVERT: F 336 ASN cc_start: 0.6011 (OUTLIER) cc_final: 0.5480 (p0) REVERT: F 483 ASP cc_start: 0.7448 (m-30) cc_final: 0.6957 (m-30) REVERT: F 487 ASP cc_start: 0.7898 (m-30) cc_final: 0.7640 (m-30) REVERT: F 561 GLU cc_start: 0.7682 (tp30) cc_final: 0.7365 (tp30) REVERT: F 616 ASN cc_start: 0.8547 (t0) cc_final: 0.7646 (t0) REVERT: F 635 LYS cc_start: 0.7389 (mmpt) cc_final: 0.7174 (mmpt) REVERT: F 671 LYS cc_start: 0.8368 (mttp) cc_final: 0.8119 (mttp) REVERT: F 672 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6956 (mp0) outliers start: 184 outliers final: 129 residues processed: 745 average time/residue: 0.1824 time to fit residues: 203.9525 Evaluate side-chains 760 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 598 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 359 HIS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 647 GLN Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 697 LYS Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 615 LYS Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 719 LEU Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 154 optimal weight: 0.0670 chunk 285 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 55 optimal weight: 0.0040 chunk 78 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 290 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 323 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN A 232 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 GLN D 229 GLN D 658 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 GLN F 57 HIS F 336 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.192571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147304 restraints weight = 47989.575| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.48 r_work: 0.3621 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28989 Z= 0.140 Angle : 0.665 17.292 39187 Z= 0.329 Chirality : 0.040 0.165 4273 Planarity : 0.005 0.068 5063 Dihedral : 6.731 69.022 3906 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.08 % Favored : 94.66 % Rotamer: Outliers : 5.55 % Allowed : 28.54 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.15), residues: 3444 helix: 1.28 (0.11), residues: 2590 sheet: None (None), residues: 0 loop : -2.40 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 661 TYR 0.037 0.002 TYR A 300 PHE 0.026 0.001 PHE B 253 TRP 0.046 0.001 TRP E 180 HIS 0.007 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00314 (28989) covalent geometry : angle 0.66527 (39187) hydrogen bonds : bond 0.04595 ( 1761) hydrogen bonds : angle 4.43655 ( 5229) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 605 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.4011 (OUTLIER) cc_final: 0.3782 (pp) REVERT: A 69 CYS cc_start: 0.7924 (t) cc_final: 0.7406 (t) REVERT: A 73 TRP cc_start: 0.7355 (t-100) cc_final: 0.7129 (t-100) REVERT: A 180 TRP cc_start: 0.6822 (OUTLIER) cc_final: 0.6558 (t-100) REVERT: A 183 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7388 (ttp) REVERT: A 219 MET cc_start: 0.7960 (mmm) cc_final: 0.7321 (mmm) REVERT: A 291 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6921 (ppt170) REVERT: A 426 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6675 (mm) REVERT: A 484 ASP cc_start: 0.8040 (m-30) cc_final: 0.7778 (m-30) REVERT: A 487 ASP cc_start: 0.7005 (m-30) cc_final: 0.6728 (m-30) REVERT: A 489 SER cc_start: 0.8594 (t) cc_final: 0.8212 (p) REVERT: A 532 ASP cc_start: 0.6962 (t0) cc_final: 0.6758 (t0) REVERT: A 632 ASP cc_start: 0.7440 (t0) cc_final: 0.6941 (t70) REVERT: A 671 LYS cc_start: 0.8284 (mttt) cc_final: 0.8062 (mptt) REVERT: A 696 GLU cc_start: 0.7932 (tp30) cc_final: 0.7655 (tm-30) REVERT: A 721 HIS cc_start: 0.8052 (t70) cc_final: 0.7825 (t70) REVERT: B 58 HIS cc_start: 0.6782 (m90) cc_final: 0.6516 (m90) REVERT: B 66 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7606 (t) REVERT: B 93 PHE cc_start: 0.7105 (t80) cc_final: 0.6540 (t80) REVERT: B 118 LEU cc_start: 0.8455 (mt) cc_final: 0.8180 (mt) REVERT: B 146 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6827 (tmm160) REVERT: B 183 MET cc_start: 0.8620 (ttm) cc_final: 0.8286 (ttm) REVERT: B 487 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: B 531 MET cc_start: 0.7146 (tpt) cc_final: 0.6873 (tpt) REVERT: B 565 ASP cc_start: 0.7590 (m-30) cc_final: 0.7205 (m-30) REVERT: B 590 GLN cc_start: 0.5152 (OUTLIER) cc_final: 0.4831 (mp10) REVERT: B 615 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8017 (mtpp) REVERT: B 680 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8132 (tt0) REVERT: C 114 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.5008 (pt0) REVERT: C 180 TRP cc_start: 0.6942 (OUTLIER) cc_final: 0.6646 (t-100) REVERT: C 183 MET cc_start: 0.7071 (tmm) cc_final: 0.6675 (tmm) REVERT: C 217 MET cc_start: 0.8149 (mpp) cc_final: 0.7765 (tpp) REVERT: C 271 MET cc_start: 0.0233 (ttt) cc_final: -0.0158 (ttt) REVERT: C 323 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.5694 (mp10) REVERT: C 429 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7221 (pt0) REVERT: C 483 ASP cc_start: 0.8044 (t0) cc_final: 0.7606 (t0) REVERT: C 487 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6823 (m-30) REVERT: C 519 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7551 (tmm) REVERT: C 529 ARG cc_start: 0.7429 (mpt-90) cc_final: 0.7098 (mpt-90) REVERT: C 554 ASN cc_start: 0.8340 (m-40) cc_final: 0.8135 (m-40) REVERT: C 606 GLU cc_start: 0.7247 (tt0) cc_final: 0.6892 (mt-10) REVERT: C 612 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7652 (t0) REVERT: C 613 ASP cc_start: 0.7795 (m-30) cc_final: 0.7391 (m-30) REVERT: C 693 GLU cc_start: 0.7363 (tp30) cc_final: 0.7098 (tp30) REVERT: D 33 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7280 (pp) REVERT: D 34 SER cc_start: 0.4508 (OUTLIER) cc_final: 0.4243 (p) REVERT: D 89 TRP cc_start: 0.6848 (OUTLIER) cc_final: 0.6379 (m-90) REVERT: D 98 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6515 (pp) REVERT: D 279 MET cc_start: 0.4545 (mmp) cc_final: 0.3904 (mmp) REVERT: D 428 ASP cc_start: 0.7092 (m-30) cc_final: 0.6889 (m-30) REVERT: D 436 GLU cc_start: 0.7299 (pp20) cc_final: 0.6971 (pp20) REVERT: D 517 ASP cc_start: 0.7368 (t0) cc_final: 0.7107 (t0) REVERT: D 538 MET cc_start: 0.7749 (mmm) cc_final: 0.7133 (mmm) REVERT: D 565 ASP cc_start: 0.7910 (t0) cc_final: 0.7630 (t0) REVERT: D 568 ARG cc_start: 0.7309 (ttm-80) cc_final: 0.7038 (ttm-80) REVERT: D 606 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7361 (mt-10) REVERT: D 612 ASP cc_start: 0.7987 (t0) cc_final: 0.7718 (t0) REVERT: E 70 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6809 (mpt90) REVERT: E 114 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.5711 (mt-10) REVERT: E 226 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.5676 (ppp) REVERT: E 227 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6474 (mm) REVERT: E 332 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6486 (mm-40) REVERT: E 429 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7258 (pt0) REVERT: E 483 ASP cc_start: 0.8296 (t0) cc_final: 0.7854 (t0) REVERT: E 493 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6325 (mpp-170) REVERT: E 550 TYR cc_start: 0.8545 (t80) cc_final: 0.7971 (t80) REVERT: E 566 MET cc_start: 0.8219 (tmm) cc_final: 0.7296 (tmm) REVERT: E 612 ASP cc_start: 0.8095 (m-30) cc_final: 0.7776 (t0) REVERT: E 632 ASP cc_start: 0.7347 (t0) cc_final: 0.7102 (t0) REVERT: E 635 LYS cc_start: 0.7010 (mptm) cc_final: 0.6706 (mptm) REVERT: E 646 SER cc_start: 0.8475 (m) cc_final: 0.8187 (p) REVERT: E 656 ILE cc_start: 0.8615 (mt) cc_final: 0.8352 (mp) REVERT: E 693 GLU cc_start: 0.7148 (tp30) cc_final: 0.6895 (tp30) REVERT: E 722 