Starting phenix.real_space_refine on Thu Sep 18 19:56:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oab_20000/09_2025/6oab_20000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oab_20000/09_2025/6oab_20000.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 { model { file = "/net/cci-nas-00/data/ceres_data/6oab_20000/09_2025/6oab_20000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oab_20000/09_2025/6oab_20000_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oab_20000/09_2025/6oab_20000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oab_20000/09_2025/6oab_20000.map" } 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= 0.014 sd= 0.087 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 P 20 5.49 5 S 87 5.16 5 Be 8 3.05 5 C 12272 2.51 5 N 3446 2.21 5 O 3833 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 210 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19690 Number of models: 1 Model: "" Number of chains: 11 Chain: "D" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4130 Classifications: {'peptide': 537} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 507} Chain breaks: 2 Chain: "E" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3383 Classifications: {'peptide': 442} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 23, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3897 Classifications: {'peptide': 509} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 481} Chain: "C" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4088 Classifications: {'peptide': 532} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 27, 'TRANS': 500} Chain breaks: 2 Chain: "A" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3770 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 465} Chain breaks: 1 Chain: "H" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {'ADP': 2, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'ADP': 2, 'BEF': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {'ADP': 2, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'ADP': 2, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.20, per 1000 atoms: 0.21 Number of scatterers: 19690 At special positions: 0 Unit cell: (146.05, 129.95, 104.65, 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) S 87 16.00 P 20 15.00 F 24 9.00 O 3833 8.00 N 3446 7.00 C 12272 6.00 Be 8 4.00 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=25, symmetry=0 Number of additional bonds: simple=25, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 690.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 12 sheets defined 41.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'D' and resid 222 through 236 removed outlier: 3.974A pdb=" N ILE D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL D 230 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 262 through 273 removed outlier: 4.237A pdb=" N ARG D 266 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 removed outlier: 3.562A pdb=" N PHE D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU D 302 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 305 " --> pdb=" O GLU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 341 removed outlier: 3.577A pdb=" N VAL D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.543A pdb=" N SER D 362 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 363 " --> pdb=" O PRO D 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 363' Processing helix chain 'D' and resid 386 through 392 removed outlier: 3.907A pdb=" N VAL D 390 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 436 Processing helix chain 'D' and resid 458 through 467 removed outlier: 3.586A pdb=" N PHE D 462 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY D 467 " --> pdb=" O ARG D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 removed outlier: 3.864A pdb=" N ARG D 475 " --> pdb=" O SER D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 504 removed outlier: 3.855A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 502 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 510 through 517 removed outlier: 3.582A pdb=" N THR D 514 " --> pdb=" O PRO D 510 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 516 " --> pdb=" O GLN D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 541 removed outlier: 3.552A pdb=" N VAL D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 578 removed outlier: 3.579A pdb=" N ILE D 572 " --> pdb=" O ASN D 568 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 592 Processing helix chain 'D' and resid 608 through 619 removed outlier: 3.618A pdb=" N MET D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP D 619 " --> pdb=" O LEU D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 670 removed outlier: 3.774A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 689 removed outlier: 3.697A pdb=" N ALA D 686 " --> pdb=" O LEU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 698 Processing helix chain 'D' and resid 701 through 708 Processing helix chain 'D' and resid 709 through 714 removed outlier: 3.613A pdb=" N ILE D 713 " --> pdb=" O ILE D 709 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 709 through 714' Processing helix chain 'D' and resid 770 through 775 removed outlier: 3.681A pdb=" N ARG D 775 " --> pdb=" O ASP D 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 228 removed outlier: 3.587A pdb=" N ILE E 226 " --> pdb=" O GLN E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 236 removed outlier: 4.309A pdb=" N LEU E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 241 removed outlier: 4.038A pdb=" N PHE E 240 " --> pdb=" O HIS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 273 removed outlier: 3.854A pdb=" N ALA E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR E 272 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.946A pdb=" N VAL E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 280 through 285' Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 296 through 306 removed outlier: 3.816A pdb=" N LYS E 305 " --> pdb=" O GLU E 301 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.691A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 335' Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.693A pdb=" N THR E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 341 " --> pdb=" O GLN E 337 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET E 342 " --> pdb=" O LEU E 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 336 through 342' Processing helix chain 'E' and resid 386 through 395 removed outlier: 3.927A pdb=" N VAL E 390 " --> pdb=" O GLY E 386 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS E 394 " --> pdb=" O VAL E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 421 through 436 removed outlier: 3.882A pdb=" N SER E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 433 " --> pdb=" O ALA E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 removed outlier: 3.746A pdb=" N PHE E 462 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 465 " --> pdb=" O ASN E 461 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY E 467 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN E 468 " --> pdb=" O PHE E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 475 removed outlier: 3.862A pdb=" N ARG E 475 " --> pdb=" O SER E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 503 removed outlier: 3.782A pdb=" N GLU E 497 " --> pdb=" O ASP E 493 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 503 " --> pdb=" O LEU E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 509 Processing helix chain 'E' and resid 509 through 517 removed outlier: 4.281A pdb=" N TYR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR E 514 " --> pdb=" O PRO E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 545 removed outlier: 4.245A pdb=" N ALA E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU E 544 