Starting phenix.real_space_refine on Tue Jun 24 09:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2i_47453/06_2025/9e2i_47453_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2i_47453/06_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_47453/06_2025/9e2i_47453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2i_47453/06_2025/9e2i_47453.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2i_47453/06_2025/9e2i_47453_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2i_47453/06_2025/9e2i_47453_neut.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.82, per 1000 atoms: 0.63 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: 6.69 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 2.79 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: 8.85 Time building geometry restraints manager: 7.94 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: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 61.100 Find NCS groups from input model: 1.550 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.040 ------------------------------------------------------------------------------- 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 : 19.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.048 0.002 TRP D 180 HIS 0.017 0.001 HIS A 488 PHE 0.056 0.002 PHE A 262 TYR 0.031 0.002 TYR D 614 ARG 0.023 0.001 ARG D 220 Details of bonding type rmsd hydrogen bonds : bond 0.31374 ( 1761) hydrogen bonds : angle 8.51747 ( 5229) covalent geometry : bond 0.00467 (28989) covalent geometry : angle 0.88760 (39187) *********************** 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 : 3.081 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: 0.4886 time to fit residues: 614.4203 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 : 3.232 ------------------------------------------------------------------------------- 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 294 optimal weight: 8.9990 chunk 264 optimal weight: 0.9990 chunk 146 optimal weight: 0.0470 chunk 90 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 273 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 316 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 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 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 677 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.196675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150966 restraints weight = 46811.129| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.67 r_work: 0.3619 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28989 Z= 0.190 Angle : 0.729 11.641 39187 Z= 0.383 Chirality : 0.043 0.270 4273 Planarity : 0.006 0.066 5063 Dihedral : 11.251 98.040 4226 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.57 % Favored : 93.99 % Rotamer: Outliers : 8.29 % Allowed : 26.09 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3444 helix: 0.06 (0.10), residues: 2538 sheet: None (None), residues: 0 loop : -2.65 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 259 HIS 0.009 0.001 HIS C 347 PHE 0.029 0.002 PHE C 47 TYR 0.032 0.002 TYR E 300 ARG 0.009 0.001 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.07038 ( 1761) hydrogen bonds : angle 5.54504 ( 5229) covalent geometry : bond 0.00396 (28989) covalent geometry : angle 0.72934 (39187) *********************** 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 923 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 666 time to evaluate : 2.935 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: A 69 CYS cc_start: 0.8139 (t) cc_final: 0.7809 (t) REVERT: A 75 GLN cc_start: 0.6605 (tp40) cc_final: 0.6200 (tp40) REVERT: A 76 PHE cc_start: 0.7540 (m-10) cc_final: 0.7198 (m-10) REVERT: A 162 LEU cc_start: 0.8095 (mt) cc_final: 0.7895 (mt) REVERT: A 172 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6830 (ttm170) REVERT: A 219 MET cc_start: 0.8253 (mmm) cc_final: 0.7611 (mmm) REVERT: A 444 LYS cc_start: 0.6476 (pttm) cc_final: 0.6065 (mtmm) REVERT: A 457 TRP cc_start: 0.8070 (m-10) cc_final: 0.7334 (m-10) REVERT: A 489 SER cc_start: 0.8652 (t) cc_final: 0.8368 (p) REVERT: A 532 ASP cc_start: 0.7373 (t0) cc_final: 0.7062 (t0) REVERT: A 557 CYS cc_start: 0.7944 (t) cc_final: 0.7694 (t) REVERT: A 606 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6163 (mt-10) REVERT: A 613 ASP cc_start: 0.7961 (m-30) cc_final: 0.7635 (m-30) REVERT: A 632 ASP cc_start: 0.7661 (t0) cc_final: 0.7137 (t70) REVERT: A 675 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8339 (tt) REVERT: A 721 HIS cc_start: 0.8055 (t70) cc_final: 0.7799 (t70) REVERT: B 105 ARG cc_start: 0.7773 (ptp90) cc_final: 0.7396 (ptp90) REVERT: B 118 LEU cc_start: 0.8575 (mt) cc_final: 0.8160 (mt) REVERT: B 146 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6711 (tmm160) REVERT: B 174 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: B 221 PHE cc_start: 0.7916 (t80) cc_final: 0.7333 (t80) REVERT: B 228 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8377 (t) REVERT: B 258 GLU cc_start: 0.7846 (tp30) cc_final: 0.7543 (tm-30) REVERT: B 304 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6839 (p90) REVERT: B 487 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: B 532 ASP cc_start: 0.7505 (m-30) cc_final: 0.7238 (m-30) REVERT: B 565 ASP cc_start: 0.7769 (m-30) cc_final: 0.7347 (m-30) REVERT: B 568 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7272 (ttm110) REVERT: B 590 GLN cc_start: 0.5067 (OUTLIER) cc_final: 0.4733 (mp10) REVERT: B 680 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 691 MET cc_start: 0.8214 (ttm) cc_final: 0.7989 (mtp) REVERT: C 73 TRP cc_start: 0.7777 (t-100) cc_final: 0.7457 (t-100) REVERT: C 158 GLN cc_start: 0.8266 (mt0) cc_final: 0.8054 (mt0) REVERT: C 183 MET cc_start: 0.6914 (tmm) cc_final: 0.6497 (tmm) REVERT: C 226 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6465 (ppp) REVERT: C 323 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6070 (mp10) REVERT: C 444 LYS cc_start: 0.6311 (pttm) cc_final: 0.5860 (mtmm) REVERT: C 459 VAL cc_start: 0.7896 (OUTLIER) cc_final: 0.7615 (p) REVERT: C 483 ASP cc_start: 0.8039 (t0) cc_final: 0.7372 (t0) REVERT: C 487 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6803 (m-30) REVERT: C 519 MET cc_start: 0.6949 (mtm) cc_final: 0.6125 (mtm) REVERT: C 566 MET cc_start: 0.8182 (ttp) cc_final: 0.7975 (tmm) REVERT: C 599 SER cc_start: 0.8369 (m) cc_final: 0.8033 (p) REVERT: C 612 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7661 (t0) REVERT: C 615 LYS cc_start: 0.8645 (mmmm) cc_final: 0.8429 (mtpp) REVERT: C 672 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7522 (mm-30) REVERT: C 685 GLU cc_start: 0.7208 (mp0) cc_final: 0.6947 (mm-30) REVERT: C 688 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7205 (mt-10) REVERT: D 25 SER cc_start: 0.7077 (OUTLIER) cc_final: 0.6714 (t) REVERT: D 98 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6346 (pp) REVERT: D 105 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7636 (mtm-85) REVERT: D 146 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6870 (tpp-160) REVERT: D 174 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: D 219 MET cc_start: 0.7438 (tmm) cc_final: 0.7157 (tmm) REVERT: D 279 MET cc_start: 0.4511 (mmp) cc_final: 0.4135 (mmp) REVERT: D 295 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8450 (pp20) REVERT: D 308 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7017 (mt) REVERT: D 315 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5985 (mp0) REVERT: D 447 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.8015 (mpt180) REVERT: D 550 TYR cc_start: 0.8304 (t80) cc_final: 0.8007 (t80) REVERT: D 554 ASN cc_start: 0.7924 (m-40) cc_final: 0.7657 (m-40) REVERT: D 568 ARG cc_start: 0.7389 (ttm-80) cc_final: 0.7139 (ttm-80) REVERT: D 633 GLU cc_start: 0.4687 (OUTLIER) cc_final: 0.4401 (mm-30) REVERT: D 649 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7209 (mmtm) REVERT: E 58 HIS cc_start: 0.1659 (OUTLIER) cc_final: 0.0588 (m-70) REVERT: E 70 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6943 (mpt90) REVERT: E 73 TRP cc_start: 0.7737 (t-100) cc_final: 0.7530 (t-100) REVERT: E 182 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: E 219 MET cc_start: 0.8305 (mtp) cc_final: 0.7398 (mtp) REVERT: E 226 MET cc_start: 0.6555 (ppp) cc_final: 0.6204 (ppp) REVERT: E 271 MET cc_start: 0.0845 (tmm) cc_final: 0.0584 (ttt) REVERT: E 342 ARG cc_start: 0.5639 (OUTLIER) cc_final: 0.5404 (mtm180) REVERT: E 475 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8316 (mt) REVERT: E 483 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7883 (t0) REVERT: E 505 GLU cc_start: 0.7312 (mp0) cc_final: 0.7101 (mp0) REVERT: E 537 GLU cc_start: 0.7809 (tp30) cc_final: 0.7172 (tp30) REVERT: E 611 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8034 (ttt-90) REVERT: E 615 LYS cc_start: 0.8466 (mmmm) cc_final: 0.8183 (mtpp) REVERT: E 635 LYS cc_start: 0.6984 (mptm) cc_final: 0.6660 (mptm) REVERT: E 646 SER cc_start: 0.8517 (m) cc_final: 0.8195 (p) REVERT: E 672 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7532 (mm-30) REVERT: E 685 GLU cc_start: 0.7385 (mp0) cc_final: 0.6987 (mm-30) REVERT: E 688 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7205 (mt-10) REVERT: E 722 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7862 (mtt180) REVERT: F 56 HIS cc_start: 0.5393 (OUTLIER) cc_final: 0.5159 (m90) REVERT: F 64 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5751 (tm-30) REVERT: F 68 ARG cc_start: 0.7301 (ttp-110) cc_final: 0.6479 (ttp-110) REVERT: F 160 LYS cc_start: 0.8075 (tptp) cc_final: 0.7873 (tptp) REVERT: F 166 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8072 (tt) REVERT: F 216 ASP cc_start: 0.8386 (t0) cc_final: 0.8105 (t0) REVERT: F 428 ASP cc_start: 0.7365 (m-30) cc_final: 0.7165 (m-30) REVERT: F 436 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: F 479 SER cc_start: 0.8172 (m) cc_final: 0.7963 (p) REVERT: F 487 ASP cc_start: 0.7846 (m-30) cc_final: 0.7621 (m-30) REVERT: F 574 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8055 (mp) REVERT: F 616 ASN cc_start: 0.8441 (t0) cc_final: 0.7466 (t0) REVERT: F 649 LYS cc_start: 0.8097 (mppt) cc_final: 0.7888 (mppt) REVERT: F 672 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6990 (mp0) outliers start: 257 outliers final: 125 residues processed: 853 average time/residue: 0.4652 time to fit residues: 588.8420 Evaluate side-chains 790 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 629 time to evaluate : 2.893 ------------------------------------------------------------------------------- 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 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 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 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 285 ASN 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 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 226 MET Chi-restraints excluded: chain C residue 290 LYS 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 317 LYS Chi-restraints excluded: chain C residue 321 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 470 SER Chi-restraints excluded: chain C residue 487 ASP 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 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 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 295 GLU 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 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 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 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 253 PHE 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 436 GLU 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 672 GLU 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 125 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 142 optimal weight: 8.9990 chunk 342 optimal weight: 0.6980 chunk 184 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 332 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 234 optimal weight: 9.9990 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 280 GLN A 285 ASN A 336 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 647 GLN D 463 HIS ** D 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 554 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.191149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146144 restraints weight = 47493.307| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.39 r_work: 0.3594 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28989 Z= 0.191 Angle : 0.673 12.063 39187 Z= 0.347 Chirality : 0.041 0.234 4273 Planarity : 0.005 0.063 5063 Dihedral : 9.175 73.218 4024 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.02 % Favored : 94.54 % Rotamer: Outliers : 7.22 % Allowed : 26.