Starting phenix.real_space_refine on Sun Sep 13 15:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tw3_56358/09_2026/9tw3_56358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tw3_56358/09_2026/9tw3_56358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tw3_56358/09_2026/9tw3_56358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tw3_56358/09_2026/9tw3_56358.map" model { file = "/net/cci-nas-00/data/ceres_data/9tw3_56358/09_2026/9tw3_56358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tw3_56358/09_2026/9tw3_56358.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 14870 2.51 5 N 4056 2.21 5 O 4361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23420 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6583 Classifications: {'peptide': 813} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 773} Chain breaks: 1 Chain: "B" Number of atoms: 9481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9481 Classifications: {'peptide': 1192} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1134} Chain breaks: 6 Chain: "C" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2907 Classifications: {'peptide': 355} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 348} Chain: "D" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2641 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 1 Chain: "E" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 982 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "G" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 103 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'GDP': 1, 'MYR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16378 SG CYS C 137 47.841 129.133 37.758 1.00 90.88 S ATOM 16402 SG CYS C 140 49.388 131.430 40.705 1.00 81.73 S ATOM 19036 SG CYS D 43 48.647 127.649 38.236 1.00 93.69 S ATOM 19057 SG CYS D 46 47.376 128.905 40.202 1.00 77.47 S ATOM 19133 SG CYS D 55 54.423 134.472 27.082 1.00102.17 S ATOM 19153 SG CYS D 58 55.104 136.219 27.564 1.00104.93 S ATOM 23301 SG CYS G 18 51.851 134.327 26.168 1.00114.45 S ATOM 23327 SG CYS G 21 53.934 135.355 25.286 1.00110.30 S Time building chain proxies: 4.78, per 1000 atoms: 0.20 Number of scatterers: 23420 At special positions: 0 Unit cell: (104.4, 181.975, 236.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 2 15.00 Mg 1 11.99 O 4361 8.00 N 4056 7.00 C 14870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 600 " pdb="ZN ZN D 600 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 600 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 600 " - pdb=" SG CYS C 137 " pdb="ZN ZN D 600 " - pdb=" SG CYS C 140 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS G 18 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 55 " pdb="ZN ZN D 601 " - pdb=" SG CYS G 21 " Number of angles added : 12 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5522 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 22 sheets defined 51.3% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 4.046A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.602A pdb=" N LYS A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.556A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 196 through 205 removed outlier: 4.151A pdb=" N GLU A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 207 No H-bonds generated for 'chain 'A' and resid 206 through 207' Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.678A pdb=" N SER A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.904A pdb=" N HIS A 284 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.600A pdb=" N PHE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.629A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.612A pdb=" N PHE A 333 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 486 through 502 removed outlier: 3.681A pdb=" N TRP A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.693A pdb=" N GLN A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.988A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 560 Processing helix chain 'A' and resid 565 through 579 removed outlier: 3.816A pdb=" N LYS A 569 " --> pdb=" O ASN A 565 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 660 removed outlier: 3.755A pdb=" N GLN A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 713 through 717 removed outlier: 3.604A pdb=" N GLY A 716 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.533A pdb=" N MET A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 788 removed outlier: 3.648A pdb=" N VAL A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 811 removed outlier: 3.812A pdb=" N GLN A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 removed outlier: 3.612A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 removed outlier: 3.692A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 4.275A pdb=" N LYS A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 868 removed outlier: 4.060A pdb=" N VAL A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 22 removed outlier: 3.689A pdb=" N SER B 18 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 21 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP B 22 " --> pdb=" O TYR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 4.159A pdb=" N ILE B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.610A pdb=" N ILE B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 114' Processing helix chain 'B' and resid 121 through 141 removed outlier: 3.686A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 187 removed outlier: 3.585A pdb=" N TYR B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 238 through 254 removed outlier: 3.941A pdb=" N PHE B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.663A pdb=" N ALA B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.575A pdb=" N LEU B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 279' Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 303 through 311 removed outlier: 3.639A pdb=" N TYR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.526A pdb=" N THR B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.717A pdb=" N ALA B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.879A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 374 through 383 removed outlier: 3.841A pdb=" N SER B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.595A pdb=" N LYS B 395 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 417 removed outlier: 3.640A pdb=" N ASP B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.514A pdb=" N PHE B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 446 removed outlier: 3.982A pdb=" N ARG B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 removed outlier: 4.084A pdb=" N ILE B 456 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 467 through 473 removed outlier: 3.903A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 472 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 473 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.815A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 506 removed outlier: 3.512A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 530 through 546 removed outlier: 3.700A pdb=" N GLU B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS B 540 " --> pdb=" O MET B 536 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 543 " --> pdb=" O GLN B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.916A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 