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 545 " --> pdb=" O VAL E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 579 removed outlier: 3.756A pdb=" N ARG E 570 " --> pdb=" O GLU E 566 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE E 572 " --> pdb=" O ASN E 568 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE E 573 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS E 575 " --> pdb=" O ASP E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 592 removed outlier: 3.936A pdb=" N SER E 591 " --> pdb=" O GLU E 588 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 592 " --> pdb=" O LEU E 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 588 through 592' Processing helix chain 'E' and resid 608 through 616 Processing helix chain 'E' and resid 640 through 645 removed outlier: 4.284A pdb=" N ARG E 645 " --> pdb=" O PRO E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 664 removed outlier: 3.540A pdb=" N LEU E 664 " --> pdb=" O GLU E 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 228 removed outlier: 4.050A pdb=" N ALA B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 removed outlier: 3.532A pdb=" N LEU B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.794A pdb=" N ARG B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.532A pdb=" N LEU B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.623A pdb=" N ILE B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 413 removed outlier: 4.087A pdb=" N ALA B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 436 removed outlier: 3.610A pdb=" N SER B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.832A pdb=" N PHE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.861A pdb=" N ARG B 475 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.521A pdb=" N THR B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Proline residue: B 506 - end of helix removed outlier: 3.606A pdb=" N HIS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 517 Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.964A pdb=" N THR B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 removed outlier: 4.182A pdb=" N ILE B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 572 " --> pdb=" O ASN B 568 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 576 " --> pdb=" O ILE B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 592 Processing helix chain 'B' and resid 593 through 597 removed outlier: 4.225A pdb=" N GLY B 597 " --> pdb=" O LYS B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 620 removed outlier: 3.783A pdb=" N VAL B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 671 removed outlier: 3.681A pdb=" N LEU B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 667 " --> pdb=" O ARG B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 695 through 716 removed outlier: 3.502A pdb=" N ILE B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 711 " --> pdb=" O TYR B 707 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 4.435A pdb=" N MET C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.922A pdb=" N VAL C 268 " --> pdb=" O MET C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 306 removed outlier: 4.120A pdb=" N ASN C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 330 through 338 removed outlier: 3.611A pdb=" N VAL C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.701A pdb=" N ARG C 368 " --> pdb=" O PRO C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 393 removed outlier: 3.640A pdb=" N ILE C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 3.694A pdb=" N LEU C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 435 removed outlier: 3.712A pdb=" N CYS C 425 " --> pdb=" O ILE C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 474 through 478 removed outlier: 3.975A pdb=" N VAL C 478 " --> pdb=" O ARG C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 removed outlier: 3.636A pdb=" N GLU C 497 " --> pdb=" O ASP C 493 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 510 through 517 removed outlier: 3.522A pdb=" N THR C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 516 " --> pdb=" O GLN C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 544 removed outlier: 3.856A pdb=" N THR C 543 " --> pdb=" O LYS C 539 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 544 " --> pdb=" O ALA C 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 539 through 544' Processing helix chain 'C' and resid 563 through 579 removed outlier: 4.842A pdb=" N ILE C 569 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 575 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 592 Processing helix chain 'C' and resid 608 through 619 removed outlier: 4.252A pdb=" N ASP C 619 " --> pdb=" O LEU C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.575A pdb=" N ARG C 672 " --> pdb=" O ASN C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 688 removed outlier: 3.765A pdb=" N ALA C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 711 removed outlier: 3.570A pdb=" N VAL C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 705 " --> pdb=" O VAL C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 760 removed outlier: 3.920A pdb=" N PHE C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 775 removed outlier: 3.802A pdb=" N ARG C 775 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.971A pdb=" N HIS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.918A pdb=" N ALA A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.634A pdb=" N VAL A 284 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.821A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 336 through 345 removed outlier: 4.044A pdb=" N THR A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.744A pdb=" N LEU A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 386 through 393 removed outlier: 4.188A pdb=" N VAL A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 4.359A pdb=" N THR A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 436 removed outlier: 3.860A pdb=" N CYS A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 4.329A pdb=" N PHE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 493 through 509 removed outlier: 3.615A pdb=" N LEU A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix removed outlier: 3.678A pdb=" N HIS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 517 removed outlier: 3.661A pdb=" N THR A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 removed outlier: 3.526A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.563A pdb=" N GLU A 556 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 557 " --> pdb=" O GLY A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 557' Processing helix chain 'A' and resid 563 through 578 removed outlier: 4.005A pdb=" N ILE A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 576 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.527A pdb=" N GLN A 613 " --> pdb=" O ARG A 609 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.803A pdb=" N GLN A 638 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 639 " --> pdb=" O PRO A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 639' Processing helix chain 'A' and resid 662 through 671 removed outlier: 3.605A pdb=" N ILE A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 689 removed outlier: 3.921A pdb=" N ALA A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 716 removed outlier: 3.620A pdb=" N TYR A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 711 " --> pdb=" O TYR A 707 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 275 through 279 removed outlier: 5.959A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA D 356 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL D 251 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL D 377 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D 252 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 