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3444 helix: 0.55 (0.10), residues: 2544 sheet: None (None), residues: 0 loop : -2.55 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 89 HIS 0.007 0.001 HIS D 463 PHE 0.030 0.002 PHE E 27 TYR 0.022 0.002 TYR A 300 ARG 0.011 0.001 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.06414 ( 1761) hydrogen bonds : angle 5.17947 ( 5229) covalent geometry : bond 0.00418 (28989) covalent geometry : angle 0.67315 (39187) *********************** 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 866 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 642 time to evaluate : 3.202 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 69 CYS cc_start: 0.7977 (t) cc_final: 0.7481 (t) REVERT: A 73 TRP cc_start: 0.7082 (t-100) cc_final: 0.6781 (t60) REVERT: A 219 MET cc_start: 0.8137 (mmm) cc_final: 0.7559 (mmm) REVERT: A 291 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7134 (ppt170) REVERT: A 426 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6282 (mm) REVERT: A 457 TRP cc_start: 0.8008 (m-10) cc_final: 0.6924 (m-10) REVERT: A 484 ASP cc_start: 0.8093 (m-30) cc_final: 0.7770 (m-30) REVERT: A 489 SER cc_start: 0.8604 (t) cc_final: 0.8297 (p) REVERT: A 532 ASP cc_start: 0.7311 (t0) cc_final: 0.7039 (t0) REVERT: A 557 CYS cc_start: 0.7916 (t) cc_final: 0.7692 (t) REVERT: A 613 ASP cc_start: 0.7941 (m-30) cc_final: 0.7592 (m-30) REVERT: A 632 ASP cc_start: 0.7711 (t0) cc_final: 0.7139 (t70) REVERT: A 671 LYS cc_start: 0.8302 (mttt) cc_final: 0.8058 (mptt) REVERT: A 688 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7210 (mt-10) REVERT: A 696 GLU cc_start: 0.7965 (tp30) cc_final: 0.7662 (tp30) REVERT: A 721 HIS cc_start: 0.8102 (t70) cc_final: 0.7858 (t70) REVERT: B 75 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: B 105 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7254 (ptp90) REVERT: B 118 LEU cc_start: 0.8566 (mt) cc_final: 0.8226 (mt) REVERT: B 146 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6742 (tmm160) REVERT: B 174 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: B 221 PHE cc_start: 0.7816 (t80) cc_final: 0.7232 (t80) REVERT: B 258 GLU cc_start: 0.7891 (tp30) cc_final: 0.7553 (tp30) REVERT: B 487 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: B 565 ASP cc_start: 0.7729 (m-30) cc_final: 0.7356 (m-30) REVERT: B 590 GLN cc_start: 0.5183 (OUTLIER) cc_final: 0.4747 (mp10) REVERT: B 593 LEU cc_start: 0.7394 (mp) cc_final: 0.7152 (mt) REVERT: B 680 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 73 TRP cc_start: 0.7908 (t-100) cc_final: 0.7575 (t-100) REVERT: C 155 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7758 (mtmm) REVERT: C 183 MET cc_start: 0.6876 (tmm) cc_final: 0.6444 (tmm) REVERT: C 444 LYS cc_start: 0.6393 (pttm) cc_final: 0.6120 (mtmm) REVERT: C 459 VAL cc_start: 0.7756 (OUTLIER) cc_final: 0.7493 (p) REVERT: C 462 ASP cc_start: 0.6209 (t0) cc_final: 0.5947 (t0) REVERT: C 466 ASN cc_start: 0.8058 (m-40) cc_final: 0.7833 (m110) REVERT: C 483 ASP cc_start: 0.8002 (t0) cc_final: 0.7648 (t0) REVERT: C 487 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: C 529 ARG cc_start: 0.7485 (mpt-90) cc_final: 0.7160 (mpt-90) REVERT: C 612 ASP cc_start: 0.7876 (m-30) cc_final: 0.7574 (t0) REVERT: C 613 ASP cc_start: 0.7862 (m-30) cc_final: 0.7653 (m-30) REVERT: C 672 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7606 (mm-30) REVERT: C 685 GLU cc_start: 0.7278 (mp0) cc_final: 0.7054 (mm-30) REVERT: D 89 TRP cc_start: 0.7094 (OUTLIER) cc_final: 0.6469 (m-90) REVERT: D 98 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6465 (pp) REVERT: D 146 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6757 (tpp-160) REVERT: D 174 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: D 219 MET cc_start: 0.7590 (tmm) cc_final: 0.7169 (tmm) REVERT: D 279 MET cc_start: 0.4552 (mmp) cc_final: 0.3952 (mmp) REVERT: D 290 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8240 (ptpp) REVERT: D 295 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8318 (pp20) REVERT: D 308 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7168 (mt) REVERT: D 315 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5998 (mp0) REVERT: D 436 GLU cc_start: 0.7326 (pp20) cc_final: 0.7000 (pp20) REVERT: D 444 LYS cc_start: 0.7633 (mtmt) cc_final: 0.6954 (mtmm) REVERT: D 447 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8031 (mpt180) REVERT: D 554 ASN cc_start: 0.7996 (m-40) cc_final: 0.7700 (m-40) REVERT: D 568 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.7025 (ttm-80) REVERT: D 606 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7156 (mt-10) REVERT: D 633 GLU cc_start: 0.4646 (OUTLIER) cc_final: 0.4414 (mm-30) REVERT: E 58 HIS cc_start: 0.1665 (OUTLIER) cc_final: 0.0810 (m-70) REVERT: E 70 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6921 (mpt90) REVERT: E 114 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6557 (pt0) REVERT: E 182 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: E 226 MET cc_start: 0.6501 (ppp) cc_final: 0.6107 (ppp) REVERT: E 271 MET cc_start: 0.0440 (tmm) cc_final: 0.0166 (ttt) REVERT: E 475 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8419 (mt) REVERT: E 483 ASP cc_start: 0.8254 (t0) cc_final: 0.7861 (t0) REVERT: E 493 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6395 (mpp-170) REVERT: E 537 GLU cc_start: 0.7858 (tp30) cc_final: 0.7520 (tp30) REVERT: E 550 TYR cc_start: 0.8601 (t80) cc_final: 0.7976 (t80) REVERT: E 560 GLU cc_start: 0.7009 (tt0) cc_final: 0.6781 (tt0) REVERT: E 611 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8014 (ttt-90) REVERT: E 612 ASP cc_start: 0.8126 (m-30) cc_final: 0.7787 (t0) REVERT: E 615 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8102 (mtpp) REVERT: E 635 LYS cc_start: 0.7041 (mptm) cc_final: 0.6774 (mptm) REVERT: E 646 SER cc_start: 0.8521 (m) cc_final: 0.8246 (p) REVERT: E 706 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7211 (mt-10) REVERT: E 722 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7885 (mtt180) REVERT: F 64 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: F 68 ARG cc_start: 0.7417 (ttp-110) cc_final: 0.7033 (ttp-110) REVERT: F 219 MET cc_start: 0.7759 (mtm) cc_final: 0.7432 (mtm) REVERT: F 251 ASP cc_start: 0.5988 (OUTLIER) cc_final: 0.5227 (t0) REVERT: F 271 MET cc_start: 0.0745 (mmt) cc_final: 0.0401 (mmt) REVERT: F 272 THR cc_start: 0.5737 (OUTLIER) cc_final: 0.4963 (m) REVERT: F 299 GLN cc_start: 0.8236 (pt0) cc_final: 0.7992 (pt0) REVERT: F 322 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6878 (mt) REVERT: F 436 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: F 479 SER cc_start: 0.8203 (m) cc_final: 0.7971 (p) REVERT: F 487 ASP cc_start: 0.7874 (m-30) cc_final: 0.7641 (m-30) REVERT: F 519 MET cc_start: 0.7677 (ttm) cc_final: 0.7035 (mtt) REVERT: F 574 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8100 (mp) REVERT: F 616 ASN cc_start: 0.8538 (t0) cc_final: 0.7568 (t0) REVERT: F 635 LYS cc_start: 0.7248 (mmpt) cc_final: 0.7039 (mmpt) REVERT: F 649 LYS cc_start: 0.8263 (mppt) cc_final: 0.8040 (mppt) REVERT: F 672 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7076 (mp0) outliers start: 224 outliers final: 126 residues processed: 811 average time/residue: 0.4753 time to fit residues: 576.0959 Evaluate side-chains 783 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 623 time to evaluate : 2.900 ------------------------------------------------------------------------------- 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 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 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 649 LYS 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 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 174 GLU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 459 VAL 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 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 B residue 703 VAL Chi-restraints excluded: chain C residue 56 HIS 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 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 292 ARG Chi-restraints excluded: chain C residue 295 GLU 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 480 LEU Chi-restraints excluded: chain C residue 487 ASP 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 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 156 GLN 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 295 GLU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 315 GLU 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 470 SER 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 574 LEU 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 616 ASN Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 35 SER 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 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 176 VAL Chi-restraints excluded: chain F residue 183 MET 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 436 GLU 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 187 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 312 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 290 optimal weight: 0.1980 chunk 296 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 340 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN C 347 HIS C 463 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN F 121 ASN F 299 GLN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.191888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146831 restraints weight = 47849.772| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.32 r_work: 0.3607 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28989 Z= 0.173 Angle : 0.649 15.003 39187 Z= 0.330 Chirality : 0.041 0.175 4273 Planarity : 0.005 0.089 5063 Dihedral : 8.379 72.405 3979 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.02 % Favored : 94.57 % Rotamer: Outliers : 7.48 % Allowed : 26.22 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3444 helix: 0.82 (0.10), residues: 2560 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 714 HIS 0.009 0.001 HIS C 347 PHE 0.020 0.002 PHE E 27 TYR 0.030 0.002 TYR B 304 ARG 0.012 0.001 ARG E 539 Details of bonding type rmsd hydrogen bonds : bond 0.05620 ( 1761) hydrogen bonds : angle 4.87508 ( 5229) covalent geometry : bond 0.00383 (28989) covalent geometry : angle 0.64900 (39187) *********************** 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 863 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 631 time to evaluate : 4.119 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: 0.7960 (t) cc_final: 0.7466 (t) REVERT: A 73 TRP cc_start: 0.7151 (t-100) cc_final: 0.6831 (t-100) REVERT: A 162 LEU cc_start: 0.8155 (mt) cc_final: 0.7949 (mm) REVERT: A 183 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7100 (ttp) REVERT: A 219 MET cc_start: 0.7953 (mmm) cc_final: 0.7401 (mmm) REVERT: A 291 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7072 (ppt170) REVERT: A 426 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6477 (mm) REVERT: A 457 TRP cc_start: 0.8021 (m-10) cc_final: 0.6918 (m-10) REVERT: A 489 SER cc_start: 0.8620 (t) cc_final: 0.8291 (p) REVERT: A 532 ASP cc_start: 0.7215 (t0) cc_final: 0.6960 (t0) REVERT: A 557 CYS cc_start: 0.7951 (t) cc_final: 0.7747 (t) REVERT: A 671 LYS cc_start: 0.8298 (mttt) cc_final: 0.8073 (mptt) REVERT: A 688 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 721 HIS cc_start: 0.8101 (t70) cc_final: 0.7863 (t70) REVERT: B 54 ARG cc_start: 0.7121 (mtm110) cc_final: 0.6479 (mtm-85) REVERT: B 72 