4.552A pdb=" N VAL B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 567 " --> pdb=" O ARG B 563 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 569 " --> pdb=" O CYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.751A pdb=" N ASN B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 removed outlier: 3.649A pdb=" N ILE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 587 removed outlier: 3.570A pdb=" N ASN B 586 " --> pdb=" O THR B 583 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 583 through 587' Processing helix chain 'B' and resid 590 through 600 removed outlier: 3.783A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 599 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 606 removed outlier: 3.877A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 611 No H-bonds generated for 'chain 'B' and resid 609 through 611' Processing helix chain 'B' and resid 612 through 624 Proline residue: B 618 - end of helix removed outlier: 3.649A pdb=" N GLN B 622 " --> pdb=" O PRO B 618 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.968A pdb=" N LYS B 634 " --> pdb=" O PHE B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 646 removed outlier: 3.770A pdb=" N CYS B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 657 removed outlier: 3.836A pdb=" N TYR B 654 " --> pdb=" O LYS B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 659 No H-bonds generated for 'chain 'B' and resid 658 through 659' Processing helix chain 'B' and resid 660 through 666 removed outlier: 3.820A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 686 removed outlier: 3.775A pdb=" N ALA B 675 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 694 removed outlier: 3.821A pdb=" N TYR B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 699 Processing helix chain 'B' and resid 712 through 718 removed outlier: 4.323A pdb=" N LEU B 716 " --> pdb=" O ARG B 712 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 717 " --> pdb=" O LYS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 734 removed outlier: 3.538A pdb=" N ARG B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 removed outlier: 4.058A pdb=" N LEU B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 777 Processing helix chain 'B' and resid 781 through 790 removed outlier: 4.146A pdb=" N ASP B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 803 removed outlier: 3.617A pdb=" N LYS B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 800 " --> pdb=" O LYS B 796 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 802 " --> pdb=" O ASN B 798 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 803 " --> pdb=" O LYS B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 825 Processing helix chain 'B' and resid 938 through 966 Processing helix chain 'B' and resid 1023 through 1027 removed outlier: 3.559A pdb=" N GLU B1026 " --> pdb=" O GLN B1023 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY B1027 " --> pdb=" O LYS B1024 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1023 through 1027' Processing helix chain 'B' and resid 1138 through 1142 Processing helix chain 'B' and resid 1249 through 1253 removed outlier: 3.638A pdb=" N GLY B1252 " --> pdb=" O PRO B1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1276 Processing helix chain 'C' and resid 110 through 127 removed outlier: 3.568A pdb=" N ARG C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP C 124 " --> pdb=" O GLY C 120 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 170 removed outlier: 3.758A pdb=" N THR C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN C 161 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 163 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 267 removed outlier: 3.869A pdb=" N GLN C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLN C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP C 200 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C 218 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN C 224 " --> pdb=" O GLU C 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 299 through 322 removed outlier: 3.808A pdb=" N ILE C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 421 through 447 removed outlier: 3.858A pdb=" N TRP C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.559A pdb=" N GLN D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 removed outlier: 4.219A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 128 removed outlier: 3.511A pdb=" N ARG D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 153 removed outlier: 3.671A pdb=" N GLY D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 205 removed outlier: 4.593A pdb=" N GLN D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS D 161 " --> pdb=" O ARG D 157 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 162 " --> pdb=" O HIS D 158 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU D 163 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 287 removed outlier: 3.541A pdb=" N GLU D 284 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 286 " --> pdb=" O TRP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 322 removed outlier: 3.780A pdb=" N ALA D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.763A pdb=" N GLU D 333 " --> pdb=" O CYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 362 Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.919A pdb=" N GLN D 368 " --> pdb=" O ASN D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 removed outlier: 3.684A pdb=" N ASN D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 378 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 381 " --> pdb=" O ASN D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.713A pdb=" N LEU D 401 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 402 " --> pdb=" O ALA D 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 398 through 402' Processing helix chain 'E' and resid 7 through 24 removed outlier: 3.748A pdb=" N GLN E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 24 " --> pdb=" O ARG E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 44 removed outlier: 3.970A pdb=" N ALA E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'E' and resid 50 through 78 removed outlier: 3.740A pdb=" N GLN E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU E 68 " --> pdb=" O HIS E 64 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU E 69 " --> pdb=" O MET E 65 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 10 through 18 removed outlier: 3.905A pdb=" N ARG F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 90 through 98 Processing sheet with id=AA1, first strand: chain 'B' and resid 818 through 820 removed outlier: 4.506A pdb=" N VAL A 224 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N HIS A 8 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 234 " --> pdb=" O HIS A 8 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 10 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 96 removed outlier: 9.034A pdb=" N TRP A 85 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU A 27 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE A 23 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU A 220 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 25 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET A 215 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 