525 through 526 removed outlier: 6.162A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASP D 587 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL D 552 " --> pdb=" O ASP D 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 353 through 356 removed outlier: 6.493A pdb=" N VAL E 251 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N VAL E 377 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU E 252 " --> pdb=" O VAL E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 275 through 276 removed outlier: 6.227A pdb=" N PHE E 275 " --> pdb=" O ILE E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 549 through 551 removed outlier: 6.787A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL E 524 " --> pdb=" O GLY E 631 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N GLY E 523 " --> pdb=" O ASP E 650 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU E 652 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU E 525 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TYR E 654 " --> pdb=" O LEU E 525 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR E 527 " --> pdb=" O TYR E 654 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 275 through 279 removed outlier: 4.229A pdb=" N ILE B 354 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 356 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 355 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 548 through 552 removed outlier: 5.860A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASP B 587 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL B 552 " --> pdb=" O ASP B 587 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 628 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 524 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR B 633 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE B 526 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 525 " --> pdb=" O GLN B 651 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 653 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 527 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 275 through 280 removed outlier: 6.175A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE C 277 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP C 314 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE C 279 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 377 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 548 through 553 removed outlier: 5.997A pdb=" N ASN C 548 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE C 585 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 550 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASP C 587 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 552 " --> pdb=" O ASP C 587 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C 524 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY C 523 " --> pdb=" O GLN C 651 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE C 653 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU C 525 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 251 through 254 Processing sheet with id=AB2, first strand: chain 'A' and resid 277 through 278 removed outlier: 7.006A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 352 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 311 " --> pdb=" O VAL A 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 548 through 551 removed outlier: 5.601A pdb=" N ASN A 548 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE A 585 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE A 550 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP A 587 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR A 582 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ILE A 630 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 584 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ALA A 632 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU A 586 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU A 525 " --> pdb=" O ILE A 653 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1221 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: 2.60 Time building geometry restraints manager: 2.17 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: 6480 1.34 - 1.46: 3683 1.46 - 1.58: 9656 1.58 - 1.70: 31 1.70 - 1.83: 164 Bond restraints: 20014 Sorted by residual: bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP C 902 " pdb=" C5 ADP C 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP D 904 " pdb=" C5 ADP D 904 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 20009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 26588 3.08 - 6.17: 352 6.17 - 9.25: 121 9.25 - 12.33: 42 12.33 - 15.42: 11 Bond angle restraints: 27114 Sorted by residual: angle pdb=" N GLY D 290 " pdb=" CA GLY D 290 " pdb=" C GLY D 290 " ideal model delta sigma weight residual 111.95 105.09 6.86 9.50e-01 1.11e+00 5.21e+01 angle pdb=" CA GLY D 290 " pdb=" C GLY D 290 " pdb=" O GLY D 290 " ideal model delta sigma weight residual 122.22 118.82 3.40 6.50e-01 2.37e+00 2.74e+01 angle pdb=" N VAL A 541 " pdb=" CA VAL A 541 " pdb=" C VAL A 541 " ideal model delta sigma weight residual 112.83 107.65 5.18 9.90e-01 1.02e+00 2.74e+01 angle pdb=" C ALA E 593 " pdb=" N LYS E 594 " pdb=" CA LYS E 594 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N GLU B 283 " pdb=" CA GLU B 283 " pdb=" C GLU B 283 " ideal model delta sigma weight residual 114.75 108.37 6.38 1.26e+00 6.30e-01 2.57e+01 ... (remaining 27109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 11978 35.21 - 70.42: 242 70.42 - 105.63: 28 105.63 - 140.84: 10 140.84 - 176.05: 7 Dihedral angle restraints: 12265 sinusoidal: 5006 harmonic: 7259 Sorted by residual: dihedral pdb=" CA ALA A 580 " pdb=" C ALA A 580 " pdb=" N PRO A 581 " pdb=" CA PRO A 581 " ideal model delta harmonic sigma weight residual 180.00 133.21 46.79 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" C2' ADP D 904 " pdb=" C1' ADP D 904 " pdb=" N9 ADP D 904 " pdb=" C4 ADP D 904 " ideal model delta sinusoidal sigma weight residual 91.55 -92.40 -176.05 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2' ADP E 901 " pdb=" C1' ADP E 901 " pdb=" N9 ADP E 901 " pdb=" C4 ADP E 901 " ideal model delta sinusoidal sigma weight residual 91.55 -94.04 -174.41 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 12262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2426 0.060 - 0.120: 524 0.120 - 0.180: 94 0.180 - 0.240: 11 0.240 - 0.300: 6 Chirality restraints: 3061 Sorted by residual: chirality pdb=" CA ALA H 17 " pdb=" N ALA H 17 " pdb=" C ALA H 17 " pdb=" CB ALA H 17 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB THR A 477 " pdb=" CA THR A 477 " pdb=" OG1 THR A 477 " pdb=" CG2 THR A 477 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL D 417 " pdb=" CA VAL D 417 " pdb=" CG1 VAL D 417 " pdb=" CG2 VAL D 417 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3058 not shown) Planarity restraints: 3543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 11 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C ALA H 11 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA H 11 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA H 12 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 677 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO D 678 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 678 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 678 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 677 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO B 678 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 678 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 678 " 0.037 5.00e-02 4.00e+02 ... (remaining 3540 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 7 1.98 - 2.71: 659 2.71 - 3.44: 27140 3.44 - 4.17: 45259 4.17 - 4.90: 78225 Nonbonded interactions: 