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6882 (t0) REVERT: B 75 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: B 76 PHE cc_start: 0.7332 (m-10) cc_final: 0.7071 (m-10) REVERT: B 118 LEU cc_start: 0.8517 (mt) cc_final: 0.8242 (mt) REVERT: B 146 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6764 (tmm160) REVERT: B 158 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7408 (tm-30) REVERT: B 220 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7514 (mmm-85) REVERT: B 221 PHE cc_start: 0.7831 (t80) cc_final: 0.7395 (t80) REVERT: B 479 SER cc_start: 0.8529 (t) cc_final: 0.8220 (p) REVERT: B 487 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: B 565 ASP cc_start: 0.7690 (m-30) cc_final: 0.7283 (m-30) REVERT: B 590 GLN cc_start: 0.5104 (OUTLIER) cc_final: 0.4713 (mp10) REVERT: B 593 LEU cc_start: 0.7363 (mp) cc_final: 0.7144 (mt) REVERT: B 680 GLN cc_start: 0.8532 (tm-30) cc_final: 0.7964 (tm-30) REVERT: B 723 LEU cc_start: 0.8643 (tp) cc_final: 0.8422 (mp) REVERT: C 114 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.5015 (pt0) REVERT: C 155 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7787 (mtmm) REVERT: C 183 MET cc_start: 0.6861 (tmm) cc_final: 0.6475 (tmm) REVERT: C 273 ASN cc_start: 0.1059 (OUTLIER) cc_final: 0.0521 (m110) REVERT: C 444 LYS cc_start: 0.6426 (pttm) cc_final: 0.5998 (mtmm) REVERT: C 462 ASP cc_start: 0.6258 (t0) cc_final: 0.5953 (t0) REVERT: C 466 ASN cc_start: 0.8002 (m-40) cc_final: 0.7688 (m110) REVERT: C 483 ASP cc_start: 0.7975 (t0) cc_final: 0.7326 (t0) REVERT: C 487 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6841 (m-30) REVERT: C 527 ASP cc_start: 0.7690 (t0) cc_final: 0.7468 (t0) REVERT: C 529 ARG cc_start: 0.7455 (mpt-90) cc_final: 0.7135 (mpt-90) REVERT: C 566 MET cc_start: 0.8222 (tmm) cc_final: 0.7674 (ttp) REVERT: C 612 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7611 (t0) REVERT: C 672 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7583 (mm-30) REVERT: C 685 GLU cc_start: 0.7243 (mp0) cc_final: 0.7028 (mm-30) REVERT: C 693 GLU cc_start: 0.7281 (tp30) cc_final: 0.7049 (tp30) REVERT: D 89 TRP cc_start: 0.6815 (OUTLIER) cc_final: 0.6187 (m-90) REVERT: D 98 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6434 (pp) REVERT: D 162 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8051 (tt) REVERT: D 219 MET cc_start: 0.7654 (tmm) cc_final: 0.7191 (tmm) REVERT: D 220 ARG cc_start: 0.7502 (ptm160) cc_final: 0.6915 (ttm170) REVERT: D 279 MET cc_start: 0.4406 (mmp) cc_final: 0.3759 (mmp) REVERT: D 290 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8460 (ptpp) REVERT: D 295 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8190 (pp20) REVERT: D 308 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7206 (mt) REVERT: D 436 GLU cc_start: 0.7298 (pp20) cc_final: 0.7014 (pp20) REVERT: D 444 LYS cc_start: 0.7692 (mtmt) cc_final: 0.7094 (mtmt) REVERT: D 447 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8032 (mpt180) REVERT: D 538 MET cc_start: 0.7793 (mmm) cc_final: 0.7316 (mmm) REVERT: D 554 ASN cc_start: 0.8014 (m-40) cc_final: 0.7728 (m-40) REVERT: D 568 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.7064 (ttm-80) REVERT: D 606 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7314 (mt-10) REVERT: D 614 TYR cc_start: 0.8458 (t80) cc_final: 0.8098 (t80) REVERT: D 633 GLU cc_start: 0.4659 (OUTLIER) cc_final: 0.4429 (mm-30) REVERT: E 58 HIS cc_start: 0.2071 (OUTLIER) cc_final: 0.1252 (m-70) REVERT: E 70 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6909 (mpt90) REVERT: E 73 TRP cc_start: 0.7897 (t-100) cc_final: 0.7686 (t-100) REVERT: E 114 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6629 (pt0) REVERT: E 226 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5698 (ppp) REVERT: E 227 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.5951 (mm) REVERT: E 300 TYR cc_start: 0.7386 (m-80) cc_final: 0.7092 (m-80) REVERT: E 455 ASN cc_start: 0.8537 (t0) cc_final: 0.8027 (t0) REVERT: E 475 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8438 (mt) REVERT: E 483 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7871 (t0) REVERT: E 493 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6364 (mpp-170) REVERT: E 537 GLU cc_start: 0.7829 (tp30) cc_final: 0.7528 (tp30) REVERT: E 560 GLU cc_start: 0.7016 (tt0) cc_final: 0.6803 (tt0) REVERT: E 611 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8079 (ttt-90) REVERT: E 612 ASP cc_start: 0.8123 (m-30) cc_final: 0.7825 (t0) REVERT: E 615 LYS cc_start: 0.8426 (mmmm) cc_final: 0.8189 (mtpp) REVERT: E 635 LYS cc_start: 0.7016 (mptm) cc_final: 0.6704 (mptm) REVERT: E 646 SER cc_start: 0.8514 (m) cc_final: 0.8230 (p) REVERT: E 672 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7515 (mm-30) REVERT: E 693 GLU cc_start: 0.7231 (tp30) cc_final: 0.7019 (tp30) REVERT: E 706 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7365 (mt-10) REVERT: E 713 ASN cc_start: 0.8410 (t0) cc_final: 0.8205 (t0) REVERT: E 722 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7886 (mtt180) REVERT: F 64 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5943 (tm-30) REVERT: F 68 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7109 (ttp-110) REVERT: F 219 MET cc_start: 0.7686 (mtm) cc_final: 0.7433 (mtm) REVERT: F 292 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7488 (mtp180) REVERT: F 299 GLN cc_start: 0.8181 (pt0) cc_final: 0.7969 (pt0) REVERT: F 322 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6759 (mt) REVERT: F 436 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: F 459 VAL cc_start: 0.8534 (t) cc_final: 0.8331 (m) REVERT: F 463 HIS cc_start: 0.7035 (p-80) cc_final: 0.6784 (p90) REVERT: F 487 ASP cc_start: 0.7849 (m-30) cc_final: 0.7638 (m-30) REVERT: F 523 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8095 (ttt-90) REVERT: F 574 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8070 (mp) REVERT: F 616 ASN cc_start: 0.8585 (t0) cc_final: 0.8294 (t0) REVERT: F 649 LYS cc_start: 0.8236 (mppt) cc_final: 0.8026 (mppt) REVERT: F 672 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7034 (mp0) outliers start: 232 outliers final: 131 residues processed: 806 average time/residue: 0.5854 time to fit residues: 707.5914 Evaluate side-chains 790 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 622 time to evaluate : 3.056 ------------------------------------------------------------------------------- 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 109 ILE 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 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 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 72 ASP 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 146 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 240 LYS 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 522 VAL 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 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 273 ASN Chi-restraints excluded: chain C residue 292 ARG 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 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 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 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 152 LEU 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 295 GLU 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 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 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 279 MET 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 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 E residue 675 LEU 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 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 167 SER Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 302 GLN 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 436 GLU Chi-restraints excluded: chain F residue 523 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 86 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 231 optimal weight: 8.9990 chunk 307 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS C 463 HIS C 506 GLN C 616 ASN D 229 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN F 307 ASN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4432 r_free = 0.4432 target = 0.191627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145984 restraints weight = 47462.571| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.35 r_work: 0.3609 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28989 Z= 0.174 Angle : 0.645 15.679 39187 Z= 0.325 Chirality : 0.040 0.183 4273 Planarity : 0.005 0.068 5063 Dihedral : 7.986 71.075 3952 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.05 % Favored : 94.60 % Rotamer: Outliers : 6.68 % Allowed : 26.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3444 helix: 0.95 (0.10), residues: 2573 sheet: None (None), residues: 0 loop : -2.45 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 180 HIS 0.016 0.001 HIS B 347 PHE 0.016 0.002 PHE E 27 TYR 0.022 0.002 TYR B 331 ARG 0.011 0.001 ARG E 539 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 1761) hydrogen bonds : angle 4.73222 ( 5229) covalent geometry : bond 0.00390 (28989) covalent geometry : angle 0.64517 (39187) *********************** 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 841 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 634 time to evaluate : 2.904 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: symmetry clash REVERT: A 69 CYS cc_start: 0.8083 (t) cc_final: 0.7580 (t) REVERT: A 73 TRP cc_start: 0.7309 (t-100) cc_final: 0.6944 (t-100) REVERT: A 183 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7139 (ttp) REVERT: A 219 MET cc_start: 0.7882 (mmm) cc_final: 0.7336 (mmm) REVERT: A 291 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6991 (ppt170) REVERT: A 426 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6672 (mm) REVERT: A 487 ASP cc_start: 0.7152 (m-30) cc_final: 0.6812 (m-30) REVERT: A 489 SER cc_start: 0.8611 (t) cc_final: 0.8253 (p) REVERT: A 532 ASP cc_start: 0.7235 (t0) cc_final: 0.6966 (t0) REVERT: A 550 TYR cc_start: 0.8596 (t80) cc_final: 0.8150 (t80) REVERT: A 606 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6717 (mt-10) REVERT: A 671 LYS cc_start: 0.8321 (mttt) cc_final: 0.8078 (mptt) REVERT: A 721 HIS cc_start: 0.8115 (t70) cc_final: 0.7883 (t70) REVERT: B 66 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.7591 (t) REVERT: B 72 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6846 (t0) REVERT: B 75 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: B 118 LEU cc_start: 0.8550 (mt) cc_final: 0.8246 (mt) REVERT: B 146 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6759 (tmm160) REVERT: B 158 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 162 LEU cc_start: 0.8147 (mm) cc_final: 0.7899 (mm) REVERT: B 479 SER cc_start: 0.8507 (t) cc_final: 0.8209 (p) REVERT: B 487 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: B 565 ASP cc_start: 0.7686 (m-30) cc_final: 0.7274 (m-30) REVERT: B 590 GLN cc_start: 0.5138 (OUTLIER) cc_final: 0.4720 (mp10) REVERT: B 593 LEU cc_start: 0.7355 (mp) cc_final: 0.7117 (mt) REVERT: B 680 GLN cc_start: 0.8516 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 73 TRP cc_start: 0.7985 (t-100) cc_final: 0.7748 (t-100) REVERT: C 114 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.5124 (pt0) REVERT: C 183 MET cc_start: 0.7086 (tmm) cc_final: 0.6693 (tmm) REVERT: C 226 MET cc_start: 0.6872 (ppp) cc_final: 0.6670 (ppp) REVERT: C 444 LYS cc_start: 0.6451 (pttm) cc_final: 0.5879 (mtmm) REVERT: C 462 ASP cc_start: 0.6251 (t0) cc_final: 0.5889 (t0) REVERT: C 466 ASN cc_start: 0.8021 (m-40) cc_final: 0.7647 (m110) REVERT: C 483 ASP cc_start: 0.7978 (t0) cc_final: 0.7345 (t0) REVERT: C 487 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6813 (m-30) REVERT: C 527 ASP cc_start: 0.7669 (t0) cc_final: 0.7443 (t0) REVERT: C 529 ARG cc_start: 0.7527 (mpt-90) cc_final: 0.7181 (mpt-90) REVERT: C 550 TYR cc_start: 0.8746 (t80) cc_final: 0.8205 (t80) REVERT: C 606 GLU cc_start: 0.7228 (tt0) cc_final: 0.6874 (mt-10) REVERT: C 612 ASP cc_start: 0.7956 (m-30) cc_final: 0.7629 (t0) REVERT: C 685 GLU cc_start: 0.7388 (mp0) cc_final: 0.7186 (mm-30) REVERT: C 688 