219 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.684A pdb=" N TYR A 58 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA A 104 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER A 128 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 106 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR A 126 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 108 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.740A pdb=" N LYS A 624 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A 604 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE A 622 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.740A pdb=" N LYS A 624 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A 604 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE A 622 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 688 through 689 removed outlier: 3.570A pdb=" N LEU A 750 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 758 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 34 removed outlier: 6.192A pdb=" N TYR B 28 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS B 44 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 30 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE B 102 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 176 removed outlier: 6.525A pdb=" N LEU B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 984 through 989 removed outlier: 6.590A pdb=" N VAL B1356 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N HIS B 988 " --> pdb=" O VAL B1354 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B1354 " --> pdb=" O HIS B 988 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B1338 " --> pdb=" O PHE B1344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B1348 " --> pdb=" O ASP B1334 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP B1334 " --> pdb=" O ALA B1348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 996 through 1001 removed outlier: 4.063A pdb=" N ARG B 998 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B1011 " --> pdb=" O ARG B 998 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1045 through 1049 removed outlier: 3.644A pdb=" N THR B1047 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B1086 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY B1070 " --> pdb=" O PRO B1084 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1098 through 1104 removed outlier: 3.971A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B1104 " --> pdb=" O VAL B1111 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B1111 " --> pdb=" O PHE B1104 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER B1120 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP B1133 " --> pdb=" O GLY B1123 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP B1125 " --> pdb=" O ASN B1131 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN B1131 " --> pdb=" O ASP B1125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 3.705A pdb=" N SER B1146 " --> pdb=" O GLY B1159 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N MET B1165 " --> pdb=" O SER B1178 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER B1178 " --> pdb=" O MET B1165 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B1174 " --> pdb=" O ASP B1169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 4.174A pdb=" N ARG B1189 " --> pdb=" O ALA B1203 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU B1209 " --> pdb=" O VAL B1204 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B1210 " --> pdb=" O LEU B1224 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B1222 " --> pdb=" O MET B1212 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU B1299 " --> pdb=" O ARG B1221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1242 through 1248 removed outlier: 3.508A pdb=" N SER B1248 " --> pdb=" O ILE B1255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.282A pdb=" N THR C 98 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N LEU F 105 " --> pdb=" O ARG F 28 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 277 through 279 removed outlier: 3.641A pdb=" N TRP C 277 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 282 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 328 through 331 removed outlier: 3.527A pdb=" N TYR C 338 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU C 349 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 395 through 397 Processing sheet with id=AC4, first strand: chain 'D' and resid 209 through 211 removed outlier: 3.805A pdb=" N GLU D 209 " --> pdb=" O SER D 262 " (cutoff:3.500A) 999 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7636 1.34 - 1.46: 4830 1.46 - 1.58: 11225 1.58 - 1.70: 3 1.70 - 1.82: 202 Bond restraints: 23896 Sorted by residual: bond pdb=" N VAL B 106 " pdb=" CA VAL B 106 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.05e+01 bond pdb=" N ARG F 40 " pdb=" CA ARG F 40 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.32e+00 bond pdb=" CA PRO F 85 " pdb=" C PRO F 85 " ideal model delta sigma weight residual 1.517 1.541 -0.024 9.30e-03 1.16e+04 6.78e+00 bond pdb=" CD2 HIS F 0 " pdb=" NE2 HIS F 0 " ideal model delta sigma weight residual 1.374 1.402 -0.028 1.10e-02 8.26e+03 6.46e+00 bond pdb=" CE1 HIS F 69 " pdb=" NE2 HIS F 69 " ideal model delta sigma weight residual 1.321 1.346 -0.025 1.00e-02 1.00e+04 6.32e+00 ... (remaining 23891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 31789 2.77 - 5.55: 437 5.55 - 8.32: 38 8.32 - 11.09: 4 11.09 - 13.87: 2 Bond angle restraints: 32270 Sorted by residual: angle pdb=" CA PHE F 60 " pdb=" CB PHE F 60 " pdb=" CG PHE F 60 " ideal model delta sigma weight residual 113.80 118.54 -4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" C LYS F 66 " pdb=" N ARG F 67 " pdb=" CA ARG F 67 " ideal model delta sigma weight residual 120.63 128.10 -7.47 1.61e+00 3.86e-01 2.15e+01 angle pdb=" CG1 ILE B 13 " pdb=" CB ILE B 13 " pdb=" CG2 ILE B 13 " ideal model delta sigma weight residual 110.70 96.83 13.87 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C CYS D 128 " pdb=" N LYS D 129 " pdb=" CA LYS D 129 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C ALA F 72 " pdb=" N GLU F 73 " pdb=" CA GLU F 73 " ideal model delta sigma weight residual 122.21 128.87 -6.66 1.48e+00 4.57e-01 2.02e+01 ... (remaining 32265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.62: 14153 28.62 - 57.23: 392 57.23 - 85.85: 45 85.85 - 114.46: 4 114.46 - 143.08: 1 Dihedral angle restraints: 14595 sinusoidal: 6089 harmonic: 8506 Sorted by residual: dihedral pdb=" O2B GDP B1402 " pdb=" O3A GDP B1402 " pdb=" PB GDP B1402 " pdb=" PA GDP B1402 " ideal model delta sinusoidal sigma weight residual 180.00 36.92 143.08 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C VAL B 106 " pdb=" N VAL B 106 " pdb=" CA VAL B 106 " pdb=" CB VAL B 106 " ideal model delta harmonic sigma weight residual -122.00 -137.22 15.22 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" CA GLU F 34 " pdb=" C GLU F 34 " pdb=" N LYS F 35 " pdb=" CA LYS F 35 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 14592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3224 0.078 - 0.157: 313 0.157 - 0.235: 20 0.235 - 0.313: 5 0.313 - 0.392: 3 Chirality restraints: 3565 Sorted by residual: chirality pdb=" CB VAL B 106 " pdb=" CA VAL B 106 " pdb=" CG1 VAL B 106 " pdb=" CG2 VAL B 