151290 Sorted by model distance: nonbonded pdb=" CG2 THR C 535 " pdb=" F2 BEF C 904 " model vdw 1.245 3.410 nonbonded pdb=" F1 BEF B 903 " pdb=" O3B ADP B 905 " model vdw 1.271 2.990 nonbonded pdb="BE BEF B 903 " pdb=" O3B ADP B 905 " model vdw 1.604 2.420 nonbonded pdb=" CB ALA E 289 " pdb=" CB ALA H 15 " model vdw 1.634 3.880 nonbonded pdb=" CG2 THR C 535 " pdb="BE BEF C 904 " model vdw 1.696 2.840 ... (remaining 151285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'B' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'C' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'D' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'E' and resid 209 through 670) } 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: 1.100 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: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.080 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 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 : 0.015 1.119 20039 Z= 1.441 Angle : 1.073 15.418 27114 Z= 0.527 Chirality : 0.053 0.300 3061 Planarity : 0.006 0.073 3543 Dihedral : 16.243 176.048 7585 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.72 % Favored : 92.08 % Rotamer: Outliers : 0.34 % Allowed : 7.85 % Favored : 91.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.58 (0.12), residues: 2513 helix: -5.04 (0.04), residues: 881 sheet: -1.68 (0.31), residues: 235 loop : -3.22 (0.13), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 645 TYR 0.016 0.001 TYR C 416 PHE 0.017 0.001 PHE C 462 TRP 0.005 0.001 TRP A 561 HIS 0.004 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00582 (20014) covalent geometry : angle 1.07300 (27114) hydrogen bonds : bond 0.34833 ( 424) hydrogen bonds : angle 10.39629 ( 1221) Misc. bond : bond 0.39908 ( 25) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 484 time to evaluate : 0.657 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: D 213 TYR cc_start: 0.8131 (m-10) cc_final: 0.7848 (m-10) REVERT: D 343 ASP cc_start: 0.7048 (p0) cc_final: 0.6787 (p0) REVERT: D 513 TYR cc_start: 0.8574 (m-80) cc_final: 0.8335 (m-10) REVERT: E 225 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7034 (tm-30) REVERT: E 430 MET cc_start: 0.8782 (tmm) cc_final: 0.8261 (tmm) REVERT: E 505 TYR cc_start: 0.7539 (m-10) cc_final: 0.7017 (m-80) REVERT: E 522 LYS cc_start: 0.8087 (tppt) cc_final: 0.7820 (tttt) REVERT: B 231 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6458 (mp0) REVERT: B 402 ASP cc_start: 0.6673 (p0) cc_final: 0.6065 (p0) REVERT: B 470 ASN cc_start: 0.6366 (p0) cc_final: 0.5656 (p0) REVERT: B 649 LEU cc_start: 0.6861 (mt) cc_final: 0.6322 (mp) REVERT: C 264 MET cc_start: 0.7548 (tpp) cc_final: 0.7042 (tpt) REVERT: C 618 MET cc_start: 0.8233 (mmt) cc_final: 0.7913 (mmm) REVERT: A 232 LEU cc_start: 0.6832 (tp) cc_final: 0.6256 (mt) REVERT: A 345 MET cc_start: 0.7636 (mmp) cc_final: 0.7380 (mmm) REVERT: A 407 GLU cc_start: 0.7652 (tp30) cc_final: 0.7267 (pm20) REVERT: A 427 GLU cc_start: 0.7093 (tp30) cc_final: 0.6409 (tm-30) REVERT: A 459 MET cc_start: 0.6657 (tpt) cc_final: 0.5792 (tpp) REVERT: A 463 ARG cc_start: 0.8356 (mmp80) cc_final: 0.7380 (mmt180) REVERT: A 557 LEU cc_start: 0.8093 (tp) cc_final: 0.7841 (tp) REVERT: A 564 GLU cc_start: 0.8500 (mp0) cc_final: 0.8231 (mp0) REVERT: A 587 ASP cc_start: 0.6411 (t0) cc_final: 0.5156 (t70) REVERT: A 659 ASP cc_start: 0.6544 (p0) cc_final: 0.5501 (p0) outliers start: 7 outliers final: 2 residues processed: 488 average time/residue: 0.1519 time to fit residues: 108.7236 Evaluate side-chains 300 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain C residue 655 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 ASN D 295 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 GLN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN ** D 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 GLN D 690 GLN D 782 GLN D 783 GLN E 225 GLN E 337 GLN E 612 ASN B 225 GLN B 670 GLN C 280 ASN C 337 GLN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN C 512 GLN C 638 GLN C 757 HIS ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 461 ASN A 568 ASN A 622 ASN A 690 GLN A 702 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.143311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.117190 restraints weight = 49514.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.120228 restraints weight = 26947.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.122193 restraints weight = 18167.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.123454 restraints weight = 14097.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.124188 restraints weight = 12039.383| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20039 Z= 0.150 Angle : 0.770 10.066 27114 Z= 0.355 Chirality : 0.047 0.274 3061 Planarity : 0.005 0.052 3543 Dihedral : 12.953 170.763 2850 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.76 % Favored : 92.12 % Rotamer: Outliers : 2.29 % Allowed : 14.67 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.34 (0.13), residues: 2513 helix: -3.51 (0.11), residues: 918 sheet: -1.41 (0.31), residues: 251 loop : -2.73 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 372 TYR 0.015 0.001 TYR A 254 PHE 0.025 0.001 PHE A 549 TRP 0.021 0.002 TRP C 486 HIS 0.009 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00332 (20014) covalent geometry : angle 0.77013 (27114) hydrogen bonds : bond 0.04832 ( 424) hydrogen bonds : angle 5.54877 ( 1221) Misc. bond : bond 0.00287 ( 25) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 331 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 345 MET cc_start: 0.6159 (tpp) cc_final: 0.5887 (tpp) REVERT: D 513 TYR cc_start: 0.8848 (m-80) cc_final: 0.8546 (m-10) REVERT: D 699 TYR cc_start: 0.6175 (t80) cc_final: 0.5759 (t80) REVERT: D 762 MET cc_start: 0.4931 (mmp) cc_final: 0.4301 (ptp) REVERT: B 264 MET cc_start: 0.7490 (mmt) cc_final: 0.7129 (mmt) REVERT: B 288 MET cc_start: 0.8153 (mmt) cc_final: 0.7816 (mmm) REVERT: B 388 LEU cc_start: 0.8774 (tp) cc_final: 0.8563 (tt) REVERT: B 402 ASP cc_start: 0.6964 (p0) cc_final: 0.6430 (p0) REVERT: B 439 LEU cc_start: 0.2729 (OUTLIER) cc_final: 0.2371 (tp) REVERT: B 470 ASN cc_start: 0.6996 (p0) cc_final: 0.6653 (p0) REVERT: B 621 MET cc_start: 0.6467 (mmm) cc_final: 0.5681 (mmm) REVERT: C 264 MET cc_start: 0.7473 (tpp) cc_final: 0.6777 (tpt) REVERT: C 459 MET cc_start: 0.7771 (mmm) cc_final: 0.7399 (tpp) REVERT: A 232 LEU cc_start: 0.6837 (tp) cc_final: 0.6234 (mt) REVERT: A 288 MET cc_start: 0.4432 (mpp) cc_final: 0.3279 (tmm) REVERT: A 403 ASP cc_start: 0.7019 (p0) cc_final: 0.6418 (p0) REVERT: A 407 GLU cc_start: 0.7939 (tp30) cc_final: 0.7476 (pm20) REVERT: A 427 GLU cc_start: 0.7348 (tp30) cc_final: 0.6825 (pt0) REVERT: A 459 MET cc_start: 0.7130 (tpt) cc_final: 0.6735 (mmm) REVERT: A 463 ARG cc_start: 0.8258 (mmp80) cc_final: 0.7847 (mmm160) REVERT: A 537 LEU cc_start: 0.7979 (tp) cc_final: 0.7464 (mt) REVERT: A 659 ASP cc_start: 0.6183 (p0) cc_final: 0.5647 (p0) outliers start: 47 outliers final: 26 residues processed: 364 average time/residue: 0.1310 time to fit residues: 73.7067 Evaluate side-chains 313 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 421 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 102 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.140548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.113854 restraints weight = 48230.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.116857 restraints weight = 26482.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.118747 restraints weight = 17882.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.119952 restraints weight = 13924.