Starting phenix.real_space_refine on Sat Sep 28 15:49:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/09_2024/6oab_20000_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/09_2024/6oab_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/09_2024/6oab_20000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/09_2024/6oab_20000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/09_2024/6oab_20000_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oab_20000/09_2024/6oab_20000_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 11.90, per 1000 atoms: 0.60 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: 5.19 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.95 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: 5.61 Time building geometry restraints manager: 5.93 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 43.610 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.060 ------------------------------------------------------------------------------- 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 : 0.006 0.109 20014 Z= 0.368 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP A 561 HIS 0.004 0.001 HIS C 236 PHE 0.017 0.001 PHE C 462 TYR 0.016 0.001 TYR C 416 ARG 0.005 0.000 ARG E 645 *********************** 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 fitting. rotamer outliers: 7 poor density : 484 time to evaluate : 2.394 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: 0.7847 (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: 0.7037 (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: 0.7043 (tpt) REVERT: C 618 MET cc_start: 0.8233 (mmt) cc_final: 0.7914 (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: 0.7266 (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: 0.3675 time to fit residues: 261.9559 Evaluate side-chains 300 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 298 time to evaluate : 2.215 ------------------------------------------------------------------------------- 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 211 optimal weight: 0.3980 chunk 190 optimal weight: 0.3980 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 0.0470 chunk 128 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20014 Z= 0.183 Angle : 0.761 9.983 27114 Z= 0.349 Chirality : 0.046 0.285 3061 Planarity : 0.005 0.052 3543 Dihedral : 12.953 175.280 2850 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.44 % Rotamer: Outliers : 1.90 % Allowed : 14.86 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.13), residues: 2513 helix: -3.57 (0.11), residues: 909 sheet: -1.37 (0.31), residues: 248 loop : -2.73 (0.14), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 486 HIS 0.017 0.001 HIS C 394 PHE 0.027 0.001 PHE B 516 TYR 0.016 0.001 TYR A 254 ARG 0.007 0.001 ARG A 372 *********************** 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 372 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 333 time to evaluate : 2.156 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: 0.5955 (tpp) cc_final: 0.5729 (tpp) REVERT: D 513 TYR cc_start: 0.8678 (m-80) cc_final: 0.8416 (m-10) REVERT: D 699 TYR cc_start: 0.6048 (t80) cc_final: 0.5729 (t80) REVERT: D 762 MET cc_start: 0.4978 (mmp) cc_final: 0.4505 (ptp) REVERT: E 430 MET cc_start: 0.8975 (tmm) cc_final: 0.8528 (tmm) REVERT: B 264 MET cc_start: 0.7517 (mmt) cc_final: 0.7156 (mmt) REVERT: B 332 ARG cc_start: 0.7789 (ptp-110) cc_final: 0.7577 (ptm160) REVERT: B 402 ASP cc_start: 0.6807 (p0) cc_final: 0.6247 (p0) REVERT: B 439 LEU cc_start: 0.3302 (OUTLIER) cc_final: 0.2906 (tp) REVERT: B 470 ASN cc_start: 0.6883 (p0) cc_final: 0.6549 (p0) REVERT: B 621 MET cc_start: 0.6625 (mmm) cc_final: 0.5763 (mmm) REVERT: B 649 LEU cc_start: 0.7128 (mt) cc_final: 0.6580 (mp) REVERT: C 264 MET cc_start: 0.7431 (tpp) cc_final: 0.6906 (tpt) REVERT: C 348 ARG cc_start: 0.6721 (tpp80) cc_final: 0.6514 (tpp80) REVERT: C 459 MET cc_start: 0.7558 (mmm) cc_final: 0.7209 (tpp) REVERT: A 232 LEU cc_start: 0.6895 (tp) cc_final: 0.6255 (mt) REVERT: A 288 MET cc_start: 0.4428 (mpp) cc_final: 0.3286 (tmm) REVERT: A 403 ASP cc_start: 0.6710 (p0) cc_final: 0.6156 (p0) REVERT: A 407 GLU cc_start: 0.7736 (tp30) cc_final: 0.7334 (pm20) REVERT: A 427 GLU cc_start: 0.7214 (tp30) cc_final: 0.6859 (pt0) REVERT: A 459 MET cc_start: 0.6992 (tpt) cc_final: 0.6697 (mmm) REVERT: A 463 ARG cc_start: 0.8214 (mmp80) cc_final: 0.7832 (mmm160) REVERT: A 537 LEU cc_start: 0.7977 (tp) cc_final: 0.7453 (mt) REVERT: A 557 LEU cc_start: 0.8254 (tp) cc_final: 0.8023 (tp) REVERT: A 659 ASP cc_start: 0.5787 (p0) cc_final: 0.5285 (p0) outliers start: 39 outliers final: 20 residues processed: 360 average time/residue: 0.3040 time to fit residues: 167.4142 Evaluate side-chains 307 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 286 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 583 VAL 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 541 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 232 LEU 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 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 126 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 228 optimal weight: 0.0570 chunk 246 