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA VAL B 106 " pdb=" N VAL B 106 " pdb=" C VAL B 106 " pdb=" CB VAL B 106 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CB ILE B 13 " pdb=" CA ILE B 13 " pdb=" CG1 ILE B 13 " pdb=" CG2 ILE B 13 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 3562 not shown) Planarity restraints: 4138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 49 " 0.079 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" CG TYR F 49 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR F 49 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR F 49 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR F 49 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR F 49 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR F 49 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR F 49 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 109 " 0.069 2.00e-02 2.50e+03 3.52e-02 2.48e+01 pdb=" CG TYR F 109 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 109 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR F 109 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR F 109 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR F 109 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR F 109 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 109 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 5 " 0.047 2.00e-02 2.50e+03 3.34e-02 2.24e+01 pdb=" CG TYR F 5 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR F 5 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR F 5 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR F 5 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR F 5 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR F 5 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR F 5 " 0.062 2.00e-02 2.50e+03 ... (remaining 4135 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5743 2.81 - 3.33: 19654 3.33 - 3.85: 34622 3.85 - 4.38: 40482 4.38 - 4.90: 71173 Nonbonded interactions: 171674 Sorted by model distance: nonbonded pdb=" O PRO F 37 " pdb=" NH2 ARG F 40 " model vdw 2.285 3.120 nonbonded pdb=" O2B GDP B1402 " pdb="MG MG B1403 " model vdw 2.340 2.170 nonbonded pdb=" O1A GDP B1402 " pdb="MG MG B1403 " model vdw 2.340 2.170 nonbonded pdb=" OD2 ASP B 166 " pdb="MG MG B1403 " model vdw 2.357 2.170 nonbonded pdb=" OD1 ASN B 153 " pdb="MG MG B1403 " model vdw 2.373 2.170 ... (remaining 171669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.710 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 23905 Z= 0.260 Angle : 1.153 64.971 32282 Z= 0.507 Chirality : 0.048 0.392 3565 Planarity : 0.006 0.078 4138 Dihedral : 13.633 143.081 9073 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 0.39 % Allowed : 4.99 % Favored : 94.62 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.13), residues: 2867 helix: -2.03 (0.12), residues: 1283 sheet: -0.30 (0.30), residues: 271 loop : -1.07 (0.15), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 189 TYR 0.079 0.003 TYR F 49 PHE 0.052 0.002 PHE F 78 TRP 0.020 0.001 TRP A 355 HIS 0.008 0.001 HIS F 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.25 (23896) covalent geometry : angle 0.80111 / 0.48 (32270) hydrogen bonds : bond 0.24453 / 15.96 ( 994) hydrogen bonds : angle 7.12341 / 4.91 ( 2850) metal coordination : bond 0.02462 / 1.63 ( 8) metal coordination : angle 43.04002 / 22.86 ( 12) Misc. bond : bond 0.10380 / 5.46 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 618 time to evaluate : 0.934 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: A 86 ASN cc_start: 0.7407 (t0) cc_final: 0.6969 (p0) REVERT: A 394 MET cc_start: 0.8010 (mtp) cc_final: 0.7551 (mtt) REVERT: A 505 ASP cc_start: 0.7692 (t0) cc_final: 0.7449 (t0) REVERT: A 546 GLN cc_start: 0.7705 (tp40) cc_final: 0.7442 (tp-100) REVERT: A 656 LYS cc_start: 0.8391 (tttt) cc_final: 0.8152 (ttpt) REVERT: A 771 LYS cc_start: 0.7834 (mttp) cc_final: 0.7292 (pttt) REVERT: A 856 VAL cc_start: 0.8703 (t) cc_final: 0.8494 (p) REVERT: B 190 SER cc_start: 0.8934 (t) cc_final: 0.8684 (p) REVERT: B 254 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7145 (pt0) REVERT: B 477 ILE cc_start: 0.8835 (tp) cc_final: 0.8357 (tt) REVERT: B 1059 ILE cc_start: 0.8859 (mt) cc_final: 0.8520 (tt) REVERT: B 1146 SER cc_start: 0.8481 (t) cc_final: 0.8237 (t) REVERT: B 1263 MET cc_start: 0.7848 (mtm) cc_final: 0.7502 (mtt) REVERT: B 1351 ASP cc_start: 0.8608 (p0) cc_final: 0.8311 (p0) REVERT: B 1353 ILE cc_start: 0.8773 (mm) cc_final: 0.7872 (tt) REVERT: D 66 TYR cc_start: 0.7919 (m-80) cc_final: 0.7685 (m-80) REVERT: D 330 CYS cc_start: 0.7801 (p) cc_final: 0.7513 (p) REVERT: D 348 VAL cc_start: 0.9317 (t) cc_final: 0.8983 (m) REVERT: D 380 TYR cc_start: 0.8243 (m-10) cc_final: 0.7574 (m-10) outliers start: 10 outliers final: 4 residues processed: 623 average time/residue: 0.1927 time to fit residues: 180.3054 Evaluate side-chains 327 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 323 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 91 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0070 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 GLN A 715 ASN A 745 HIS A 860 GLN B 131 GLN B 140 HIS B 469 HIS B 559 ASN B 622 GLN B 644 GLN B 744 HIS ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1152 HIS B1243 HIS B1305 GLN C 230 GLN C 286 ASN C 363 ASN C 446 GLN C 449 ASN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.169267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110556 restraints weight = 40525.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110950 restraints weight = 25865.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110375 restraints weight = 20037.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111301 restraints weight = 22047.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111463 restraints weight = 18654.582| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23905 Z= 0.231 Angle : 0.896 53.393 32282 Z= 0.382 Chirality : 0.045 0.268 3565 Planarity : 0.005 0.062 4138 Dihedral : 6.030 129.670 3176 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.36 % Allowed : 11.56 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 2867 helix: -0.41 (0.14), residues: 1291 sheet: -0.10 (0.30), residues: 268 loop : -0.89 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 15 TYR 0.021 0.002 TYR A 803 PHE 0.023 0.002 PHE F 60 TRP 0.022 0.002 TRP B 670 HIS 0.009 0.001 HIS D 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.23 (23896) covalent geometry : angle 0.70987 / 0.37 (32270) hydrogen bonds : bond 0.05682 / 3.65 ( 994) hydrogen bonds : angle 4.85731 / 3.34 ( 2850) metal coordination : bond 0.01764 / 0.90 ( 8) metal coordination : angle 28.34370 / 14.76 ( 12) Misc. bond : bond 0.00555 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 347 time to evaluate : 0.975 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: A 86 ASN cc_start: 0.8182 (t0) cc_final: 0.7725 (p0) REVERT: A 263 GLU cc_start: 0.5655 (mt-10) cc_final: 0.5370 (mt-10) REVERT: A 516 MET cc_start: 0.8521 (tmm) cc_final: 0.8205 (tmm) REVERT: A 771 LYS cc_start: 0.8059 (mttp) cc_final: 0.7680 (pttt) REVERT: A 865 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7963 (mm-30) REVERT: B 72 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: B 190 SER cc_start: 0.9214 (t) cc_final: 0.8931 (p) REVERT: B 982 