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.120704 restraints weight = 11878.372| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20039 Z= 0.138 Angle : 0.711 9.435 27114 Z= 0.330 Chirality : 0.045 0.172 3061 Planarity : 0.005 0.049 3543 Dihedral : 12.478 177.129 2850 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Rotamer: Outliers : 2.58 % Allowed : 15.50 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.15), residues: 2513 helix: -2.46 (0.14), residues: 940 sheet: -1.33 (0.30), residues: 274 loop : -2.42 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 375 TYR 0.017 0.001 TYR A 505 PHE 0.015 0.001 PHE A 549 TRP 0.021 0.001 TRP C 486 HIS 0.018 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00299 (20014) covalent geometry : angle 0.71141 (27114) hydrogen bonds : bond 0.03430 ( 424) hydrogen bonds : angle 4.81328 ( 1221) Misc. bond : bond 0.00242 ( 25) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 513 TYR cc_start: 0.8825 (m-80) cc_final: 0.8523 (m-10) REVERT: D 532 THR cc_start: 0.8569 (p) cc_final: 0.8121 (t) REVERT: D 699 TYR cc_start: 0.6120 (t80) cc_final: 0.5826 (t80) REVERT: D 762 MET cc_start: 0.5098 (mmp) cc_final: 0.4512 (ptp) REVERT: E 223 MET cc_start: 0.7296 (mpp) cc_final: 0.6971 (mpp) REVERT: E 572 ILE cc_start: 0.8570 (tp) cc_final: 0.8313 (tp) REVERT: B 232 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8368 (mm) REVERT: B 288 MET cc_start: 0.8227 (mmt) cc_final: 0.8004 (mmm) REVERT: B 402 ASP cc_start: 0.7026 (p0) cc_final: 0.6534 (p0) REVERT: B 439 LEU cc_start: 0.3060 (OUTLIER) cc_final: 0.2645 (tp) REVERT: B 470 ASN cc_start: 0.7072 (p0) cc_final: 0.6777 (p0) REVERT: B 495 ILE cc_start: 0.7472 (mt) cc_final: 0.7148 (mt) REVERT: B 621 MET cc_start: 0.6632 (mmm) cc_final: 0.5881 (mmm) REVERT: C 230 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8504 (p) REVERT: C 264 MET cc_start: 0.7459 (tpp) cc_final: 0.6791 (tpt) REVERT: C 459 MET cc_start: 0.7577 (mmm) cc_final: 0.7326 (tpp) REVERT: A 232 LEU cc_start: 0.6806 (tp) cc_final: 0.6234 (mt) REVERT: A 253 MET cc_start: 0.3374 (ppp) cc_final: 0.3018 (ppp) REVERT: A 271 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: A 407 GLU cc_start: 0.7760 (tp30) cc_final: 0.7411 (pm20) REVERT: A 427 GLU cc_start: 0.7381 (tp30) cc_final: 0.6841 (pt0) REVERT: A 437 MET cc_start: 0.7924 (mmm) cc_final: 0.7471 (tpp) REVERT: A 459 MET cc_start: 0.7141 (tpt) cc_final: 0.6762 (tpp) REVERT: A 537 LEU cc_start: 0.8036 (tp) cc_final: 0.7578 (mt) REVERT: A 574 ASP cc_start: 0.6896 (t0) cc_final: 0.6631 (t0) REVERT: A 659 ASP cc_start: 0.6321 (p0) cc_final: 0.5556 (p0) outliers start: 53 outliers final: 25 residues processed: 342 average time/residue: 0.1337 time to fit residues: 71.4508 Evaluate side-chains 296 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 171 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 240 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 126 optimal weight: 0.5980 chunk 233 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 HIS ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 GLN C 782 GLN ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.130432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.102931 restraints weight = 47860.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.105848 restraints weight = 26274.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.107714 restraints weight = 17824.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108894 restraints weight = 13951.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.109612 restraints weight = 11983.471| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20039 Z= 0.224 Angle : 0.839 13.640 27114 Z= 0.394 Chirality : 0.050 0.225 3061 Planarity : 0.006 0.065 3543 Dihedral : 12.502 165.922 2849 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.07 % Favored : 90.81 % Rotamer: Outliers : 4.24 % Allowed : 17.69 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.16), residues: 2513 helix: -1.67 (0.16), residues: 939 sheet: -1.26 (0.30), residues: 275 loop : -2.16 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 463 TYR 0.024 0.002 TYR C 254 PHE 0.022 0.002 PHE A 585 TRP 0.053 0.003 TRP C 486 HIS 0.015 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00506 (20014) covalent geometry : angle 0.83856 (27114) hydrogen bonds : bond 0.03494 ( 424) hydrogen bonds : angle 4.70341 ( 1221) Misc. bond : bond 0.00485 ( 25) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 300 time to evaluate : 0.579 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: D 213 TYR cc_start: 0.8541 (m-10) cc_final: 0.8160 (m-10) REVERT: D 513 TYR cc_start: 0.9030 (m-80) cc_final: 0.8768 (m-10) REVERT: D 635 ARG cc_start: 0.5512 (ptt180) cc_final: 0.5240 (ptt180) REVERT: D 762 MET cc_start: 0.5082 (mmp) cc_final: 0.4708 (ptp) REVERT: E 223 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6403 (tpp) REVERT: E 430 MET cc_start: 0.8733 (tmm) cc_final: 0.8488 (tmm) REVERT: E 459 MET cc_start: 0.7308 (tpt) cc_final: 0.6817 (tpt) REVERT: E 572 ILE cc_start: 0.8560 (tp) cc_final: 0.8292 (tp) REVERT: B 264 MET cc_start: 0.7290 (mmt) cc_final: 0.6857 (mmt) REVERT: B 293 GLU cc_start: 0.7145 (mp0) cc_final: 0.6298 (mp0) REVERT: B 317 ASP cc_start: 0.5598 (t0) cc_final: 0.5386 (t70) REVERT: B 364 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.6329 (t0) REVERT: B 402 ASP cc_start: 0.7271 (p0) cc_final: 0.6801 (p0) REVERT: B 439 LEU cc_start: 0.3142 (OUTLIER) cc_final: 0.2615 (tp) REVERT: B 557 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8805 (pp) REVERT: B 562 TYR cc_start: 0.8253 (t80) cc_final: 0.8045 (t80) REVERT: B 569 ILE cc_start: 0.8778 (pp) cc_final: 0.8565 (pp) REVERT: C 288 MET cc_start: 0.7620 (mmt) cc_final: 0.7388 (mmm) REVERT: C 301 GLU cc_start: 0.8542 (pp20) cc_final: 0.8298 (pp20) REVERT: C 459 MET cc_start: 0.7828 (mmm) cc_final: 0.7435 (tpp) REVERT: C 474 LEU cc_start: 0.8225 (pt) cc_final: 0.7890 (pp) REVERT: C 498 GLU cc_start: 0.7986 (tp30) cc_final: 0.7769 (tm-30) REVERT: A 271 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: A 407 GLU cc_start: 0.7983 (tp30) cc_final: 0.7649 (pm20) REVERT: A 537 LEU cc_start: 0.8128 (tp) cc_final: 0.7785 (mt) outliers start: 87 outliers final: 35 residues processed: 363 average time/residue: 0.1351 time to fit residues: 76.4214 Evaluate side-chains 289 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 244 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 243 optimal weight: 0.0470 chunk 57 optimal weight: 0.3980 chunk 215 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 237 optimal weight: 0.0070 chunk 151 optimal weight: 4.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 306 ASN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.133362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.105957 restraints weight = 47309.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.108967 restraints weight = 25782.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.110894 restraints weight = 17319.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112095 restraints weight = 13403.