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7867 (mtt180) REVERT: F 64 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6172 (tm-30) REVERT: F 68 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7212 (ttp-110) REVERT: F 98 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7321 (pt) REVERT: F 219 MET cc_start: 0.7812 (mtm) cc_final: 0.7556 (mtm) REVERT: F 251 ASP cc_start: 0.5463 (OUTLIER) cc_final: 0.5220 (t0) REVERT: F 295 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7458 (pp20) REVERT: F 483 ASP cc_start: 0.7464 (m-30) cc_final: 0.6978 (m-30) REVERT: F 487 ASP cc_start: 0.7893 (m-30) cc_final: 0.7627 (m-30) REVERT: F 561 GLU cc_start: 0.7523 (tp30) cc_final: 0.7246 (tp30) REVERT: F 616 ASN cc_start: 0.8539 (t0) cc_final: 0.7657 (t0) REVERT: F 635 LYS cc_start: 0.7299 (mmpt) cc_final: 0.7093 (mmpt) REVERT: F 671 LYS cc_start: 0.8325 (mttp) cc_final: 0.8115 (mttp) REVERT: F 672 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: F 724 LYS cc_start: 0.7928 (mttp) cc_final: 0.7641 (mttp) outliers start: 172 outliers final: 127 residues processed: 732 average time/residue: 0.1801 time to fit residues: 198.5013 Evaluate side-chains 751 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 594 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 359 HIS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 699 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 524 GLN Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 697 LYS Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 615 LYS Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 86 optimal weight: 5.9990 chunk 206 optimal weight: 0.6980 chunk 228 optimal weight: 0.6980 chunk 342 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 271 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 GLN D 158 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN F 336 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.191365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145810 restraints weight = 47611.953| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.44 r_work: 0.3601 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28989 Z= 0.171 Angle : 0.689 18.037 39187 Z= 0.341 Chirality : 0.041 0.175 4273 Planarity : 0.005 0.068 5063 Dihedral : 6.613 68.913 3901 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.11 % Favored : 94.63 % Rotamer: Outliers : 5.26 % Allowed : 28.86 % Favored : 65.88 % 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 aren not related in a simple way. whole: 0.51 (0.15), residues: 3444 helix: 1.23 (0.10), residues: 2596 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 661 TYR 0.030 0.002 TYR A 300 PHE 0.040 0.002 PHE D 262 TRP 0.042 0.001 TRP E 180 HIS 0.009 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00389 (28989) covalent geometry : angle 0.68922 (39187) hydrogen bonds : bond 0.04974 ( 1761) hydrogen bonds : angle 4.49304 ( 5229) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 599 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.3914 (OUTLIER) cc_final: 0.3645 (pp) REVERT: A 69 CYS cc_start: 0.7971 (t) cc_final: 0.7461 (t) REVERT: A 73 TRP cc_start: 0.7420 (t-100) cc_final: 0.7185 (t-100) REVERT: A 180 TRP cc_start: 0.6813 (OUTLIER) cc_final: 0.6560 (t-100) REVERT: A 219 MET cc_start: 0.7967 (mmm) cc_final: 0.7335 (mmm) REVERT: A 291 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6911 (ppt170) REVERT: A 426 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6904 (mm) REVERT: A 444 LYS cc_start: 0.6458 (pttm) cc_final: 0.6084 (mtmm) REVERT: A 484 ASP cc_start: 0.8024 (m-30) cc_final: 0.7756 (m-30) REVERT: A 487 ASP cc_start: 0.7104 (m-30) cc_final: 0.6814 (m-30) REVERT: A 489 SER cc_start: 0.8614 (t) cc_final: 0.8205 (p) REVERT: A 532 ASP cc_start: 0.7059 (t0) cc_final: 0.6828 (t0) REVERT: A 550 TYR cc_start: 0.8557 (t80) cc_final: 