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8351 (mppt) REVERT: B 1222 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: B 1263 MET cc_start: 0.7933 (mtm) cc_final: 0.7520 (mtt) REVERT: B 1351 ASP cc_start: 0.8881 (p0) cc_final: 0.8440 (p0) REVERT: B 1353 ILE cc_start: 0.8688 (mm) cc_final: 0.8184 (mm) REVERT: C 229 TYR cc_start: 0.8623 (t80) cc_final: 0.8341 (t80) REVERT: C 254 MET cc_start: 0.9100 (tmm) cc_final: 0.8631 (tpp) REVERT: C 315 HIS cc_start: 0.9234 (t-90) cc_final: 0.8946 (m-70) REVERT: C 321 MET cc_start: 0.8950 (mtp) cc_final: 0.8691 (mtp) REVERT: C 328 TYR cc_start: 0.7826 (m-80) cc_final: 0.7506 (m-80) REVERT: C 333 TYR cc_start: 0.7081 (t80) cc_final: 0.6043 (t80) REVERT: D 37 TYR cc_start: 0.7611 (m-80) cc_final: 0.7393 (m-10) REVERT: D 158 HIS cc_start: 0.8795 (m-70) cc_final: 0.8509 (m-70) REVERT: D 308 CYS cc_start: 0.8886 (p) cc_final: 0.8267 (p) REVERT: D 330 CYS cc_start: 0.8149 (p) cc_final: 0.7798 (p) REVERT: D 379 MET cc_start: 0.9106 (mtp) cc_final: 0.8826 (mtt) REVERT: E -2 MET cc_start: 0.5245 (mpp) cc_final: 0.4829 (pmm) REVERT: E 76 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8219 (mtpt) REVERT: F 27 ASP cc_start: 0.8128 (t0) cc_final: 0.7771 (t0) REVERT: G 16 PHE cc_start: 0.8095 (m-80) cc_final: 0.7702 (m-80) outliers start: 61 outliers final: 33 residues processed: 381 average time/residue: 0.1676 time to fit residues: 99.2916 Evaluate side-chains 333 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1222 PHE Chi-restraints excluded: chain B residue 1349 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 178 optimal weight: 8.9990 chunk 232 optimal weight: 50.0000 chunk 175 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 239 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 238 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 HIS A 545 GLN B 45 HIS B 82 GLN B 427 ASN B 644 GLN B1152 HIS C 286 ASN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.170976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113914 restraints weight = 40325.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112033 restraints weight = 27360.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112195 restraints weight = 23502.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112385 restraints weight = 23489.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112814 restraints weight = 21771.773| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23905 Z= 0.154 Angle : 0.694 45.278 32282 Z= 0.307 Chirality : 0.042 0.182 3565 Planarity : 0.004 0.049 4138 Dihedral : 5.617 124.333 3172 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.93 % Allowed : 12.92 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 2867 helix: 0.30 (0.15), residues: 1316 sheet: -0.04 (0.31), residues: 271 loop : -0.83 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 28 TYR 0.026 0.001 TYR A 803 PHE 0.014 0.001 PHE D 395 TRP 0.015 0.001 TRP C 442 HIS 0.009 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (23896) covalent geometry : angle 0.58343 / 0.30 (32270) hydrogen bonds : bond 0.04769 / 3.05 ( 994) hydrogen bonds : angle 4.46498 / 3.08 ( 2850) metal coordination : bond 0.01642 / 0.96 ( 8) metal coordination : angle 19.48568 / 9.57 ( 12) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 314 time to evaluate : 1.052 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: A 86 ASN cc_start: 0.8123 (t0) cc_final: 0.7723 (p0) REVERT: A 172 MET cc_start: 0.4520 (mtt) cc_final: 0.4314 (mmt) REVERT: A 263 GLU cc_start: 0.5521 (mt-10) cc_final: 0.5226 (mt-10) REVERT: A 771 LYS cc_start: 0.8053 (mttp) cc_final: 0.7750 (pttt) REVERT: A 803 TYR cc_start: 0.7774 (p90) cc_final: 0.7412 (p90) REVERT: A 865 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7899 (mm-30) REVERT: B 190 SER cc_start: 0.9251 (t) cc_final: 0.8977 (p) REVERT: B 982 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8403 (mppt) REVERT: B 1021 ASN cc_start: 0.8827 (t0) cc_final: 0.8492 (t0) REVERT: B 1025 MET cc_start: 0.8249 (mtp) cc_final: 0.7805 (mpp) REVERT: B 1044 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7919 (mtt180) REVERT: B 1263 MET cc_start: 0.7873 (mtm) cc_final: 0.7483 (mtt) REVERT: B 1353 ILE cc_start: 0.8757 (mm) cc_final: 0.7959 (tt) REVERT: C 229 TYR cc_start: 0.8687 (t80) cc_final: 0.8361 (t80) REVERT: C 254 MET cc_start: 0.8927 (tmm) cc_final: 0.8633 (tpp) REVERT: C 315 HIS cc_start: 0.9124 (t-90) cc_final: 0.8886 (m-70) REVERT: C 333 TYR cc_start: 0.6689 (t80) cc_final: 0.5799 (t80) REVERT: C 413 TYR cc_start: 0.4452 (m-10) cc_final: 0.4226 (m-80) REVERT: D 158 HIS cc_start: 0.8597 (m-70) cc_final: 0.8295 (m-70) REVERT: D 301 TYR cc_start: 0.7260 (m-80) cc_final: 0.6409 (m-80) REVERT: D 304 SER cc_start: 0.8579 (m) cc_final: 0.8307 (p) REVERT: D 308 CYS cc_start: 0.8481 (p) cc_final: 0.8113 (p) REVERT: D 330 CYS cc_start: 0.8158 (p) cc_final: 0.7831 (p) REVERT: D 348 VAL cc_start: 0.9470 (t) cc_final: 0.9251 (p) REVERT: E -2 MET cc_start: 0.5173 (mpp) cc_final: 0.4767 (pmm) REVERT: F 19 GLU cc_start: 0.8449 (tp30) cc_final: 0.7971 (mt-10) REVERT: F 27 ASP cc_start: 0.8143 (t0) cc_final: 0.7848 (t0) REVERT: F 51 VAL cc_start: 0.7821 (t) cc_final: 0.7584 (p) REVERT: F 95 TYR cc_start: 0.7639 (t80) cc_final: 0.7423 (t80) REVERT: G 23 GLN cc_start: 0.7471 (mp10) cc_final: 0.7217 (mp10) outliers start: 50 outliers final: 33 residues processed: 339 average time/residue: 0.1711 time to fit residues: 90.9159 Evaluate side-chains 327 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1349 SER Chi-restraints excluded: chain B residue 1362 THR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain E residue -1 GLU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 280 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 GLN B 506 ASN B1152 HIS ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN E 54 HIS ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.166000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105986 restraints weight = 40426.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105293 restraints weight = 26963.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105477 restraints weight = 21036.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106392 restraints weight = 21813.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106529 restraints weight = 19357.328| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23905 Z= 0.222 Angle : 0.697 36.997 32282 Z= 0.331 Chirality : 0.045 0.183 3565 Planarity : 0.004 0.057 4138 Dihedral : 5.661 124.465 3172 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.71 % Allowed : 12.99 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2867 helix: 0.55 (0.15), residues: 1318 sheet: -0.11 (0.30), residues: 273 loop : -0.90 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 114 TYR 0.026 0.002 TYR A 803 PHE 0.028 0.002 PHE B1147 TRP 0.018 0.002 TRP B 127 HIS 0.005 0.001 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.22 (23896) covalent geometry : angle 0.64124 / 0.33 (32270) hydrogen bonds : bond 0.05079 / 3.26 ( 994) hydrogen bonds : angle 4.47633 / 3.09 ( 2850) metal coordination : bond 0.01197 / 0.70 ( 8) metal coordination : angle 14.19536 / 6.60 ( 12) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 302 time to evaluate : 0.987 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: A 203 MET cc_start: 0.8604 (tmm) cc_final: 0.8280 (mpp) REVERT: A 516 MET cc_start: 0.8547 (tmm) cc_final: 0.8248 (tmm) REVERT: A 771 LYS cc_start: 0.8263 (mttp) cc_final: 0.7836 (pttt) REVERT: A 803 TYR cc_start: 0.7847 (p90) cc_final: 0.7426 (p90) REVERT: A 865 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7979 (mm-30) REVERT: B 72 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: B 190 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.9175 (p) REVERT: B 292 GLN cc_start: 0.8114 (mt0) cc_final: 0.7904 (tt0) REVERT: B 982 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8392 (mppt) REVERT: B 1025 MET cc_start: 0.8334 (mtp) cc_final: 0.7825 (mpp) REVERT: B 1140 LYS cc_start: 0.9200 (mptt) cc_final: 0.8976 (mmtp) REVERT: B 1358 LYS cc_start: 0.8461 (pttt) cc_final: 0.8018 (pttt) REVERT: C 254 MET cc_start: 0.9057 (tmm) cc_final: 0.8689 (tpp) REVERT: C 315 HIS cc_start: 0.9294 (t-90) cc_final: 0.9028 (m-70) REVERT: C 333 TYR cc_start: 0.7227 (t80) cc_final: 0.6075 (t80) REVERT: C 432 MET cc_start: 0.9408 (tpp) cc_final: 0.8923 (tpp) REVERT: C 436 LEU cc_start: 0.9560 (mt) cc_final: 0.9191 (mt) REVERT: D 280 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: D 304 SER cc_start: 0.8599 (m) cc_final: 0.8235 (p) REVERT: D 308 CYS cc_start: 0.8538 (p) cc_final: 0.8173 (p) REVERT: D 330 CYS cc_start: 0.8138 (p) cc_final: 0.7824 (p) REVERT: D 379 MET cc_start: 0.9202 (mtp) cc_final: 0.8957 (mtm) REVERT: E -2 MET cc_start: 0.5207 (mpp) cc_final: 0.4628 (pmm) REVERT: F 27 ASP cc_start: 0.8149 (t0) cc_final: 0.7831 (t0) REVERT: F 50 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8542 (mp) outliers start: 70 outliers final: 44 residues processed: 341 average time/residue: 0.1647 time to fit residues: 88.4649 Evaluate side-chains 329 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 281 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1349 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue -1 GLU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 4 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 279 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 506 ASN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.167804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119006 restraints weight = 39758.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119861 restraints weight = 38918.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119857 restraints weight = 29280.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.119372 restraints weight = 21199.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119745 restraints weight = 21382.869| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 23905 Z= 0.109 Angle : 0.588 31.324 32282 Z= 0.276 Chirality : 0.040 0.238 3565 Planarity : 0.004 0.051 4138 Dihedral : 5.242 116.371 3170 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.78 % Allowed : 14.39 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2867 helix: 1.04 (0.15), residues: 1299 sheet: -0.12 (0.29), residues: 290 loop : -0.76 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 14 TYR 0.025 0.001 TYR A 803 PHE 0.032 0.001 PHE B1338 TRP 0.014 0.001 TRP B 127 HIS 0.004 0.001 HIS B1137 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (23896) covalent geometry : angle 0.53362 / 0.27 (32270) hydrogen bonds : bond 0.03969 / 2.52 ( 994) hydrogen bonds : angle 4.14019 / 2.85 ( 2850) metal coordination : bond 0.01133 / 0.62 ( 8) metal coordination : angle 12.81091 / 6.20 ( 12) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 306 time to evaluate : 1.145 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: A 86 ASN cc_start: 0.8162 (t0) cc_final: 0.7818 (p0) REVERT: A 142 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: A 172 MET cc_start: 0.3910 (mmt) cc_final: 0.3200 (mmt) REVERT: A 250 PHE cc_start: 0.7845 (m-80) cc_final: 0.7525 (m-80) REVERT: A 572 ARG cc_start: 0.7708 (tpp80) cc_final: 0.6929 (tpp80) REVERT: A 636 LYS cc_start: 0.8245 (mttt) cc_final: 0.7986 (mttm) REVERT: A 771 LYS cc_start: 0.8132 (mttp) cc_final: 0.7835 (pttt) REVERT: A 803 TYR cc_start: 0.7628 (p90) cc_final: 0.7344 (p90) REVERT: A 865 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7799 (mm-30) REVERT: B 1038 TYR cc_start: 0.7105 (t80) cc_final: 0.6580 (t80) REVERT: B 1044 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7481 (mmt90) REVERT: B 1140 LYS cc_start: 0.8901 (mptt) cc_final: 0.8692 (mmtp) REVERT: D 280 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: D 301 TYR cc_start: 0.6847 (m-80) cc_final: 0.6010 (m-80) REVERT: D 308 CYS cc_start: 0.7970 (p) cc_final: 0.7634 (p) REVERT: F 27 ASP cc_start: 0.7801 (t0) cc_final: 0.7521 (t0) REVERT: G 23 GLN cc_start: 0.7573 (mp10) cc_final: 0.7299 (mp10) outliers start: 46 outliers final: 33 residues processed: 327 average time/residue: 0.1699 time to fit residues: 86.8649 Evaluate side-chains 318 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1349 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 9 HIS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 164 optimal weight: 1.9990 chunk 87 optimal weight: 0.0000 chunk 213 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 253 optimal weight: 0.0370 chunk 143 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN B 506 ASN C 216 GLN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.168398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109696 restraints weight = 40250.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108724 restraints weight = 28699.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108495 restraints weight = 29310.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109142 restraints weight = 25507.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109448 restraints weight = 23818.500| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23905 Z= 0.172 Angle : 0.624 32.998 32282 Z= 0.297 Chirality : 0.042 0.174 3565 Planarity : 0.004 0.049 4138 Dihedral : 5.238 116.929 3170 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.20 % Allowed : 14.85 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2867 helix: 1.04 (0.15), residues: 1299 sheet: -0.13 (0.30), residues: 282 loop : -0.81 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 346 TYR 0.025 0.001 TYR A 803 PHE 0.031 0.002 PHE B1147 TRP 0.016 0.001 TRP B 127 HIS 0.005 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (23896) covalent geometry : angle 0.57553 / 0.29 (32270) hydrogen bonds : bond 0.04412 / 2.82 ( 994) hydrogen bonds : angle 4.20073 / 2.89 ( 2850) metal coordination : bond 0.01314 / 0.79 ( 8) metal coordination : angle 12.52909 / 5.89 ( 12) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 1.079 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: A 516 MET cc_start: 0.8437 (tmm) cc_final: 0.8214 (tmm) REVERT: A 636 LYS cc_start: 0.8193 (mttt) cc_final: 0.7877 (mttm) REVERT: A 771 LYS cc_start: 0.8257 (mttp) cc_final: 0.7851 (pttt) REVERT: A 803 TYR cc_start: 0.7791 (p90) cc_final: 0.7404 (p90) REVERT: A 865 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7962 (mm-30) REVERT: B 190 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.9137 (p) REVERT: B 1025 MET cc_start: 0.7828 (mpp) cc_final: 0.7405 (mpp) REVERT: B 1140 LYS cc_start: 0.9179 (mptt) cc_final: 0.8952 (mmtp) REVERT: B 1355 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8063 (mmtt) REVERT: C 328 TYR