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.112828 restraints weight = 11484.636| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20039 Z= 0.119 Angle : 0.738 10.361 27114 Z= 0.337 Chirality : 0.046 0.162 3061 Planarity : 0.004 0.051 3543 Dihedral : 12.135 168.837 2848 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.12 % Favored : 92.84 % Rotamer: Outliers : 2.34 % Allowed : 20.76 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.16), residues: 2513 helix: -1.22 (0.17), residues: 924 sheet: -1.09 (0.30), residues: 271 loop : -1.96 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 372 TYR 0.023 0.002 TYR D 699 PHE 0.016 0.001 PHE D 692 TRP 0.017 0.001 TRP C 486 HIS 0.010 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00269 (20014) covalent geometry : angle 0.73784 (27114) hydrogen bonds : bond 0.02780 ( 424) hydrogen bonds : angle 4.43386 ( 1221) Misc. bond : bond 0.00204 ( 25) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 274 time to evaluate : 0.762 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: D 215 ASP cc_start: 0.8025 (m-30) cc_final: 0.7330 (t0) REVERT: D 280 ASN cc_start: 0.7789 (m110) cc_final: 0.6003 (m-40) REVERT: D 513 TYR cc_start: 0.8933 (m-80) cc_final: 0.8522 (m-10) REVERT: D 532 THR cc_start: 0.8862 (p) cc_final: 0.8542 (t) REVERT: D 621 MET cc_start: 0.8607 (tpp) cc_final: 0.8403 (tpp) REVERT: E 223 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6671 (mpp) REVERT: E 225 GLN cc_start: 0.8297 (pp30) cc_final: 0.7702 (pp30) REVERT: E 229 MET cc_start: 0.8505 (ttm) cc_final: 0.8299 (ttm) REVERT: E 459 MET cc_start: 0.7432 (tpt) cc_final: 0.7024 (tpt) REVERT: E 560 MET cc_start: 0.7101 (mmm) cc_final: 0.6724 (mmm) REVERT: E 572 ILE cc_start: 0.8439 (tp) cc_final: 0.8141 (tp) REVERT: B 293 GLU cc_start: 0.7128 (mp0) cc_final: 0.6321 (mp0) REVERT: B 402 ASP cc_start: 0.7244 (p0) cc_final: 0.6796 (p0) REVERT: B 439 LEU cc_start: 0.2903 (OUTLIER) cc_final: 0.2300 (tp) REVERT: C 229 MET cc_start: 0.7910 (tmm) cc_final: 0.7497 (tmm) REVERT: C 288 MET cc_start: 0.7601 (mmt) cc_final: 0.7376 (mmm) REVERT: C 301 GLU cc_start: 0.8448 (pp20) cc_final: 0.8192 (pp20) REVERT: C 498 GLU cc_start: 0.8023 (tp30) cc_final: 0.7756 (tp30) REVERT: C 615 LEU cc_start: 0.9574 (mt) cc_final: 0.9226 (mt) REVERT: C 706 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9050 (tttp) REVERT: A 271 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: A 407 GLU cc_start: 0.7989 (tp30) cc_final: 0.7625 (pm20) REVERT: A 427 GLU cc_start: 0.7687 (tp30) cc_final: 0.7095 (pt0) REVERT: A 430 MET cc_start: 0.8548 (mmm) cc_final: 0.8013 (mmm) REVERT: A 459 MET cc_start: 0.6698 (mmm) cc_final: 0.6276 (mmm) REVERT: A 537 LEU cc_start: 0.7940 (tp) cc_final: 0.7647 (mt) REVERT: A 659 ASP cc_start: 0.7039 (p0) cc_final: 0.6761 (p0) outliers start: 48 outliers final: 29 residues processed: 309 average time/residue: 0.1319 time to fit residues: 63.9199 Evaluate side-chains 286 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 624 LYS Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 706 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 627 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 57 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 207 optimal weight: 0.0770 chunk 198 optimal weight: 0.9980 chunk 250 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 ASN B 414 HIS B 670 GLN A 236 HIS A 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.129447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101401 restraints weight = 48342.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.104250 restraints weight = 27003.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.106083 restraints weight = 18576.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.107252 restraints weight = 14694.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.107840 restraints weight = 12701.961| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20039 Z= 0.160 Angle : 0.757 11.976 27114 Z= 0.349 Chirality : 0.047 0.175 3061 Planarity : 0.004 0.049 3543 Dihedral : 12.013 177.138 2848 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.32 % Favored : 91.64 % Rotamer: Outliers : 3.36 % Allowed : 20.52 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.17), residues: 2513 helix: -1.02 (0.17), residues: 954 sheet: -1.26 (0.30), residues: 287 loop : -1.91 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 359 TYR 0.027 0.002 TYR D 416 PHE 0.012 0.001 PHE C 462 TRP 0.037 0.002 TRP C 486 HIS 0.005 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00370 (20014) covalent geometry : angle 0.75654 (27114) hydrogen bonds : bond 0.02703 ( 424) hydrogen bonds : angle 4.32090 ( 1221) Misc. bond : bond 0.00195 ( 25) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 0.716 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: D 215 ASP cc_start: 0.7933 (m-30) cc_final: 0.7516 (t0) REVERT: D 264 MET cc_start: 0.7811 (mmt) cc_final: 0.7460 (tpp) REVERT: D 513 TYR cc_start: 0.8953 (m-80) cc_final: 0.8619 (m-10) REVERT: D 532 THR cc_start: 0.8945 (p) cc_final: 0.8666 (t) REVERT: D 615 LEU cc_start: 0.9276 (mt) cc_final: 0.8956 (mp) REVERT: D 621 MET cc_start: 0.8674 (tpp) cc_final: 0.8444 (tpp) REVERT: E 223 MET cc_start: 0.7317 (mpp) cc_final: 0.6734 (mpp) REVERT: E 225 GLN cc_start: 0.8264 (pp30) cc_final: 0.7981 (pp30) REVERT: E 430 MET cc_start: 0.9013 (tmm) cc_final: 0.8756 (tmm) REVERT: E 459 MET cc_start: 0.7457 (tpt) cc_final: 0.7167 (tpt) REVERT: E 505 TYR cc_start: 0.8615 (m-80) cc_final: 0.8274 (m-80) REVERT: E 572 ILE cc_start: 0.8409 (tp) cc_final: 0.8152 (tp) REVERT: B 354 ILE cc_start: 0.9097 (mt) cc_final: 0.8844 (mt) REVERT: B 378 ASP cc_start: 0.6927 (t0) cc_final: 0.6673 (t0) REVERT: B 402 ASP cc_start: 0.7172 (p0) cc_final: 0.6789 (p0) REVERT: B 439 LEU cc_start: 0.2928 (OUTLIER) cc_final: 0.2447 (tp) REVERT: B 470 ASN cc_start: 0.7223 (p0) cc_final: 0.7020 (p0) REVERT: C 288 MET cc_start: 0.7699 (mmt) cc_final: 0.7445 (mmm) REVERT: C 301 GLU cc_start: 0.8372 (pp20) cc_final: 0.8120 (pp20) REVERT: C 498 GLU cc_start: 0.8023 (tp30) cc_final: 0.7764 (tm-30) REVERT: C 706 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8687 (tptm) REVERT: A 271 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: A 342 MET cc_start: 0.7844 (ppp) cc_final: 0.7236 (ppp) REVERT: A 359 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7657 (mmm160) REVERT: A 407 GLU cc_start: 0.7969 (tp30) cc_final: 0.7626 (pm20) REVERT: A 430 MET cc_start: 0.8688 (mmm) cc_final: 0.8227 (mmm) REVERT: A 437 MET cc_start: 0.8072 (mmm) cc_final: 0.7563 (tpp) REVERT: A 459 MET cc_start: 0.6756 (mmm) cc_final: 0.6309 (mmm) REVERT: A 537 LEU cc_start: 0.8154 (tp) cc_final: 0.7837 (mt) REVERT: A 574 ASP cc_start: 0.6363 (p0) cc_final: 0.6090 (t0) REVERT: A 659 ASP cc_start: 0.7638 (p0) cc_final: 0.7277 (p0) outliers start: 69 outliers final: 40 residues processed: 310 average time/residue: 0.1262 time to fit residues: 61.2241 Evaluate side-chains 288 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 624 LYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 706 LYS Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 627 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 179 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 242 optimal weight: 0.0570 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 140 optimal weight: 0.0170 chunk 64 optimal weight: 6.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 ASN B 222 GLN B 414 HIS B 670 GLN A 236 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.131514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103938 restraints weight = 47912.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106889 restraints weight = 26086.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.108769 restraints weight = 17638.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109962 restraints weight = 13782.