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7262 (mt-10) REVERT: C 693 GLU cc_start: 0.7290 (tp30) cc_final: 0.7014 (tp30) REVERT: D 33 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7375 (pp) REVERT: D 89 TRP cc_start: 0.6769 (OUTLIER) cc_final: 0.6149 (m-90) REVERT: D 98 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6435 (pp) REVERT: D 162 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8028 (tt) REVERT: D 220 ARG cc_start: 0.7488 (ptm160) cc_final: 0.6990 (ttm170) REVERT: D 279 MET cc_start: 0.4444 (mmp) cc_final: 0.3799 (mmp) REVERT: D 290 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8333 (ptpp) REVERT: D 295 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8155 (pp20) REVERT: D 308 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7207 (mt) REVERT: D 428 ASP cc_start: 0.7184 (m-30) cc_final: 0.6962 (m-30) REVERT: D 436 GLU cc_start: 0.7341 (pp20) cc_final: 0.7024 (pp20) REVERT: D 444 LYS cc_start: 0.7689 (mtmt) cc_final: 0.7048 (mtmt) REVERT: D 447 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8055 (mpt180) REVERT: D 517 ASP cc_start: 0.7366 (t0) cc_final: 0.7033 (t0) REVERT: D 519 MET cc_start: 0.7495 (ptm) cc_final: 0.7195 (ptp) REVERT: D 538 MET cc_start: 0.7870 (mmm) cc_final: 0.7294 (mmm) REVERT: D 554 ASN cc_start: 0.8037 (m-40) cc_final: 0.7810 (m110) REVERT: D 568 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.7025 (ttm-80) REVERT: D 606 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7308 (mt-10) REVERT: D 614 TYR cc_start: 0.8549 (t80) cc_final: 0.8261 (t80) REVERT: D 633 GLU cc_start: 0.4683 (OUTLIER) cc_final: 0.4463 (mm-30) REVERT: E 58 HIS cc_start: 0.1756 (OUTLIER) cc_final: 0.0936 (m170) REVERT: E 70 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6925 (mpt90) REVERT: E 114 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6757 (pt0) REVERT: E 226 MET cc_start: 0.6035 (ppp) cc_final: 0.5617 (ppp) REVERT: E 227 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.5739 (mm) REVERT: E 300 TYR cc_start: 0.7316 (m-80) cc_final: 0.6932 (m-80) REVERT: E 483 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7799 (t0) REVERT: E 493 ARG cc_start: 0.6738 (mpt180) cc_final: 0.6361 (mpp-170) REVERT: E 519 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6509 (ptp) REVERT: E 537 GLU cc_start: 0.7861 (tp30) cc_final: 0.7543 (tp30) REVERT: E 550 TYR cc_start: 0.8573 (t80) cc_final: 0.7930 (t80) REVERT: E 560 GLU cc_start: 0.7047 (tt0) cc_final: 0.6827 (tt0) REVERT: E 611 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8062 (ttt-90) REVERT: E 612 ASP cc_start: 0.8108 (m-30) cc_final: 0.7798 (t0) REVERT: E 615 LYS cc_start: 0.8432 (mmmm) cc_final: 0.8188 (mtpp) REVERT: E 616 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8133 (t0) REVERT: E 635 LYS cc_start: 0.7084 (mptm) cc_final: 0.6764 (mptm) REVERT: E 646 SER cc_start: 0.8509 (m) cc_final: 0.8232 (p) REVERT: E 688 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7247 (mt-10) REVERT: E 693 GLU cc_start: 0.7217 (tp30) cc_final: 0.6967 (tp30) REVERT: E 706 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7476 (mt-10) REVERT: E 722 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7905 (mtt180) REVERT: F 64 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5931 (tm-30) REVERT: F 68 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.7145 (ttp-110) REVERT: F 160 LYS cc_start: 0.7994 (tptp) cc_final: 0.7793 (tptp) REVERT: F 219 MET cc_start: 0.7684 (mtm) cc_final: 0.7423 (mtm) REVERT: F 251 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.5210 (t0) REVERT: F 272 THR cc_start: 0.5777 (OUTLIER) cc_final: 0.4874 (m) REVERT: F 322 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6479 (mt) REVERT: F 345 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.5956 (mtp-110) REVERT: F 436 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: F 483 ASP cc_start: 0.7444 (m-30) cc_final: 0.6989 (m-30) REVERT: F 487 ASP cc_start: 0.7890 (m-30) cc_final: 0.7660 (m-30) REVERT: F 574 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8000 (mp) REVERT: F 616 ASN cc_start: 0.8597 (t0) cc_final: 0.8323 (t0) REVERT: F 635 LYS cc_start: 0.7245 (mmpt) cc_final: 0.7005 (mmpt) REVERT: F 724 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7643 (mtmp) outliers start: 207 outliers final: 134 residues processed: 793 average time/residue: 0.4829 time to fit residues: 568.6247 Evaluate side-chains 792 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 622 time to evaluate : 3.265 ------------------------------------------------------------------------------- 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 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 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 166 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 LYS 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 459 VAL 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 522 VAL 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 B residue 703 VAL 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 114 GLU Chi-restraints excluded: chain C residue 292 ARG 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 470 SER 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 589 GLN 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 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 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 295 GLU 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 342 ARG Chi-restraints excluded: chain D residue 343 CYS 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 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 227 LEU Chi-restraints excluded: chain E residue 261 GLU 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 475 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 519 MET 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 671 LYS Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 697 LYS 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 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 167 SER 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 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 322 LEU Chi-restraints excluded: chain F residue 331 TYR 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 436 GLU 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 Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 66 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 316 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 259 optimal weight: 20.0000 chunk 312 optimal weight: 0.7980 chunk 286 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 232 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS C 616 ASN C 647 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 GLN E 650 ASN F 307 ASN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.191373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146194 restraints weight = 47639.509| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.40 r_work: 0.3585 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28989 Z= 0.183 Angle : 0.651 16.182 39187 Z= 0.326 Chirality : 0.041 0.174 4273 Planarity : 0.005 0.076 5063 Dihedral : 7.890 70.071 3948 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.05 % Favored : 94.66 % Rotamer: Outliers : 7.03 % Allowed : 26.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3444 helix: 0.99 (0.10), residues: 2588 sheet: None (None), residues: 0 loop : -2.46 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 180 HIS 0.018 0.001 HIS B 347 PHE 0.039 0.002 PHE C 278 TYR 0.019 0.002 TYR B 550 ARG 0.010 0.001 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.05438 ( 1761) hydrogen bonds : angle 4.66105 ( 5229) covalent geometry : bond 0.00416 (28989) covalent geometry : angle 0.65072 (39187) *********************** 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 850 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 632 time to evaluate : 2.840 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: A 69 CYS cc_start: 0.8025 (t) cc_final: 0.7538 (t) REVERT: A 73 TRP cc_start: 0.7318 (t-100) cc_final: 0.6920 (t-100) REVERT: A 106 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6810 (tt) REVERT: A 162 LEU cc_start: 0.8153 (mp) cc_final: 0.7913 (mm) REVERT: A 183 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7313 (ttp) REVERT: A 219 MET cc_start: 0.7925 (mmm) cc_final: 0.7366 (mmm) REVERT: A 291 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6989 (ppt170) REVERT: A 426 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6796 (mm) REVERT: A 487 ASP cc_start: 0.7225 (m-30) cc_final: 0.6875 (m-30) REVERT: A 489 SER cc_start: 0.8627 (t) cc_final: 0.8253 (p) REVERT: A 532 ASP cc_start: 0.7257 (t0) cc_final: 0.6969 (t0) REVERT: A 606 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6843 (mt-10) REVERT: A 671 LYS cc_start: 0.8331 (mttt) cc_final: 0.8080 (mptt) REVERT: A 721 HIS cc_start: 0.8085 (t70) cc_final: 0.7846 (t70) REVERT: B 66 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7603 (t) REVERT: B 118 LEU cc_start: 0.8521 (mt) cc_final: 0.8223 (mt) REVERT: B 158 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6893 (tm-30) REVERT: B 162 LEU cc_start: 0.8149 (mm) cc_final: 0.7922 (mm) REVERT: B 253 PHE cc_start: 0.6089 (t80) cc_final: 0.5835 (t80) REVERT: B 299 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 444 LYS cc_start: 0.7660 (pttm) cc_final: 0.7084 (pttm) REVERT: B 487 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: B 565 ASP cc_start: 0.7693 (m-30) cc_final: 0.7242 (m-30) REVERT: B 568 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7226 (ttm110) REVERT: B 590 GLN cc_start: 0.5178 (OUTLIER) cc_final: 0.4773 (mp10) REVERT: B 593 LEU cc_start: 0.7370 (mp) cc_final: 0.7161 (mt) REVERT: B 680 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 114 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.5075 (pt0) REVERT: C 180 TRP cc_start: 0.7143 (OUTLIER) cc_final: 0.6841 (t-100) REVERT: C 183 MET cc_start: 0.7137 (tmm) cc_final: 0.6738 (tmm) REVERT: C 226 MET cc_start: 0.6837 (ppp) cc_final: 0.6617 (ppp) REVERT: C 323 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.5806 (mp10) REVERT: C 429 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7331 (pt0) REVERT: C 462 ASP cc_start: 0.6276 (t0) cc_final: 0.6073 (t0) REVERT: C 466 ASN cc_start: 0.8003 (m-40) cc_final: 0.7665 (m-40) REVERT: C 483 ASP cc_start: 0.7978 (t0) cc_final: 0.7353 (t0) REVERT: C 487 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: C 527 ASP cc_start: 0.7643 (t0) cc_final: 0.7442 (t0) REVERT: C 529 ARG cc_start: 0.7509 (mpt-90) cc_final: 0.7116 (mpt-90) REVERT: C 550 TYR cc_start: 0.8751 (t80) cc_final: 0.8185 (t80) REVERT: C 606 GLU cc_start: 0.7249 (tt0) cc_final: 0.6963 (mt-10) REVERT: C 612 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7650 (t0) REVERT: C 688 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7289 (mt-10) REVERT: C 693 GLU cc_start: 0.7356 (tp30) cc_final: 0.7080 (tp30) REVERT: D 33 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7355 (pp) REVERT: D 89 TRP cc_start: 0.6855 (OUTLIER) cc_final: 0.6420 (m-90) REVERT: D 98 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6487 (pp) REVERT: D 162 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8110 (tt) REVERT: D 219 MET cc_start: 0.7706 (tmm) cc_final: 0.7351 (tmm) REVERT: D 278 PHE cc_start: 0.0189 (OUTLIER) cc_final: -0.1159 (m-10) REVERT: D 279 MET cc_start: 0.4537 (mmp) cc_final: 0.3980 (mmp) REVERT: D 308 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7258 (mt) REVERT: D 428 ASP cc_start: 0.7148 (m-30) cc_final: 0.6933 (m-30) REVERT: D 436 GLU cc_start: 0.7336 (pp20) cc_final: 0.7031 (pp20) REVERT: D 444 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7025 (mtmt) REVERT: D 517 ASP cc_start: 0.7400 (t0) cc_final: 0.7082 (t0) REVERT: D 538 MET cc_start: 0.7931 (mmm) cc_final: 0.7332 (mmm) REVERT: D 554 ASN cc_start: 0.8071 (m-40) cc_final: 0.7852 (m110) REVERT: D 565 ASP cc_start: 0.7925 (t0) cc_final: 0.7640 (t0) REVERT: D 568 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.7068 (ttm-80) REVERT: D 606 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7395 (mt-10) REVERT: E 58 HIS cc_start: 0.1716 (OUTLIER) cc_final: 0.0857 (m170) REVERT: E 70 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6910 (mpt90) REVERT: E 73 TRP cc_start: 0.7903 (t-100) cc_final: 0.7699 (t-100) REVERT: E 114 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6719 (pt0) REVERT: E 226 MET cc_start: 0.6185 (ppp) cc_final: 0.5633 (ppp) REVERT: E 271 MET cc_start: -0.0947 (ttt) cc_final: -0.1654 (ttp) REVERT: E 300 TYR cc_start: 0.7517 (m-80) cc_final: 0.7173 (m-80) REVERT: E 327 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7740 (mtpt) REVERT: E 332 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6466 (mm-40) REVERT: E 448 GLU cc_start: 0.6956 (mp0) cc_final: 0.6674 (mp0) REVERT: E 455 ASN cc_start: 0.8545 (t0) cc_final: 0.7987 (t0) REVERT: E 483 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7786 (t0) REVERT: E 493 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6358 (mpp-170) REVERT: E 537 GLU cc_start: 0.7856 (tp30) cc_final: 0.7542 (tp30) REVERT: E 550 TYR cc_start: 0.8563 (t80) cc_final: 0.7978 (t80) REVERT: E 560 GLU cc_start: 0.7074 (tt0) cc_final: 0.6847 (tt0) REVERT: E 611 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8103 (ttt-90) REVERT: E 612 ASP cc_start: 0.8110 (m-30) cc_final: 0.7796 (t0) REVERT: E 615 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8186 (mtpp) REVERT: E 635 LYS cc_start: 0.7088 (mptm) cc_final: 0.6767 (mptm) REVERT: E 646 SER cc_start: 0.8509 (m) cc_final: 0.8218 (p) REVERT: E 688 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7246 (mt-10) REVERT: E 693 GLU cc_start: 0.7236 (tp30) cc_final: 0.6996 (tp30) REVERT: E 706 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7535 (mt-10) REVERT: E 722 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7900 (mtt180) REVERT: F 64 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5900 (tm-30) REVERT: F 68 ARG cc_start: 0.7630 (ttp-110) cc_final: 0.7079 (ttp-110) REVERT: F 166 LEU cc_start: 0.8524 (mt) cc_final: 0.8152 (tt) REVERT: F 219 MET cc_start: 0.7823 (mtm) cc_final: 0.7591 (mtm) REVERT: F 251 ASP cc_start: 0.5649 (OUTLIER) cc_final: 0.5307 (t0) REVERT: F 272 THR cc_start: 0.5372 (OUTLIER) cc_final: 0.5016 (m) REVERT: F 295 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: F 299 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: F 345 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.5916 (mtp-110) REVERT: F 436 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: F 483 ASP cc_start: 0.7434 (m-30) cc_final: 0.6990 (m-30) REVERT: F 487 ASP cc_start: 0.7889 (m-30) cc_final: 0.7674 (m-30) REVERT: F 574 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8006 (mp) REVERT: F 616 ASN cc_start: 0.8600 (t0) cc_final: 0.8286 (m-40) REVERT: F 671 LYS cc_start: 0.8381 (mttp) cc_final: 0.7991 (mttp) REVERT: F 724 LYS cc_start: 0.7942 (mttp) cc_final: 0.7715 (mtmp) outliers start: 218 outliers final: 141 residues processed: 797 average time/residue: 0.4662 time to fit residues: 557.8578 Evaluate side-chains 796 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 621 time to evaluate : 4.153 ------------------------------------------------------------------------------- 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 106 LEU 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 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 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 612 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 720 ILE 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 217 MET Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 321 LYS 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 459 VAL 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 522 VAL 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 B residue 703 VAL Chi-restraints excluded: chain C residue 57 HIS 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 292 ARG 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 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 470 SER 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 570 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 647 GLN 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 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 150 SER 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 278 PHE 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 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 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 27 PHE 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 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 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 470 SER 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 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 E residue 675 LEU Chi-restraints excluded: chain E residue 697 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 120 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 167 SER 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 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 299 GLN 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 436 GLU Chi-restraints excluded: chain F residue 535 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 193 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 294 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 276 optimal weight: 0.2980 chunk 239 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 463 HIS C 647 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN F 156 GLN F 329 GLN F 336 ASN F 506 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.191837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146750 restraints weight = 47436.546| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.39 r_work: 0.3600 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28989 Z= 0.163 Angle : 0.652 16.377 39187 Z= 0.325 Chirality : 0.040 0.172 4273 Planarity : 0.005 0.073 5063 Dihedral : 7.446 69.641 3929 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.08 % Favored : 94.63 % Rotamer: Outliers : 6.45 % Allowed : 27.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3444 helix: 1.07 (0.10), residues: 2597 sheet: None (None), residues: 0 loop : -2.46 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 180 HIS 0.012 0.001 HIS B 347 PHE 0.043 0.002 PHE C 262 TYR 0.022 0.002 TYR B 550 ARG 0.010 0.001 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 1761) hydrogen bonds : angle 4.56910 ( 5229) covalent geometry : bond 0.00368 (28989) covalent geometry : angle 0.65215 (39187) *********************** 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 820 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 620 time to evaluate : 2.939 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: A 69 CYS cc_start: 0.8121 (t) cc_final: 0.7650 (t) REVERT: A 73 TRP cc_start: 0.7332 (t-100) cc_final: 0.7032 (t-100) REVERT: A 180 TRP cc_start: 0.6831 (OUTLIER) cc_final: 0.6471 (t-100) REVERT: A 183 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7572 (ttp) REVERT: A 219 MET cc_start: 0.8079 (mmm) cc_final: 0.7447 (mmm) REVERT: A 291 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6950 (ppt170) REVERT: A 426 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6859 (mm) REVERT: A 487 ASP cc_start: 0.7168 (m-30) cc_final: 0.6839 (m-30) REVERT: A 489 SER cc_start: 0.8617 (t) cc_final: 0.8226 (p) REVERT: A 532 ASP cc_start: 0.7194 (t0) cc_final: 0.6929 (t0) REVERT: A 550 TYR cc_start: 0.8563 (t80) cc_final: 0.8131 (t80) REVERT: A 606 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6834 (mt-10) REVERT: A 614 TYR cc_start: 0.8417 (t80) cc_final: 0.8096 (t80) REVERT: A 671 LYS cc_start: 0.8304 (mttt) cc_final: 0.8055 (mptt) REVERT: A 696 GLU cc_start: 0.7967 (tp30) cc_final: 0.7641 (tm-30) REVERT: A 721 HIS cc_start: 0.8073 (t70) cc_final: 0.7843 (t70) REVERT: B 66 SER cc_start: 0.7859 (OUTLIER) cc_final: 0.7587 (t) REVERT: B 75 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: B 118 LEU cc_start: 0.8509 (mt) cc_final: 0.8208 (mt) REVERT: B 146 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6792 (tmm160) REVERT: B 230 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: B 253 PHE cc_start: 0.6085 (t80) cc_final: 0.5787 (t80) REVERT: B 304 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6969 (p90) REVERT: B 487 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: B 565 ASP cc_start: 0.7667 (m-30) cc_final: 0.7268 (m-30) REVERT: B 590 GLN cc_start: 0.5174 (OUTLIER) cc_final: 0.4784 (mp10) REVERT: B 593 LEU cc_start: 0.7329 (mp) cc_final: 0.7110 (mt) REVERT: B 680 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8187 (tt0) REVERT: C 73 TRP cc_start: 0.8072 (t-100) cc_final: 0.7825 (t-100) REVERT: C 114 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.5052 (pt0) REVERT: C 180 TRP cc_start: 0.7188 (OUTLIER) cc_final: 0.6862 (t-100) REVERT: C 183 MET cc_start: 0.7064 (tmm) cc_final: 0.6678 (tmm) REVERT: C 226 MET cc_start: 0.6805 (ppp) cc_final: 0.6553 (ppp) REVERT: C 429 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7319 (pt0) REVERT: C 462 ASP cc_start: 0.6229 (t0) cc_final: 0.5845 (t0) REVERT: C 466 ASN cc_start: 0.7973 (m-40) cc_final: 0.7553 (m110) REVERT: C 469 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8379 (ttmt) REVERT: C 483 ASP cc_start: 0.7952 (t0) cc_final: 0.7317 (t0) REVERT: C 487 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6791 (m-30) REVERT: C 527 ASP cc_start: 0.7677 (t0) cc_final: 0.7465 (t0) REVERT: C 529 ARG cc_start: 0.7520 (mpt-90) cc_final: 0.7115 (mpt-90) REVERT: C 606 GLU cc_start: 0.7214 (tt0) cc_final: 0.6885 (mt-10) REVERT: C 612 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7641 (t0) REVERT: C 693 GLU cc_start: 0.7307 (tp30) cc_final: 0.7025 (tp30) REVERT: D 33 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7263 (pp) REVERT: D 34 SER cc_start: 0.4241 (OUTLIER) cc_final: 0.3968 (p) REVERT: D 89 TRP cc_start: 0.6936 (OUTLIER) cc_final: 0.6506 (m-90) REVERT: D 98 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6508 (pp) REVERT: D 219 MET cc_start: 0.7673 (tmm) cc_final: 0.7339 (tmm) REVERT: D 278 PHE cc_start: -0.0104 (OUTLIER) cc_final: -0.1276 (m-10) REVERT: D 279 MET cc_start: 0.4580 (mmp) cc_final: 0.4010 (mmp) REVERT: D 280 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7989 (pp30) REVERT: D 308 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7270 (mt) REVERT: D 428 ASP cc_start: 0.7177 (m-30) cc_final: 0.6951 (m-30) REVERT: D 444 LYS cc_start: 0.7687 (mtmt) cc_final: 0.7035 (mtmt) REVERT: D 517 ASP cc_start: 0.7399 (t0) cc_final: 0.7070 (t0) REVERT: D 538 MET cc_start: 0.7897 (mmm) cc_final: 0.7298 (mmm) REVERT: D 554 ASN cc_start: 0.8094 (m-40) cc_final: 0.7863 (m110) REVERT: D 565 ASP cc_start: 0.7928 (t0) cc_final: 0.7638 (t0) REVERT: D 568 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.7071 (ttm-80) REVERT: D 606 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7384 (mt-10) REVERT: D 612 ASP cc_start: 0.7924 (t0) cc_final: 0.7674 (t0) REVERT: E 70 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6892 (mpt90) REVERT: E 73 TRP cc_start: 0.7871 (t-100) cc_final: 0.7632 (t-100) REVERT: E 114 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6796 (pt0) REVERT: E 226 MET cc_start: 0.6189 (ppp) cc_final: 0.5844 (ppp) REVERT: E 271 MET cc_start: -0.1090 (ttt) cc_final: -0.1596 (ttp) REVERT: E 300 TYR cc_start: 0.7361 (m-80) cc_final: 0.7075 (m-80) REVERT: E 327 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7783 (mtpt) REVERT: E 332 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6462 (mm-40) REVERT: E 483 ASP cc_start: 0.8231 (t0) cc_final: 0.7783 (t0) REVERT: E 493 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6314 (mpp-170) REVERT: E 537 GLU cc_start: 0.7871 (tp30) cc_final: 0.7542 (tp30) REVERT: E 550 TYR cc_start: 0.8550 (t80) cc_final: 0.7918 (t80) REVERT: E 560 GLU cc_start: 0.7049 (tt0) cc_final: 0.6818 (tt0) REVERT: E 611 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8112 (ttt-90) REVERT: E 612 ASP cc_start: 0.8105 (m-30) cc_final: 0.7793 (t0) REVERT: E 615 LYS cc_start: 0.8432 (mmmm) cc_final: 0.8182 (mtpp) REVERT: E 635 LYS cc_start: 0.7086 (mptm) cc_final: 0.6744 (mptm) REVERT: E 646 SER cc_start: 0.8466 (m) cc_final: 0.8158 (p) REVERT: E 693 GLU cc_start: 0.7224 (tp30) cc_final: 0.6963 (tp30) REVERT: E 706 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7502 (mt-10) REVERT: E 722 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7866 (mtt180) REVERT: F 64 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5923 (tm-30) REVERT: F 68 ARG cc_start: 0.7630 (ttp-110) cc_final: 0.7004 (ttp-110) REVERT: F 106 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6574 (tt) REVERT: F 166 LEU cc_start: 0.8532 (mt) cc_final: 0.8209 (tt) REVERT: F 219 MET cc_start: 0.7831 (mtm) cc_final: 0.7622 (mtm) REVERT: F 251 ASP cc_start: 0.5483 (OUTLIER) cc_final: 0.5206 (t0) REVERT: F 272 THR cc_start: 0.5352 (OUTLIER) cc_final: 0.5014 (m) REVERT: F 295 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: F 336 ASN cc_start: 0.6020 (OUTLIER) cc_final: 0.5518 (p0) REVERT: F 436 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: F 483 ASP cc_start: 0.7422 (m-30) cc_final: 0.6952 (m-30) REVERT: F 487 ASP cc_start: 0.7898 (m-30) cc_final: 0.7661 (m-30) REVERT: F 561 GLU cc_start: 0.7655 (tp30) cc_final: 0.7332 (tp30) REVERT: F 574 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7972 (mp) REVERT: F 616 ASN cc_start: 0.8577 (t0) cc_final: 0.8318 (m-40) REVERT: F 635 LYS cc_start: 0.7225 (mmpt) cc_final: 0.6947 (mmpt) REVERT: F 671 LYS cc_start: 0.8349 (mttp) cc_final: 0.7971 (mttp) REVERT: F 672 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: F 724 LYS cc_start: 0.7891 (mttp) cc_final: 0.7635 (mtmp) outliers start: 200 outliers final: 136 residues processed: 779 average time/residue: 0.5970 time to fit residues: 692.3957 Evaluate side-chains 781 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 608 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 155 LYS 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 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 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 146 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 216 ASP Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 304 TYR 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 459 VAL 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 522 VAL 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 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 B residue 703 VAL 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 114 GLU Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 324 THR 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 470 SER 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 504 THR 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 570 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 647 GLN Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 34 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 156 GLN 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 278 PHE Chi-restraints excluded: chain D residue 280 GLN 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 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 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 27 PHE 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 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 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 470 SER 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 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 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 697 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 106 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 167 SER 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 436 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 297 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 319 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 346 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN C 463 HIS C 647 GLN D 263 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS F 121 ASN ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.191288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145990 restraints weight = 47817.878| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.48 r_work: 0.3588 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28989 Z= 0.187 Angle : 0.673 16.799 39187 Z= 0.334 Chirality : 0.041 0.194 4273 Planarity : 0.005 0.069 5063 Dihedral : 7.374 69.331 3927 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.26 % Favored : 94.48 % Rotamer: Outliers : 6.51 % Allowed : 27.64 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3444 helix: 1.06 (0.10), residues: 2596 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 180 HIS 0.014 0.001 HIS B 347 PHE 0.028 0.002 PHE C 278 TYR 0.020 0.001 TYR B 550 ARG 0.012 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 1761) hydrogen bonds : angle 4.57439 ( 5229) covalent geometry : bond 0.00426 (28989) covalent geometry : angle 0.67291 (39187) *********************** 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 810 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 608 time to evaluate : 2.926 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: 0.3999 (OUTLIER) cc_final: 0.3686 (pp) REVERT: A 69 CYS cc_start: 0.8062 (t) cc_final: 0.7545 (t) REVERT: A 73 TRP cc_start: 0.7418 (t-100) cc_final: 0.7180 (t-100) REVERT: A 106 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6809 (tt) REVERT: A 180 TRP cc_start: 0.6797 (OUTLIER) cc_final: 0.6489 (t-100) REVERT: A 183 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7357 (ttp) REVERT: A 219 MET cc_start: 0.7963 (mmm) cc_final: 0.7376 (mmm) REVERT: A 291 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6932 (ppt170) REVERT: A 426 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6787 (mm) REVERT: A 459 VAL cc_start: 0.8208 (p) cc_final: 0.7989 (m) REVERT: A 487 ASP cc_start: 0.7209 (m-30) cc_final: 0.6878 (m-30) REVERT: A 489 SER cc_start: 0.8623 (t) cc_final: 0.8232 (p) REVERT: A 532 ASP cc_start: 0.7220 (t0) cc_final: 0.6955 (t0) REVERT: A 550 TYR cc_start: 0.8587 (t80) cc_final: 0.8119 (t80) REVERT: A 606 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6694 (mt-10) REVERT: A 671 LYS cc_start: 0.8323 (mttt) cc_final: 0.8072 (mptt) REVERT: A 721 HIS cc_start: 0.8083 (t70) cc_final: 0.7859 (t70) REVERT: B 58 HIS cc_start: 0.7002 (m90) cc_final: 0.6746 (m90) REVERT: B 66 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7598 (t) REVERT: B 93 PHE cc_start: 0.7159 (t80) cc_final: 0.6487 (t80) REVERT: B 118 LEU cc_start: 0.8531 (mt) cc_final: 0.8233 (mt) REVERT: B 146 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6842 (tmm160) REVERT: B 230 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: B 253 PHE cc_start: 0.6079 (t80) cc_final: 0.5693 (t80) REVERT: B 304 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.7009 (p90) REVERT: B 487 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: B 565 ASP cc_start: 0.7659 (m-30) cc_final: 0.7252 (m-30) REVERT: B 590 GLN cc_start: 0.5220 (OUTLIER) cc_final: 0.4814 (mp10) REVERT: B 593 LEU cc_start: 0.7386 (mp) cc_final: 0.7146 (mt) REVERT: B 680 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8189 (tt0) REVERT: C 73 TRP cc_start: 0.8035 (t-100) cc_final: 0.7775 (t-100) REVERT: C 114 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.5140 (pt0) REVERT: C 180 TRP cc_start: 0.7121 (OUTLIER) cc_final: 0.6824 (t-100) REVERT: C 183 MET cc_start: 0.7075 (tmm) cc_final: 0.6678 (tmm) REVERT: C 226 MET cc_start: 0.6802 (ppp) cc_final: 0.6526 (ppp) REVERT: C 323 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.5696 (mp10) REVERT: C 429 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7335 (pt0) REVERT: C 444 LYS cc_start: 0.6512 (pttm) cc_final: 0.6084 (mtmm) REVERT: C 483 ASP cc_start: 0.7929 (t0) cc_final: 0.7347 (t0) REVERT: C 487 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: C 519 MET cc_start: 0.6653 (mtm) cc_final: 0.6441 (mtm) REVERT: C 527 ASP cc_start: 0.7673 (t0) cc_final: 0.7464 (t0) REVERT: C 529 ARG cc_start: 0.7552 (mpt-90) cc_final: 0.7157 (mpt-90) REVERT: C 606 GLU cc_start: 0.7230 (tt0) cc_final: 0.6902 (mt-10) REVERT: C 612 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7690 (t0) REVERT: C 679 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7474 (mtm-85) REVERT: C 693 GLU cc_start: 0.7345 (tp30) cc_final: 0.7067 (tp30) REVERT: D 33 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7290 (pp) REVERT: D 34 SER cc_start: 0.4303 (OUTLIER) cc_final: 0.4097 (p) REVERT: D 89 TRP cc_start: 0.6877 (OUTLIER) cc_final: 0.6438 (m-90) REVERT: D 98 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6523 (pp) REVERT: D 219 MET cc_start: 0.7696 (tmm) cc_final: 0.7347 (tmm) REVERT: D 278 PHE cc_start: -0.0223 (OUTLIER) cc_final: -0.1421 (m-10) REVERT: D 279 MET cc_start: 0.4775 (mmp) cc_final: 0.4215 (mmp) REVERT: D 280 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7957 (pp30) REVERT: D 308 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7395 (mt) REVERT: D 428 ASP cc_start: 0.7187 (m-30) cc_final: 0.6970 (m-30) REVERT: D 444 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7158 (mtmt) REVERT: D 517 ASP cc_start: 0.7407 (t0) cc_final: 0.7101 (t0) REVERT: D 538 MET cc_start: 0.7956 (mmm) cc_final: 0.7316 (mmm) REVERT: D 565 ASP cc_start: 0.7920 (t0) cc_final: 0.7637 (t0) REVERT: D 568 ARG cc_start: 0.7346 (ttm-80) cc_final: 0.7054 (ttm-80) REVERT: D 606 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7377 (mt-10) REVERT: D 612 ASP cc_start: 0.7998 (t0) cc_final: 0.7759 (t0) REVERT: E 70 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6916 (mpt90) REVERT: E 114 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6766 (pt0) REVERT: E 226 MET cc_start: 0.5998 (ppp) cc_final: 0.5646 (ppp) REVERT: E 271 MET cc_start: -0.1554 (ttt) cc_final: -0.1789 (ttp) REVERT: E 327 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7739 (mtpt) REVERT: E 332 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6423 (mm-40) REVERT: E 429 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7336 (mt-10) REVERT: E 483 ASP cc_start: 0.8228 (t0) cc_final: 0.7808 (t0) REVERT: E 493 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6337 (mpp-170) REVERT: E 519 MET cc_start: 0.7423 (ttp) cc_final: 0.7006 (ttm) REVERT: E 537 GLU cc_start: 0.7860 (tp30) cc_final: 0.7549 (tp30) REVERT: E 550 TYR cc_start: 0.8560 (t80) cc_final: 0.8000 (t80) REVERT: E 560 GLU cc_start: 0.7096 (tt0) cc_final: 0.6866 (tt0) REVERT: E 611 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8069 (ttt-90) REVERT: E 612 ASP cc_start: 0.8134 (m-30) cc_final: 0.7788 (t0) REVERT: E 615 LYS cc_start: 0.8472 (mmmm) cc_final: 0.8204 (mtpp) REVERT: E 635 LYS cc_start: 0.7133 (mptm) cc_final: 0.6782 (mptm) REVERT: E 646 SER cc_start: 0.8521 (m) cc_final: 0.8192 (t) REVERT: E 693 GLU cc_start: 0.7249 (tp30) cc_final: 0.6987 (tp30) REVERT: E 706 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7507 (mt-10) REVERT: E 722 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7927 (mtt180) REVERT: F 64 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5975 (tm-30) REVERT: F 68 ARG cc_start: 0.7721 (ttp-110) cc_final: 0.7109 (ttp-110) REVERT: F 166 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8250 (tt) REVERT: F 219 MET cc_start: 0.7817 (mtm) cc_final: 0.7587 (mtm) REVERT: F 251 ASP cc_start: 0.5301 (OUTLIER) cc_final: 0.5029 (t0) REVERT: F 272 THR cc_start: 0.5265 (OUTLIER) cc_final: 0.4948 (m) REVERT: F 295 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7483 (pp20) REVERT: F 436 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: F 483 ASP cc_start: 0.7425 (m-30) cc_final: 0.6966 (m-30) REVERT: F 487 ASP cc_start: 0.7933 (m-30) cc_final: 0.7698 (m-30) REVERT: F 519 MET cc_start: 0.7487 (ttm) cc_final: 0.7176 (mtt) REVERT: F 520 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7241 (tt0) REVERT: F 561 GLU cc_start: 0.7712 (tp30) cc_final: 0.7399 (tp30) REVERT: F 616 ASN cc_start: 0.8604 (t0) cc_final: 0.8352 (m-40) REVERT: F 671 LYS cc_start: 0.8398 (mttp) cc_final: 0.8028 (mttp) REVERT: F 672 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7064 (mp0) outliers start: 202 outliers final: 142 residues processed: 764 average time/residue: 0.4841 time to fit residues: 551.0025 Evaluate side-chains 781 