cc_start: 0.6599 (m-10) cc_final: 0.6383 (m-10) REVERT: C 333 TYR cc_start: 0.7317 (t80) cc_final: 0.6986 (t80) REVERT: C 432 MET cc_start: 0.9291 (tpp) cc_final: 0.9072 (tpp) REVERT: D 280 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: D 308 CYS cc_start: 0.8492 (p) cc_final: 0.8115 (p) REVERT: D 344 PHE cc_start: 0.8381 (m-80) cc_final: 0.8151 (m-80) REVERT: D 362 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7609 (tp-100) REVERT: D 379 MET cc_start: 0.9551 (mtp) cc_final: 0.9224 (mtm) REVERT: F 27 ASP cc_start: 0.8208 (t0) cc_final: 0.7822 (t0) REVERT: G 23 GLN cc_start: 0.7779 (mp10) cc_final: 0.7466 (mp10) outliers start: 57 outliers final: 46 residues processed: 319 average time/residue: 0.1666 time to fit residues: 83.8980 Evaluate side-chains 327 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 278 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 982 LYS Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1349 SER Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 3.9990 chunk 60 optimal weight: 0.0000 chunk 221 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 205 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 230 GLN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.165710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115920 restraints weight = 39791.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116652 restraints weight = 38286.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115662 restraints weight = 25280.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114454 restraints weight = 21398.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114758 restraints weight = 22363.953| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23905 Z= 0.149 Angle : 0.601 30.954 32282 Z= 0.286 Chirality : 0.042 0.306 3565 Planarity : 0.004 0.046 4138 Dihedral : 5.112 114.099 3170 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.32 % Allowed : 15.43 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2867 helix: 1.16 (0.15), residues: 1299 sheet: -0.10 (0.30), residues: 276 loop : -0.79 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 734 TYR 0.024 0.001 TYR A 803 PHE 0.031 0.001 PHE B1147 TRP 0.016 0.001 TRP B 127 HIS 0.004 0.001 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (23896) covalent geometry : angle 0.55701 / 0.28 (32270) hydrogen bonds : bond 0.04147 / 2.64 ( 994) hydrogen bonds : angle 4.15809 / 2.86 ( 2850) metal coordination : bond 0.01129 / 0.66 ( 8) metal coordination : angle 11.74360 / 5.49 ( 12) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 283 time to evaluate : 0.880 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: A 516 MET cc_start: 0.8418 (tmm) cc_final: 0.8161 (tmm) REVERT: A 636 LYS cc_start: 0.8268 (mttt) cc_final: 0.7966 (mttm) REVERT: A 771 LYS cc_start: 0.8199 (mttp) cc_final: 0.7883 (pttt) REVERT: A 803 TYR cc_start: 0.7638 (p90) cc_final: 0.7346 (p90) REVERT: A 865 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7822 (mm-30) REVERT: B 72 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: B 190 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9131 (p) REVERT: B 1263 MET cc_start: 0.8242 (mtm) cc_final: 0.7833 (ptp) REVERT: B 1355 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8071 (mmtt) REVERT: D 280 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6855 (m-80) REVERT: D 294 MET cc_start: 0.1578 (ppp) cc_final: 0.1368 (ttp) REVERT: F 27 ASP cc_start: 0.7951 (t0) cc_final: 0.7667 (t0) REVERT: G 23 GLN cc_start: 0.7813 (mp10) cc_final: 0.7598 (mp10) outliers start: 60 outliers final: 46 residues processed: 314 average time/residue: 0.1626 time to fit residues: 81.2898 Evaluate side-chains 321 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1101 MET Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1349 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 9 HIS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 110 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 157 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 336 HIS ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.167073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115126 restraints weight = 40058.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114878 restraints weight = 37980.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109538 restraints weight = 24893.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109881 restraints weight = 24905.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110231 restraints weight = 22222.283| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23905 Z= 0.199 Angle : 0.655 31.075 32282 Z= 0.312 Chirality : 0.043 0.206 3565 Planarity : 0.004 0.044 4138 Dihedral : 5.238 116.393 3170 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.51 % Allowed : 15.47 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2867 helix: 1.04 (0.15), residues: 1304 sheet: -0.17 (0.30), residues: 280 loop : -0.78 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 572 TYR 0.049 0.002 TYR C 328 PHE 0.044 0.002 PHE C 365 TRP 0.016 0.001 TRP B 127 HIS 0.005 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 (23896) covalent geometry : angle 0.60894 / 0.31 (32270) hydrogen bonds : bond 0.04603 / 2.95 ( 994) hydrogen bonds : angle 4.27523 / 2.94 ( 2850) metal coordination : bond 0.01375 / 0.88 ( 8) metal coordination : angle 12.59179 / 5.93 ( 12) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 288 time to evaluate : 0.856 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: A 572 ARG cc_start: 0.7863 (tpp80) cc_final: 0.6992 (tpp80) REVERT: A 636 LYS cc_start: 0.8252 (mttt) cc_final: 0.8034 (mttm) REVERT: A 771 LYS cc_start: 0.8271 (mttp) cc_final: 0.7926 (pttt) REVERT: A 803 TYR cc_start: 0.7686 (p90) cc_final: 0.7379 (p90) REVERT: A 865 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7857 (mm-30) REVERT: B 1355 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8125 (mmtt) REVERT: C 432 MET cc_start: 0.8800 (tpp) cc_final: 0.8559 (tpp) REVERT: D 280 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: D 308 CYS cc_start: 0.8159 (p) cc_final: 0.7864 (p) REVERT: F 27 ASP cc_start: 0.8091 (t0) cc_final: 0.7784 (t0) REVERT: G 23 GLN cc_start: 0.7935 (mp10) cc_final: 0.7387 (mp10) outliers start: 65 outliers final: 53 residues processed: 323 average time/residue: 0.1645 time to fit residues: 83.8939 Evaluate side-chains 328 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1101 MET Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1349 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 9 HIS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 10 optimal weight: 0.9990 chunk 140 optimal weight: 0.0570 chunk 49 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 225 optimal weight: 40.0000 chunk 282 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 251 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 387 GLN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.168795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116477 restraints weight = 40116.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116417 restraints weight = 36366.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112420 restraints weight = 24530.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112538 restraints weight = 26446.