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.110553 restraints weight = 11806.601| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20039 Z= 0.115 Angle : 0.724 11.970 27114 Z= 0.330 Chirality : 0.045 0.163 3061 Planarity : 0.004 0.088 3543 Dihedral : 11.955 178.675 2848 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.24 % Favored : 92.72 % Rotamer: Outliers : 2.44 % Allowed : 21.44 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.17), residues: 2513 helix: -0.85 (0.17), residues: 958 sheet: -1.15 (0.30), residues: 275 loop : -1.90 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 775 TYR 0.020 0.001 TYR D 416 PHE 0.010 0.001 PHE A 549 TRP 0.028 0.001 TRP C 486 HIS 0.013 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00260 (20014) covalent geometry : angle 0.72379 (27114) hydrogen bonds : bond 0.02515 ( 424) hydrogen bonds : angle 4.26657 ( 1221) Misc. bond : bond 0.00368 ( 25) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 0.724 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: D 213 TYR cc_start: 0.8578 (m-10) cc_final: 0.8061 (m-10) REVERT: D 215 ASP cc_start: 0.7978 (m-30) cc_final: 0.7450 (t0) REVERT: D 280 ASN cc_start: 0.7432 (m-40) cc_final: 0.6911 (t0) REVERT: D 513 TYR cc_start: 0.8860 (m-80) cc_final: 0.8461 (m-10) REVERT: D 532 THR cc_start: 0.8759 (p) cc_final: 0.8470 (t) REVERT: D 615 LEU cc_start: 0.9265 (mt) cc_final: 0.8963 (mp) REVERT: D 621 MET cc_start: 0.8626 (tpp) cc_final: 0.8352 (tpp) REVERT: E 223 MET cc_start: 0.7340 (mpp) cc_final: 0.6335 (tpp) REVERT: E 225 GLN cc_start: 0.8223 (pp30) cc_final: 0.8014 (pp30) REVERT: E 459 MET cc_start: 0.7476 (tpt) cc_final: 0.7173 (tpt) REVERT: E 505 TYR cc_start: 0.8577 (m-80) cc_final: 0.8158 (m-80) REVERT: E 513 TYR cc_start: 0.8785 (m-80) cc_final: 0.7804 (m-80) REVERT: E 560 MET cc_start: 0.7088 (mmm) cc_final: 0.6762 (mmm) REVERT: E 572 ILE cc_start: 0.8357 (tp) cc_final: 0.8096 (tp) REVERT: E 588 GLU cc_start: 0.6899 (pm20) cc_final: 0.6684 (pt0) REVERT: B 231 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6855 (mp0) REVERT: B 402 ASP cc_start: 0.7285 (p0) cc_final: 0.6873 (p0) REVERT: B 439 LEU cc_start: 0.3103 (OUTLIER) cc_final: 0.2536 (tp) REVERT: B 483 ASN cc_start: 0.6380 (m-40) cc_final: 0.6144 (t0) REVERT: C 301 GLU cc_start: 0.8352 (pp20) cc_final: 0.8076 (pp20) REVERT: C 498 GLU cc_start: 0.8034 (tp30) cc_final: 0.7744 (tm-30) REVERT: C 615 LEU cc_start: 0.9596 (mt) cc_final: 0.9288 (mt) REVERT: C 706 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8689 (tptm) REVERT: A 271 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: A 342 MET cc_start: 0.7911 (ppp) cc_final: 0.7374 (ppp) REVERT: A 407 GLU cc_start: 0.7933 (tp30) cc_final: 0.7606 (pm20) REVERT: A 430 MET cc_start: 0.8724 (mmm) cc_final: 0.8235 (mmm) REVERT: A 537 LEU cc_start: 0.8078 (tp) cc_final: 0.7862 (mt) REVERT: A 659 ASP cc_start: 0.7582 (p0) cc_final: 0.7182 (p0) outliers start: 50 outliers final: 34 residues processed: 307 average time/residue: 0.1274 time to fit residues: 61.5431 Evaluate side-chains 291 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 624 LYS Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 670 GLN Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 706 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 627 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 64 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 169 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 88 optimal weight: 0.4980 chunk 68 optimal weight: 0.1980 chunk 146 optimal weight: 0.0970 chunk 229 optimal weight: 20.0000 chunk 107 optimal weight: 0.4980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN A 236 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.132335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.104912 restraints weight = 47692.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107871 restraints weight = 26016.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.109753 restraints weight = 17589.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.110940 restraints weight = 13728.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111695 restraints weight = 11762.221| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20039 Z= 0.110 Angle : 0.716 10.945 27114 Z= 0.325 Chirality : 0.045 0.154 3061 Planarity : 0.004 0.081 3543 Dihedral : 11.840 179.921 2848 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.96 % Favored : 92.00 % Rotamer: Outliers : 2.14 % Allowed : 22.56 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.17), residues: 2513 helix: -0.65 (0.17), residues: 954 sheet: -0.98 (0.31), residues: 262 loop : -1.82 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 635 TYR 0.014 0.001 TYR D 416 PHE 0.010 0.001 PHE A 549 TRP 0.029 0.002 TRP D 486 HIS 0.012 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00251 (20014) covalent geometry : angle 0.71611 (27114) hydrogen bonds : bond 0.02360 ( 424) hydrogen bonds : angle 4.14177 ( 1221) Misc. bond : bond 0.00212 ( 25) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 0.733 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: D 215 ASP cc_start: 0.7833 (m-30) cc_final: 0.7365 (t0) REVERT: D 316 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7904 (mm) REVERT: D 513 TYR cc_start: 0.8848 (m-80) cc_final: 0.8426 (m-10) REVERT: D 532 THR cc_start: 0.8712 (p) cc_final: 0.8458 (t) REVERT: D 574 ASP cc_start: 0.7874 (m-30) cc_final: 0.7664 (m-30) REVERT: D 615 LEU cc_start: 0.9201 (mt) cc_final: 0.8923 (mp) REVERT: D 621 MET cc_start: 0.8476 (tpp) cc_final: 0.8254 (tpp) REVERT: E 223 MET cc_start: 0.7380 (mpp) cc_final: 0.6300 (tpp) REVERT: E 225 GLN cc_start: 0.8314 (pp30) cc_final: 0.8025 (pp30) REVERT: E 459 MET cc_start: 0.7412 (tpt) cc_final: 0.7154 (tpt) REVERT: E 505 TYR cc_start: 0.8511 (m-80) cc_final: 0.8059 (m-80) REVERT: E 513 TYR cc_start: 0.8771 (m-80) cc_final: 0.7828 (m-80) REVERT: E 560 MET cc_start: 0.7067 (mmm) cc_final: 0.6736 (mmm) REVERT: E 572 ILE cc_start: 0.8285 (tp) cc_final: 0.8069 (tp) REVERT: B 402 ASP cc_start: 0.7197 (p0) cc_final: 0.6809 (p0) REVERT: B 439 LEU cc_start: 0.3047 (OUTLIER) cc_final: 0.2661 (tp) REVERT: B 483 ASN cc_start: 0.6468 (m-40) cc_final: 0.6180 (t0) REVERT: C 229 MET cc_start: 0.8619 (ttp) cc_final: 0.8046 (tmm) REVERT: C 301 GLU cc_start: 0.8281 (pp20) cc_final: 0.8015 (pp20) REVERT: C 459 MET cc_start: 0.7480 (mmt) cc_final: 0.7207 (tpp) REVERT: C 498 GLU cc_start: 0.8049 (tp30) cc_final: 0.7764 (tm-30) REVERT: C 615 LEU cc_start: 0.9596 (mt) cc_final: 0.9202 (mt) REVERT: C 706 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8733 (tptm) REVERT: A 271 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: A 342 MET cc_start: 0.8010 (ppp) cc_final: 0.7458 (ppp) REVERT: A 407 GLU cc_start: 0.7913 (tp30) cc_final: 0.7604 (pm20) REVERT: A 430 MET cc_start: 0.8737 (mmm) cc_final: 0.8226 (mmm) REVERT: A 659 ASP cc_start: 0.7634 (p0) cc_final: 0.7300 (p0) outliers start: 44 outliers final: 35 residues processed: 291 average time/residue: 0.1327 time to fit residues: 60.1375 Evaluate side-chains 286 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 706 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 627 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 131 optimal weight: 0.0370 chunk 185 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 15 optimal weight: 0.0570 chunk 50 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS B 670 GLN A 236 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.131925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104419 restraints weight = 47837.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.107310 restraints weight = 26612.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.109169 restraints weight = 18218.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.110332 restraints weight = 14333.