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 602 time to evaluate : 3.528 ------------------------------------------------------------------------------- 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 106 LEU 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 155 LYS 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 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 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 146 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 216 ASP Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 304 TYR 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 459 VAL 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 522 VAL 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 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 B residue 699 THR Chi-restraints excluded: chain B residue 703 VAL 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 114 GLU Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 292 ARG 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 333 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 470 SER 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 504 THR 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 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 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 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 156 GLN 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 278 PHE Chi-restraints excluded: chain D residue 280 GLN 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 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 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 27 PHE 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 220 ARG 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 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 475 LEU Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 524 GLN 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 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 675 LEU 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 120 ASP Chi-restraints excluded: chain F residue 146 ARG 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 167 SER 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 345 ARG Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 436 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 92 optimal weight: 0.0980 chunk 318 optimal weight: 5.9990 chunk 276 optimal weight: 0.0670 chunk 247 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 154 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 255 optimal weight: 30.0000 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 B 56 HIS ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 273 ASN C 647 GLN D 336 ASN D 658 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.192370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.147836 restraints weight = 47960.317| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.64 r_work: 0.3597 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4450 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= 0.142 Angle : 0.657 16.813 39187 Z= 0.326 Chirality : 0.039 0.185 4273 Planarity : 0.005 0.069 5063 Dihedral : 7.235 69.229 3925 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.05 % Favored : 94.69 % Rotamer: Outliers : 5.39 % Allowed : 28.76 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3444 helix: 1.24 (0.10), residues: 2590 sheet: None (None), residues: 0 loop : -2.48 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP E 180 HIS 0.009 0.001 HIS B 347 PHE 0.027 0.001 PHE C 278 TYR 0.029 0.001 TYR E 300 ARG 0.013 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 1761) hydrogen bonds : angle 4.42189 ( 5229) covalent geometry : bond 0.00319 (28989) covalent geometry : angle 0.65657 (39187) *********************** 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 781 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 614 time to evaluate : 5.685 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: A 29 LEU cc_start: 0.3811 (OUTLIER) cc_final: 0.3611 (pp) REVERT: A 69 CYS cc_start: 0.7964 (t) cc_final: 0.7419 (t) REVERT: A 73 TRP cc_start: 0.7388 (t-100) cc_final: 0.7169 (t-100) REVERT: A 106 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6604 (tt) REVERT: A 180 TRP cc_start: 0.6796 (OUTLIER) cc_final: 0.6517 (t-100) REVERT: A 219 MET cc_start: 0.7898 (mmm) cc_final: 0.7281 (mmm) REVERT: A 426 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6865 (mm) REVERT: A 459 VAL cc_start: 0.8211 (p) cc_final: 0.7997 (m) REVERT: A 487 ASP cc_start: 0.7137 (m-30) cc_final: 0.6836 (m-30) REVERT: A 489 SER cc_start: 0.8600 (t) cc_final: 0.8212 (p) REVERT: A 532 ASP cc_start: 0.7094 (t0) cc_final: 0.6864 (t0) REVERT: A 537 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: A 550 TYR cc_start: 0.8558 (t80) cc_final: 0.8078 (t80) REVERT: A 606 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6674 (mt-10) REVERT: A 671 LYS cc_start: 0.8322 (mttt) cc_final: 0.8081 (mptt) REVERT: A 696 GLU cc_start: 0.7822 (tp30) cc_final: 0.7546 (tp30) REVERT: A 721 HIS cc_start: 0.8003 (t70) cc_final: 0.7785 (t70) REVERT: B 58 HIS cc_start: 0.6808 (m90) cc_final: 0.6556 (m90) REVERT: B 66 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7633 (t) REVERT: B 93 PHE cc_start: 0.7117 (t80) cc_final: 0.6541 (t80) REVERT: B 118 LEU cc_start: 0.8495 (mt) cc_final: 0.8207 (mt) REVERT: B 146 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6976 (tmm160) REVERT: B 253 PHE cc_start: 0.6248 (t80) cc_final: 0.5794 (t80) REVERT: B 304 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.7053 (p90) REVERT: B 487 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: B 565 ASP cc_start: 0.7631 (m-30) cc_final: 0.7219 (m-30) REVERT: B 590 GLN cc_start: 0.5197 (OUTLIER) cc_final: 0.4847 (mp10) REVERT: B 680 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8145 (tt0) REVERT: C 73 TRP cc_start: 0.7968 (t-100) cc_final: 0.7698 (t-100) REVERT: C 114 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.5023 (pt0) REVERT: C 183 MET cc_start: 0.7072 (tmm) cc_final: 0.6691 (tmm) REVERT: C 226 MET cc_start: 0.6766 (ppp) cc_final: 0.6470 (ppp) REVERT: C 323 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.5655 (mp10) REVERT: C 429 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7287 (pt0) REVERT: C 444 LYS cc_start: 0.6513 (pttm) cc_final: 0.6075 (mtmm) REVERT: C 483 ASP cc_start: 0.8057 (t0) cc_final: 0.7636 (t0) REVERT: C 487 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: C 529 ARG cc_start: 0.7486 (mpt-90) cc_final: 0.7151 (mpt-90) REVERT: C 606 GLU cc_start: 0.7251 (tt0) cc_final: 0.6909 (mt-10) REVERT: C 612 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7617 (t0) REVERT: C 613 ASP cc_start: 0.7843 (m-30) cc_final: 0.7452 (m-30) REVERT: C 679 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7540 (mtm-85) REVERT: C 693 GLU cc_start: 0.7361 (tp30) cc_final: 0.7102 (tp30) REVERT: D 33 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7247 (pp) REVERT: D 34 SER cc_start: 0.4434 (OUTLIER) cc_final: 0.4161 (p) REVERT: D 89 TRP cc_start: 0.6845 (OUTLIER) cc_final: 0.6412 (m-90) REVERT: D 98 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6507 (pp) REVERT: D 219 MET cc_start: 0.7739 (tmm) cc_final: 0.7385 (tmm) REVERT: D 279 MET cc_start: 0.4706 (mmp) cc_final: 0.4131 (mmp) REVERT: D 280 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7926 (pp30) REVERT: D 308 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7508 (mt) REVERT: D 428 ASP cc_start: 0.7118 (m-30) cc_final: 0.6879 (m-30) REVERT: D 444 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7161 (mtmt) REVERT: D 517 ASP cc_start: 0.7192 (t0) cc_final: 0.6892 (t0) REVERT: D 538 MET cc_start: 0.7779 (mmm) cc_final: 0.7117 (mmm) REVERT: D 565 ASP cc_start: 0.7993 (t0) cc_final: 0.7710 (t0) REVERT: D 568 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7117 (ttm-80) REVERT: D 606 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7323 (mt-10) REVERT: D 612 ASP cc_start: 0.7963 (t0) cc_final: 0.7733 (t0) REVERT: E 70 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6879 (mpt90) REVERT: E 73 TRP cc_start: 0.7798 (t-100) cc_final: 0.7592 (t-100) REVERT: E 114 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6711 (pt0) REVERT: E 226 MET cc_start: 0.5908 (ppp) cc_final: 0.5421 (ppp) REVERT: E 327 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7721 (mtpt) REVERT: E 332 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6440 (mm-40) REVERT: E 429 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7267 (mt-10) REVERT: E 483 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7868 (t0) REVERT: E 493 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6263 (mpp-170) REVERT: E 537 GLU cc_start: 0.7821 (tp30) cc_final: 0.7513 (tp30) REVERT: E 550 TYR cc_start: 0.8576 (t80) cc_final: 0.7977 (t80) REVERT: E 560 GLU cc_start: 0.7067 (tt0) cc_final: 0.6817 (tt0) REVERT: E 566 MET cc_start: 0.8137 (tmm) cc_final: 0.7473 (tmm) REVERT: E 611 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8167 (ttt-90) REVERT: E 615 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8252 (mtpp) REVERT: E 635 LYS cc_start: 0.7044 (mptm) cc_final: 0.6682 (mptm) REVERT: E 646 SER cc_start: 0.8466 (m) cc_final: 0.8180 (t) REVERT: E 693 GLU cc_start: 0.7209 (tp30) cc_final: 0.6953 (tp30) REVERT: E 706 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7422 (mt-10) REVERT: E 722 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7926 (mtt180) REVERT: F 64 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6160 (tm-30) REVERT: F 68 ARG cc_start: 0.7656 (ttp-110) cc_final: 0.7023 (ttp-110) REVERT: F 166 LEU cc_start: 0.8571 (mt) cc_final: 0.8304 (tt) REVERT: F 219 MET cc_start: 0.8076 (mtm) cc_final: 0.7831 (mtm) REVERT: F 251 ASP cc_start: 0.5291 (OUTLIER) cc_final: 0.5041 (t0) REVERT: F 271 MET cc_start: 0.0842 (mmp) cc_final: 0.0474 (mmt) REVERT: F 436 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: F 483 ASP cc_start: 0.7420 (m-30) cc_final: 0.6952 (m-30) REVERT: F 487 ASP cc_start: 0.7915 (m-30) cc_final: 0.7662 (m-30) REVERT: F 519 MET cc_start: 0.7533 (ttm) cc_final: 0.7320 (ttm) REVERT: F 561 GLU cc_start: 0.7596 (tp30) cc_final: 0.7292 (tp30) REVERT: F 616 ASN cc_start: 0.8552 (t0) cc_final: 0.7664 (t0) REVERT: F 635 LYS cc_start: 0.7359 (mmpt) cc_final: 0.7107 (mmpt) REVERT: F 661 ARG cc_start: 0.7518 (ttm110) cc_final: 0.7126 (ttm110) REVERT: F 671 LYS cc_start: 0.8371 (mttp) cc_final: 0.8051 (mttp) REVERT: F 672 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: F 724 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7661 (mtmp) outliers start: 167 outliers final: 120 residues processed: 740 average time/residue: 0.6106 time to fit residues: 685.6558 Evaluate side-chains 755 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 603 time to evaluate : 3.258 ------------------------------------------------------------------------------- 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 106 LEU 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 280 GLN 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 537 GLU 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 685 GLU Chi-restraints excluded: chain A residue 686 TYR 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 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 217 MET Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 304 TYR 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 629 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 699 THR 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 114 GLU Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 292 ARG 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 514 LEU 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 723 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 34 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 156 GLN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 280 GLN 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 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 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 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 