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112869 restraints weight = 22088.238| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23905 Z= 0.126 Angle : 0.608 28.215 32282 Z= 0.289 Chirality : 0.041 0.192 3565 Planarity : 0.004 0.043 4138 Dihedral : 5.054 109.843 3170 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.93 % Allowed : 16.43 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2867 helix: 1.26 (0.15), residues: 1290 sheet: -0.09 (0.30), residues: 284 loop : -0.73 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 572 TYR 0.053 0.001 TYR C 333 PHE 0.031 0.001 PHE B1147 TRP 0.034 0.001 TRP B1199 HIS 0.004 0.001 HIS B1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (23896) covalent geometry : angle 0.56486 / 0.29 (32270) hydrogen bonds : bond 0.03993 / 2.54 ( 994) hydrogen bonds : angle 4.16505 / 2.86 ( 2850) metal coordination : bond 0.01155 / 0.69 ( 8) metal coordination : angle 11.73572 / 5.61 ( 12) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 291 time to evaluate : 0.933 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: A 572 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7002 (tpp80) REVERT: A 617 MET cc_start: 0.8526 (mtm) cc_final: 0.8294 (mtp) REVERT: A 636 LYS cc_start: 0.8221 (mttt) cc_final: 0.7892 (mttm) REVERT: A 771 LYS cc_start: 0.8261 (mttp) cc_final: 0.7889 (pttt) REVERT: A 803 TYR cc_start: 0.7636 (p90) cc_final: 0.7283 (p90) REVERT: A 865 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7863 (mm-30) REVERT: B 1355 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8120 (mmtt) REVERT: C 432 MET cc_start: 0.8775 (tpp) cc_final: 0.8515 (tpp) REVERT: D 308 CYS cc_start: 0.8068 (p) cc_final: 0.7754 (p) REVERT: F 27 ASP cc_start: 0.8026 (t0) cc_final: 0.7739 (t0) REVERT: G 23 GLN cc_start: 0.7926 (mp10) cc_final: 0.7366 (mp10) outliers start: 50 outliers final: 44 residues processed: 318 average time/residue: 0.1631 time to fit residues: 82.1575 Evaluate side-chains 325 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1101 MET Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1349 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 9 HIS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 31 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 272 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 HIS ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.165710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104829 restraints weight = 40405.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105057 restraints weight = 27122.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105332 restraints weight = 22592.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105999 restraints weight = 20825.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106215 restraints weight = 19516.058| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 23905 Z= 0.238 Angle : 0.710 31.451 32282 Z= 0.340 Chirality : 0.045 0.264 3565 Planarity : 0.004 0.044 4138 Dihedral : 5.304 113.694 3170 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 2.05 % Allowed : 16.40 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2867 helix: 1.00 (0.15), residues: 1299 sheet: -0.25 (0.30), residues: 290 loop : -0.82 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 572 TYR 0.025 0.002 TYR A 803 PHE 0.035 0.002 PHE B1338 TRP 0.028 0.002 TRP B1199 HIS 0.007 0.001 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.24 (23896) covalent geometry : angle 0.66954 / 0.34 (32270) hydrogen bonds : bond 0.04882 / 3.12 ( 994) hydrogen bonds : angle 4.40202 / 3.02 ( 2850) metal coordination : bond 0.01492 / 0.92 ( 8) metal coordination : angle 12.30421 / 5.71 ( 12) Misc. bond : bond 0.00051 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 0.869 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: A 572 ARG cc_start: 0.7720 (tpp80) cc_final: 0.6957 (tpp80) REVERT: A 617 MET cc_start: 0.8461 (mtm) cc_final: 0.8197 (mtp) REVERT: A 636 LYS cc_start: 0.8185 (mttt) cc_final: 0.7898 (mttp) REVERT: A 722 MET cc_start: 0.8242 (mmt) cc_final: 0.8037 (tpp) REVERT: A 771 LYS cc_start: 0.8386 (mttp) cc_final: 0.7950 (pttt) REVERT: A 803 TYR cc_start: 0.7784 (p90) cc_final: 0.7409 (p90) REVERT: A 865 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7957 (mm-30) REVERT: B 72 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: B 731 TYR cc_start: 0.7834 (t80) cc_final: 0.7465 (t80) REVERT: B 1025 MET cc_start: 0.8497 (ptp) cc_final: 0.7884 (pmm) REVERT: B 1339 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7593 (mm-40) REVERT: B 1355 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8057 (mmtt) REVERT: C 432 MET cc_start: 0.9201 (tpp) cc_final: 0.8681 (tpp) REVERT: C 436 LEU cc_start: 0.9541 (mt) cc_final: 0.9201 (mt) REVERT: D 308 CYS cc_start: 0.8289 (p) cc_final: 0.7999 (p) REVERT: D 373 HIS cc_start: 0.6757 (OUTLIER) cc_final: 0.6413 (t-90) REVERT: D 379 MET cc_start: 0.9509 (mtp) cc_final: 0.9152 (mpp) REVERT: F 19 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7842 (mt-10) REVERT: F 27 ASP cc_start: 0.8273 (t0) cc_final: 0.7940 (t0) REVERT: F 91 MET cc_start: 0.8535 (ppp) cc_final: 0.8320 (ppp) REVERT: G 23 GLN cc_start: 0.7992 (mp10) cc_final: 0.7275 (mp10) outliers start: 53 outliers final: 45 residues processed: 313 average time/residue: 0.1636 time to fit residues: 80.6885 Evaluate side-chains 326 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1101 MET Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain B residue 1349 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 9 HIS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 177 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 235 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 253 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 276 optimal weight: 0.8980 chunk 247 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 702 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.167156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110016 restraints weight = 40134.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107442 restraints weight = 28262.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109009 restraints weight = 26350.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109121 restraints weight = 23155.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109582 restraints weight = 22391.623| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23905 Z= 0.123 Angle : 0.634 28.102 32282 Z= 0.300 Chirality : 0.041 0.306 3565 Planarity : 0.004 0.041 4138 Dihedral : 5.038 104.641 3170 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 1.86 % Allowed : 16.67 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2867 helix: 1.25 (0.15), residues: 1295 sheet: -0.14 (0.30), residues: 284 loop : -0.74 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 572 TYR 0.024 0.001 TYR A 803 PHE 0.031 0.001 PHE B1147 TRP 0.024 0.001 TRP B1199 HIS 0.003 0.001 HIS B1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (23896) covalent geometry : angle 0.59416 / 0.30 (32270) hydrogen bonds : bond 0.04010 / 2.55 ( 994) hydrogen bonds : angle 4.21336 / 2.89 ( 2850) metal coordination : bond 0.01172 / 0.68 ( 8) metal coordination : angle 11.53170 / 5.48 ( 12) Misc. bond : bond 0.00018 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5188.40 seconds wall clock time: 89 minutes 51.04 seconds (5391.04 seconds total)