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111052 restraints weight = 12366.321| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20039 Z= 0.113 Angle : 0.728 10.786 27114 Z= 0.328 Chirality : 0.045 0.157 3061 Planarity : 0.004 0.073 3543 Dihedral : 11.739 177.698 2848 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.14 % Allowed : 23.00 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.17), residues: 2513 helix: -0.50 (0.17), residues: 954 sheet: -0.91 (0.31), residues: 262 loop : -1.76 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 359 TYR 0.012 0.001 TYR D 416 PHE 0.010 0.001 PHE E 277 TRP 0.031 0.002 TRP D 486 HIS 0.009 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00261 (20014) covalent geometry : angle 0.72788 (27114) hydrogen bonds : bond 0.02325 ( 424) hydrogen bonds : angle 4.09133 ( 1221) Misc. bond : bond 0.00221 ( 25) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 0.699 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: D 215 ASP cc_start: 0.7826 (m-30) cc_final: 0.7421 (t0) REVERT: D 316 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7925 (mm) REVERT: D 513 TYR cc_start: 0.8845 (m-80) cc_final: 0.8429 (m-10) REVERT: D 532 THR cc_start: 0.8623 (p) cc_final: 0.8393 (t) REVERT: D 574 ASP cc_start: 0.7839 (m-30) cc_final: 0.7624 (m-30) REVERT: D 590 ASP cc_start: 0.7276 (t0) cc_final: 0.6964 (t0) REVERT: D 615 LEU cc_start: 0.9195 (mt) cc_final: 0.8887 (mp) REVERT: E 223 MET cc_start: 0.7385 (mpp) cc_final: 0.6288 (tpp) REVERT: E 225 GLN cc_start: 0.8216 (pp30) cc_final: 0.8011 (pp30) REVERT: E 505 TYR cc_start: 0.8509 (m-80) cc_final: 0.8107 (m-80) REVERT: E 513 TYR cc_start: 0.8785 (m-80) cc_final: 0.7840 (m-80) REVERT: B 231 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6796 (mp0) REVERT: B 402 ASP cc_start: 0.7079 (p0) cc_final: 0.6714 (p0) REVERT: B 439 LEU cc_start: 0.3128 (OUTLIER) cc_final: 0.2735 (tp) REVERT: C 229 MET cc_start: 0.8493 (ttp) cc_final: 0.7912 (tmm) REVERT: C 301 GLU cc_start: 0.8195 (pp20) cc_final: 0.7962 (pp20) REVERT: C 345 MET cc_start: 0.7251 (tpp) cc_final: 0.6849 (tpt) REVERT: C 459 MET cc_start: 0.7502 (mmt) cc_final: 0.7230 (tpp) REVERT: C 498 GLU cc_start: 0.8011 (tp30) cc_final: 0.7737 (tm-30) REVERT: C 615 LEU cc_start: 0.9615 (mt) cc_final: 0.9362 (mt) REVERT: C 706 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8760 (tptm) REVERT: A 264 MET cc_start: 0.6492 (mmt) cc_final: 0.5710 (mmt) REVERT: A 271 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: A 342 MET cc_start: 0.7954 (ppp) cc_final: 0.7436 (ppp) REVERT: A 407 GLU cc_start: 0.7898 (tp30) cc_final: 0.7610 (pm20) REVERT: A 430 MET cc_start: 0.8734 (mmm) cc_final: 0.8223 (mmm) REVERT: A 659 ASP cc_start: 0.7575 (p0) cc_final: 0.7240 (p0) outliers start: 44 outliers final: 32 residues processed: 292 average time/residue: 0.1296 time to fit residues: 58.9326 Evaluate side-chains 279 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 706 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 627 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 112 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.0470 chunk 140 optimal weight: 0.6980 chunk 164 optimal weight: 0.2980 chunk 146 optimal weight: 0.5980 chunk 241 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 ASN B 225 GLN ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 670 GLN C 702 GLN A 236 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.132940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105425 restraints weight = 47831.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108363 restraints weight = 26330.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.110263 restraints weight = 17864.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.111430 restraints weight = 13922.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111962 restraints weight = 11953.359| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20039 Z= 0.113 Angle : 0.735 10.591 27114 Z= 0.333 Chirality : 0.045 0.157 3061 Planarity : 0.004 0.071 3543 Dihedral : 11.666 175.525 2848 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.05 % Allowed : 23.20 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.17), residues: 2513 helix: -0.37 (0.17), residues: 952 sheet: -0.79 (0.32), residues: 258 loop : -1.76 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 249 TYR 0.013 0.001 TYR A 505 PHE 0.010 0.001 PHE E 277 TRP 0.016 0.001 TRP C 486 HIS 0.009 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00261 (20014) covalent geometry : angle 0.73452 (27114) hydrogen bonds : bond 0.02332 ( 424) hydrogen bonds : angle 4.07340 ( 1221) Misc. bond : bond 0.00282 ( 25) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.810 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: D 215 ASP cc_start: 0.7907 (m-30) cc_final: 0.7489 (t0) REVERT: D 316 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7920 (mm) REVERT: D 513 TYR cc_start: 0.8833 (m-80) cc_final: 0.8376 (m-10) REVERT: D 532 THR cc_start: 0.8531 (p) cc_final: 0.8314 (t) REVERT: D 574 ASP cc_start: 0.7851 (m-30) cc_final: 0.7650 (m-30) REVERT: D 615 LEU cc_start: 0.9181 (mt) cc_final: 0.8880 (mp) REVERT: D 706 LYS cc_start: 0.6900 (pttt) cc_final: 0.6136 (pttm) REVERT: E 223 MET cc_start: 0.7375 (mpp) cc_final: 0.6307 (tpp) REVERT: E 225 GLN cc_start: 0.8198 (pp30) cc_final: 0.7991 (pp30) REVERT: E 505 TYR cc_start: 0.8486 (m-80) cc_final: 0.8093 (m-80) REVERT: E 513 TYR cc_start: 0.8816 (m-80) cc_final: 0.7942 (m-80) REVERT: B 231 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6804 (mp0) REVERT: B 253 MET cc_start: 0.8242 (mtp) cc_final: 0.7877 (mtt) REVERT: B 402 ASP cc_start: 0.7072 (p0) cc_final: 0.6722 (p0) REVERT: B 439 LEU cc_start: 0.4051 (OUTLIER) cc_final: 0.3776 (tp) REVERT: C 229 MET cc_start: 0.8582 (ttp) cc_final: 0.8008 (tmm) REVERT: C 301 GLU cc_start: 0.8210 (pp20) cc_final: 0.7967 (pp20) REVERT: C 345 MET cc_start: 0.7220 (tpp) cc_final: 0.6858 (tpt) REVERT: C 459 MET cc_start: 0.7510 (mmt) cc_final: 0.7272 (tpp) REVERT: C 615 LEU cc_start: 0.9605 (mt) cc_final: 0.9210 (mt) REVERT: C 706 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8792 (tptm) REVERT: A 264 MET cc_start: 0.6445 (mmt) cc_final: 0.5743 (mmt) REVERT: A 271 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: A 342 MET cc_start: 0.7901 (ppp) cc_final: 0.7399 (ppp) REVERT: A 407 GLU cc_start: 0.7912 (tp30) cc_final: 0.7616 (pm20) REVERT: A 430 MET cc_start: 0.8762 (mmm) cc_final: 0.8252 (mmm) REVERT: A 659 ASP cc_start: 0.7670 (p0) cc_final: 0.7317 (p0) outliers start: 42 outliers final: 31 residues processed: 286 average time/residue: 0.1305 time to fit residues: 58.3764 Evaluate side-chains 275 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 706 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 627 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 96 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 98 optimal weight: 0.0570 chunk 95 optimal weight: 4.9990 chunk 242 optimal weight: 0.4980 chunk 190 optimal weight: 9.9990 chunk 200 optimal weight: 40.0000 chunk 162 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 213 optimal weight: 0.0370 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 ASN B 397 ASN ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 670 GLN ** A 236 HIS ** 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 = 0.4039 r_free = 0.4039 target = 0.132969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.105085 restraints weight = 47916.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.108001 restraints weight = 26622.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.109820 restraints weight = 18257.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.110974 restraints weight = 14407.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.111581 restraints weight = 12437.961| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20039 Z= 0.116 Angle : 0.754 13.188 27114 Z= 0.341 Chirality : 0.045 0.170 3061 Planarity : 0.004 0.073 3543 Dihedral : 11.621 174.695 2848 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.90 % Allowed : 23.54 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.17), residues: 2513 helix: -0.33 (0.17), residues: 950 sheet: -0.68 (0.32), residues: 249 loop : -1.73 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 249 TYR 0.020 0.001 TYR A 505 PHE 0.011 0.001 PHE E 277 TRP 0.014 0.001 TRP C 486 HIS 0.008 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00270 (20014) covalent geometry : angle 0.75399 (27114) hydrogen bonds : bond 0.02367 ( 424) hydrogen bonds : angle 4.06098 ( 1221) Misc. bond : bond 0.00245 ( 25) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3525.82 seconds wall clock time: 61 minutes 19.38 seconds (3679.38 seconds total)