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 524 GLN 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 668 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 697 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 120 ASP Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 167 SER 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 345 ARG Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 436 GLU 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 719 LEU Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 57 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 314 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 281 optimal weight: 0.0980 chunk 212 optimal weight: 0.2980 chunk 102 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 273 ASN C 584 GLN C 647 GLN D 336 ASN D 658 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.197843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.151492 restraints weight = 47326.977| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.53 r_work: 0.3634 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28989 Z= 0.133 Angle : 0.669 20.804 39187 Z= 0.330 Chirality : 0.040 0.176 4273 Planarity : 0.005 0.078 5063 Dihedral : 6.951 68.945 3911 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.08 % Favored : 94.66 % Rotamer: Outliers : 4.90 % Allowed : 29.15 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3444 helix: 1.34 (0.11), residues: 2582 sheet: None (None), residues: 0 loop : -2.42 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP A 259 HIS 0.009 0.001 HIS C 60 PHE 0.032 0.001 PHE D 262 TYR 0.021 0.001 TYR F 304 ARG 0.014 0.001 ARG E 661 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 1761) hydrogen bonds : angle 4.35330 ( 5229) covalent geometry : bond 0.00294 (28989) covalent geometry : angle 0.66869 (39187) ********************** 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 753 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 601 time to evaluate : 3.084 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: 0.3977 (OUTLIER) cc_final: 0.3747 (pp) REVERT: A 69 CYS cc_start: 0.8078 (t) cc_final: 0.7556 (t) REVERT: A 73 TRP cc_start: 0.7507 (t-100) cc_final: 0.7291 (t-100) REVERT: A 106 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6585 (tt) REVERT: A 180 TRP cc_start: 0.7014 (OUTLIER) cc_final: 0.6745 (t-100) REVERT: A 219 MET cc_start: 0.7940 (mmm) cc_final: 0.7384 (mmm) REVERT: A 426 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6863 (mm) REVERT: A 487 ASP cc_start: 0.7211 (m-30) cc_final: 0.6907 (m-30) REVERT: A 489 SER cc_start: 0.8799 (t) cc_final: 0.8425 (p) REVERT: A 532 ASP cc_start: 0.7379 (t0) cc_final: 0.7152 (t0) REVERT: A 537 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: A 550 TYR cc_start: 0.8664 (t80) cc_final: 0.8278 (t80) REVERT: A 671 LYS cc_start: 0.8487 (mttt) cc_final: 0.8268 (mptt) REVERT: A 721 HIS cc_start: 0.8174 (t70) cc_final: 0.7958 (t70) REVERT: B 58 HIS cc_start: 0.6969 (m90) cc_final: 0.6692 (m90) REVERT: B 66 SER cc_start: 0.7981 (OUTLIER) cc_final: 0.7724 (t) REVERT: B 76 PHE cc_start: 0.7260 (m-10) cc_final: 0.7025 (m-10) REVERT: B 93 PHE cc_start: 0.7184 (t80) cc_final: 0.6572 (t80) REVERT: B 118 LEU cc_start: 0.8562 (mt) cc_final: 0.8296 (mt) REVERT: B 146 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6926 (tmm160) REVERT: B 164 GLU cc_start: 0.8260 (tp30) cc_final: 0.7858 (tp30) REVERT: B 220 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7686 (mmm-85) REVERT: B 253 PHE cc_start: 0.6265 (t80) cc_final: 0.5780 (t80) REVERT: B 261 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 290 LYS cc_start: 0.8634 (pttm) cc_final: 0.8400 (pttm) REVERT: B 487 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: B 565 ASP cc_start: 0.8020 (m-30) cc_final: 0.7632 (m-30) REVERT: B 590 GLN cc_start: 0.5412 (OUTLIER) cc_final: 0.5031 (mp10) REVERT: B 615 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8107 (mtpp) REVERT: B 680 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8402 (tt0) REVERT: C 73 TRP cc_start: 0.8170 (t-100) cc_final: 0.7907 (t-100) REVERT: C 180 TRP cc_start: 0.7135 (OUTLIER) cc_final: 0.6838 (t-100) REVERT: C 183 MET cc_start: 0.7239 (tmm) cc_final: 0.6825 (tmm) REVERT: C 226 MET cc_start: 0.6858 (ppp) cc_final: 0.6551 (ppp) REVERT: C 323 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.5746 (mp10) REVERT: C 429 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7674 (pt0) REVERT: C 444 LYS cc_start: 0.6777 (pttm) cc_final: 0.6298 (mtmm) REVERT: C 483 ASP cc_start: 0.8241 (t0) cc_final: 0.7831 (t0) REVERT: C 487 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: C 529 ARG cc_start: 0.7715 (mpt-90) cc_final: 0.7351 (mpt-90) REVERT: C 550 TYR cc_start: 0.8839 (t80) cc_final: 0.8450 (t80) REVERT: C 606 GLU cc_start: 0.7706 (tt0) cc_final: 0.7351 (mt-10) REVERT: C 612 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8040 (t0) REVERT: C 613 ASP cc_start: 0.8162 (m-30) cc_final: 0.7789 (m-30) REVERT: C 679 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7762 (mtm-85) REVERT: C 688 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7591 (mt-10) REVERT: C 693 GLU cc_start: 0.7718 (tp30) cc_final: 0.7482 (tp30) REVERT: D 33 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7246 (pp) REVERT: D 34 SER cc_start: 0.4560 (OUTLIER) cc_final: 0.4280 (p) REVERT: D 58 HIS cc_start: 0.7050 (m90) cc_final: 0.6692 (m90) REVERT: D 89 TRP cc_start: 0.6838 (OUTLIER) cc_final: 0.6413 (m-90) REVERT: D 98 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6457 (pp) REVERT: D 219 MET cc_start: 0.7964 (tmm) cc_final: 0.7681 (tmm) REVERT: D 279 MET cc_start: 0.4583 (mmp) cc_final: 0.3943 (mmp) REVERT: D 280 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7940 (pp30) REVERT: D 336 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.7023 (t0) REVERT: D 444 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7171 (mtmt) REVERT: D 517 ASP cc_start: 0.7581 (t0) cc_final: 0.7272 (t0) REVERT: D 538 MET cc_start: 0.7907 (mmm) cc_final: 0.7305 (mmm) REVERT: D 568 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7366 (ttm-80) REVERT: D 606 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7791 (mt-10) REVERT: D 671 LYS cc_start: 0.8345 (mmtp) cc_final: 0.8015 (mmtt) REVERT: E 70 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6941 (mpt90) REVERT: E 73 TRP cc_start: 0.8013 (t-100) cc_final: 0.7782 (t-100) REVERT: E 114 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6774 (pt0) REVERT: E 226 MET cc_start: 0.6122 (ppp) cc_final: 0.5727 (ppp) REVERT: E 327 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7780 (mtpt) REVERT: E 332 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6544 (mm-40) REVERT: E 475 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8488 (mt) REVERT: E 483 ASP cc_start: 0.8513 (t0) cc_final: 0.8077 (t0) REVERT: E 493 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6561 (mpp-170) REVERT: E 519 MET cc_start: 0.7548 (ttm) cc_final: 0.6856 (mtp) REVERT: E 537 GLU cc_start: 0.8047 (tp30) cc_final: 0.7723 (tp30) REVERT: E 550 TYR cc_start: 0.8658 (t80) cc_final: 0.8162 (t80) REVERT: E 560 GLU cc_start: 0.7432 (tt0) cc_final: 0.7200 (tt0) REVERT: E 611 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8186 (ttt-90) REVERT: E 615 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8397 (mtpp) REVERT: E 635 LYS cc_start: 0.7177 (mptm) cc_final: 0.6826 (mptm) REVERT: E 646 SER cc_start: 0.8538 (m) cc_final: 0.8248 (t) REVERT: E 672 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7933 (mm-30) REVERT: E 693 GLU cc_start: 0.7604 (tp30) cc_final: 0.7339 (tp30) REVERT: E 706 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7610 (mt-10) REVERT: E 722 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.8078 (mtt180) REVERT: F 64 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6367 (tm-30) REVERT: F 68 ARG cc_start: 0.7825 (ttp-110) cc_final: 0.7294 (ttp-110) REVERT: F 166 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (tt) REVERT: F 336 ASN cc_start: 0.6247 (OUTLIER) cc_final: 0.5724 (p0) REVERT: F 436 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: F 483 ASP cc_start: 0.7775 (m-30) cc_final: 0.7314 (m-30) REVERT: F 487 ASP cc_start: 0.8143 (m-30) cc_final: 0.7922 (m-30) REVERT: F 531 MET cc_start: 0.7819 (tpt) cc_final: 0.7603 (tpt) REVERT: F 561 GLU cc_start: 0.7966 (tp30) cc_final: 0.7596 (tp30) REVERT: F 574 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8072 (mp) REVERT: F 616 ASN cc_start: 0.8647 (t0) cc_final: 0.7808 (t0) REVERT: F 661 ARG cc_start: 0.7737 (ttm110) cc_final: 0.7393 (ttm110) REVERT: F 671 LYS cc_start: 0.8502 (mttp) cc_final: 0.8299 (mttp) REVERT: F 672 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: F 724 LYS cc_start: 0.8081 (mtmp) cc_final: 0.7812 (mtmp) outliers start: 152 outliers final: 108 residues processed: 717 average time/residue: 0.4829 time to fit residues: 516.0573 Evaluate side-chains 729 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 589 time to evaluate : 3.050 ------------------------------------------------------------------------------- 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 106 LEU 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 426 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 537 GLU 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 685 GLU Chi-restraints excluded: chain A residue 686 TYR 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 217 MET Chi-restraints excluded: chain B residue 268 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 487 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 686 TYR Chi-restraints excluded: chain B residue 699 THR 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 180 TRP Chi-restraints excluded: chain C residue 292 ARG 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 514 LEU 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 647 GLN Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 34 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 156 GLN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 456 VAL 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 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 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 475 LEU Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 611 ARG 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 675 LEU 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 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 226 MET Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 292 ARG 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 436 GLU 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 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 238 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 40 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 270 optimal weight: 0.9980 chunk 320 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 273 ASN C 584 GLN C 647 GLN D 307 ASN D 336 ASN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 GLN F 336 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.197565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.150693 restraints weight = 47434.392| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.50 r_work: 0.3619 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28989 Z= 0.146 Angle : 0.691 19.646 39187 Z= 0.338 Chirality : 0.041 0.263 4273 Planarity : 0.005 0.068 5063 Dihedral : 6.780 68.612 3902 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.82 % Favored : 94.92 % Rotamer: Outliers : 4.80 % Allowed : 29.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3444 helix: 1.38 (0.11), residues: 2582 sheet: None (None), residues: 0 loop : -2.40 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 259 HIS 0.008 0.001 HIS C 347 PHE 0.025 0.001 PHE C 278 TYR 0.022 0.002 TYR D 304 ARG 0.012 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 1761) hydrogen bonds : angle 4.36931 ( 5229) covalent geometry : bond 0.00330 (28989) covalent geometry : angle 0.69085 (39187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18583.90 seconds wall clock time: 330 minutes 0.49 seconds (19800.49 seconds total)