0.8261 (t80) REVERT: A 696 GLU cc_start: 0.7968 (tp30) cc_final: 0.7637 (tp30) REVERT: A 721 HIS cc_start: 0.8105 (t70) cc_final: 0.7874 (t70) REVERT: B 58 HIS cc_start: 0.6823 (m90) cc_final: 0.6564 (m90) REVERT: B 66 SER cc_start: 0.7862 (OUTLIER) cc_final: 0.7562 (t) REVERT: B 68 ARG cc_start: 0.8386 (ttp-110) cc_final: 0.7748 (ttp-110) REVERT: B 93 PHE cc_start: 0.7124 (t80) cc_final: 0.6548 (t80) REVERT: B 118 LEU cc_start: 0.8463 (mt) cc_final: 0.8188 (mt) REVERT: B 146 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6826 (tmm160) REVERT: B 158 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7497 (tp40) REVERT: B 164 GLU cc_start: 0.8134 (tp30) cc_final: 0.7733 (tp30) REVERT: B 183 MET cc_start: 0.8666 (ttm) cc_final: 0.8322 (ttm) REVERT: B 487 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: B 565 ASP cc_start: 0.7569 (m-30) cc_final: 0.7106 (m-30) REVERT: B 568 ARG cc_start: 0.7347 (ttp-110) cc_final: 0.7143 (ttp-110) REVERT: B 569 GLN cc_start: 0.8165 (mt0) cc_final: 0.7917 (mt0) REVERT: B 590 GLN cc_start: 0.5190 (OUTLIER) cc_final: 0.4852 (mp10) REVERT: B 593 LEU cc_start: 0.7383 (mp) cc_final: 0.7132 (mt) REVERT: B 615 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8006 (mtpp) REVERT: B 680 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8131 (tt0) REVERT: C 114 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.5034 (pt0) REVERT: C 180 TRP cc_start: 0.6991 (OUTLIER) cc_final: 0.6701 (t-100) REVERT: C 183 MET cc_start: 0.7085 (tmm) cc_final: 0.6670 (tmm) REVERT: C 217 MET cc_start: 0.8150 (mpp) cc_final: 0.7774 (tpp) REVERT: C 271 MET cc_start: -0.0001 (ttt) cc_final: -0.0246 (ttt) REVERT: C 323 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.5680 (mp10) REVERT: C 429 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7253 (pt0) REVERT: C 483 ASP cc_start: 0.8041 (t0) cc_final: 0.7629 (t0) REVERT: C 487 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: C 519 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7434 (tmm) REVERT: C 529 ARG cc_start: 0.7430 (mpt-90) cc_final: 0.7119 (mpt-90) REVERT: C 612 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7669 (t0) REVERT: C 613 ASP cc_start: 0.7830 (m-30) cc_final: 0.7428 (m-30) REVERT: C 693 GLU cc_start: 0.7382 (tp30) cc_final: 0.7120 (tp30) REVERT: D 33 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7310 (pp) REVERT: D 34 SER cc_start: 0.4370 (OUTLIER) cc_final: 0.4116 (p) REVERT: D 89 TRP cc_start: 0.6896 (OUTLIER) cc_final: 0.6468 (m-90) REVERT: D 98 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6560 (pp) REVERT: D 444 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7014 (mtmt) REVERT: D 517 ASP cc_start: 0.7428 (t0) cc_final: 0.7123 (t0) REVERT: D 538 MET cc_start: 0.7896 (mmm) cc_final: 0.7229 (mmm) REVERT: D 550 TYR cc_start: 0.8364 (t80) cc_final: 0.8049 (t80) REVERT: D 565 ASP cc_start: 0.7915 (t0) cc_final: 0.7630 (t0) REVERT: D 568 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.7028 (ttm-80) REVERT: D 606 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7341 (mt-10) REVERT: D 612 ASP cc_start: 0.8056 (t0) cc_final: 0.7703 (t0) REVERT: E 70 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6785 (mpt90) REVERT: E 114 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.5712 (mt-10) REVERT: E 226 MET cc_start: 0.6259 (ppp) cc_final: 0.5864 (ppp) REVERT: E 227 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6347 (mm) REVERT: E 332 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6523 (mm-40) REVERT: E 429 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7256 (pt0) REVERT: E 483 ASP cc_start: 0.8290 (t0) cc_final: 0.7869 (t0) REVERT: E 493 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6348 (mpp-170) REVERT: E 550 TYR cc_start: 0.8560 (t80) cc_final: 0.7991 (t80) REVERT: E 566 MET cc_start: 0.8208 (tmm) cc_final: 0.7376 (tmm) REVERT: E 612 ASP cc_start: 0.8097 (m-30) cc_final: 0.7765 (t0) REVERT: E 632 ASP cc_start: 0.7355 (t0) cc_final: 0.7093 (t0) REVERT: E 635 LYS cc_start: 0.7068 (mptm) cc_final: 0.6760 (mptm) REVERT: E 646 SER cc_start: 0.8468 (m) cc_final: 0.8176 (p) REVERT: E 656 ILE cc_start: 0.8639 (mt) cc_final: 0.8366 (mp) REVERT: E 693 GLU cc_start: 0.7128 (tp30) cc_final: 0.6880 (tp30) REVERT: E 722 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7879 (mtt180) REVERT: F 64 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6242 (tm-30) REVERT: F 68 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7201 (ttp-110) REVERT: F 98 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7280 (pt) REVERT: F 219 MET cc_start: 0.7782 (mtm) cc_final: 0.7514 (mtm) REVERT: F 251 ASP cc_start: 0.5315 (OUTLIER) cc_final: 0.5070 (t0) REVERT: F 271 MET cc_start: -0.0823 (mmt) cc_final: -0.1048 (mmt) REVERT: F 295 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7473 (pp20) REVERT: F 483 ASP cc_start: 0.7468 (m-30) cc_final: 0.7005 (m-30) REVERT: F 487 ASP cc_start: 0.7906 (m-30) cc_final: 0.7629 (m-30) REVERT: F 561 GLU cc_start: 0.7593 (tp30) cc_final: 0.7302 (tp30) REVERT: F 616 ASN cc_start: 0.8574 (t0) cc_final: 0.8279 (m-40) REVERT: F 635 LYS cc_start: 0.7296 (mmpt) cc_final: 0.6999 (mmpt) REVERT: F 671 LYS cc_start: 0.8384 (mttp) cc_final: 0.8159 (mttp) REVERT: F 672 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: F 724 LYS cc_start: 0.7961 (mttp) cc_final: 0.7697 (mtmp) outliers start: 163 outliers final: 124 residues processed: 723 average time/residue: 0.1840 time to fit residues: 199.1553 Evaluate side-chains 745 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 593 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 359 HIS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 699 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 57 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 327 LYS Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain E residue 346 TYR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 524 GLN Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 697 LYS Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain F residue 345 ARG Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 719 LEU Chi-restraints excluded: chain F residue 720 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 293 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.0870 chunk 215 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 337 optimal weight: 0.6980 chunk 336 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN A 658 GLN B 332 GLN C 60 HIS ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 GLN D 329 GLN D 554 ASN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.191751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146661 restraints weight = 47555.559| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.36 r_work: 0.3616 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28989 Z= 0.166 Angle : 0.694 19.636 39187 Z= 0.342 Chirality : 0.041 0.173 4273 Planarity : 0.005 0.068 5063 Dihedral : 6.521 68.745 3898 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.82 % Favored : 94.95 % Rotamer: Outliers : 5.26 % Allowed : 28.73 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.15), residues: 3444 helix: 1.28 (0.10), residues: 2595 sheet: None (None), residues: 0 loop : -2.46 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 661 TYR 0.030 0.002 TYR A 300 PHE 0.035 0.002 PHE D 262 TRP 0.054 0.001 TRP E 180 HIS 0.009 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00379 (28989) covalent geometry : angle 0.69389 (39187) hydrogen bonds : bond 0.04893 ( 1761) hydrogen bonds : angle 4.44106 ( 5229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6920.06 seconds wall clock time: 119 minutes 5.14 seconds (7145.14 seconds total)