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 226 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.7702 ------------------------------------------------------------------------------- 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 C 350 ASN C 432 GLN ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20014 Z= 0.175 Angle : 0.704 10.050 27114 Z= 0.321 Chirality : 0.044 0.171 3061 Planarity : 0.004 0.049 3543 Dihedral : 12.437 178.129 2850 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.04 % Favored : 92.84 % Rotamer: Outliers : 2.68 % Allowed : 15.20 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.15), residues: 2513 helix: -2.43 (0.14), residues: 927 sheet: -1.00 (0.32), residues: 235 loop : -2.39 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 486 HIS 0.016 0.001 HIS C 394 PHE 0.014 0.001 PHE A 549 TYR 0.013 0.001 TYR A 505 ARG 0.007 0.000 ARG B 323 *********************** 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 364 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 309 time to evaluate : 2.333 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: 0.8685 (m-80) cc_final: 0.8426 (m-10) REVERT: D 532 THR cc_start: 0.8269 (p) cc_final: 0.7790 (t) REVERT: D 762 MET cc_start: 0.5030 (mmp) cc_final: 0.4538 (ptp) REVERT: E 223 MET cc_start: 0.7328 (mpp) cc_final: 0.7001 (mpp) REVERT: E 430 MET cc_start: 0.8928 (tmm) cc_final: 0.8408 (tmm) REVERT: E 572 ILE cc_start: 0.8562 (tp) cc_final: 0.8310 (tp) REVERT: B 232 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8301 (mm) REVERT: B 323 ARG cc_start: 0.4942 (mmm160) cc_final: 0.3594 (tpp80) REVERT: B 402 ASP cc_start: 0.6819 (p0) cc_final: 0.6296 (p0) REVERT: B 424 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8885 (tp) REVERT: B 439 LEU cc_start: 0.3447 (OUTLIER) cc_final: 0.3137 (tp) REVERT: B 470 ASN cc_start: 0.6794 (p0) cc_final: 0.6517 (p0) REVERT: B 495 ILE cc_start: 0.7206 (mt) cc_final: 0.6908 (mt) REVERT: B 621 MET cc_start: 0.6562 (mmm) cc_final: 0.5793 (mmm) REVERT: C 264 MET cc_start: 0.7416 (tpp) cc_final: 0.6807 (tpt) REVERT: C 348 ARG cc_start: 0.6916 (tpp80) cc_final: 0.6688 (tpp80) REVERT: C 615 LEU cc_start: 0.9373 (mt) cc_final: 0.9047 (mt) REVERT: A 271 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: A 407 GLU cc_start: 0.7636 (tp30) cc_final: 0.7338 (pm20) REVERT: A 427 GLU cc_start: 0.7232 (tp30) cc_final: 0.6848 (pt0) REVERT: A 437 MET cc_start: 0.7760 (mmm) cc_final: 0.7539 (tpp) REVERT: A 459 MET cc_start: 0.7038 (tpt) cc_final: 0.6661 (tpp) REVERT: A 537 LEU cc_start: 0.8014 (tp) cc_final: 0.7580 (mt) REVERT: A 557 LEU cc_start: 0.8298 (tp) cc_final: 0.8097 (tp) REVERT: A 574 ASP cc_start: 0.7022 (t0) cc_final: 0.6774 (t0) REVERT: A 659 ASP cc_start: 0.6083 (p0) cc_final: 0.5366 (p0) outliers start: 55 outliers final: 29 residues processed: 348 average time/residue: 0.3046 time to fit residues: 163.4417 Evaluate side-chains 301 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 268 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 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 330 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 424 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 556 GLU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 278 LEU 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 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 414 HIS Chi-restraints excluded: chain A residue 464 PHE 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 225 optimal weight: 0.0870 chunk 171 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 229 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20014 Z= 0.184 Angle : 0.712 12.920 27114 Z= 0.324 Chirality : 0.045 0.189 3061 Planarity : 0.004 0.061 3543 Dihedral : 12.241 172.266 2849 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.12 % Favored : 92.76 % Rotamer: Outliers : 2.83 % Allowed : 17.35 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.16), residues: 2513 helix: -1.70 (0.16), residues: 936 sheet: -0.91 (0.32), residues: 254 loop : -2.19 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 486 HIS 0.007 0.001 HIS C 394 PHE 0.014 0.001 PHE A 585 TYR 0.011 0.001 TYR B 562 ARG 0.006 0.000 ARG D 703 *********************** 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 347 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 289 time to evaluate : 2.190 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 513 TYR cc_start: 0.8723 (m-80) cc_final: 0.8446 (m-10) REVERT: D 532 THR cc_start: 0.8528 (p) cc_final: 0.8192 (t) REVERT: D 762 MET cc_start: 0.4920 (mmp) cc_final: 0.4644 (ptp) REVERT: E 223 MET cc_start: 0.7297 (mpp) cc_final: 0.6195 (tpp) REVERT: E 229 MET cc_start: 0.8735 (tmm) cc_final: 0.8389 (tmm) REVERT: E 313 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8848 (pt) REVERT: E 572 ILE cc_start: 0.8577 (tp) cc_final: 0.8306 (tp) REVERT: E 667 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8022 (pt) REVERT: B 378 ASP cc_start: 0.5954 (t70) cc_final: 0.5723 (t70) REVERT: B 402 ASP cc_start: 0.6853 (p0) cc_final: 0.6367 (p0) REVERT: B 424 LEU cc_start: 0.9165 (tt) cc_final: 0.8933 (tp) REVERT: B 439 LEU cc_start: 0.3669 (OUTLIER) cc_final: 0.3254 (tp) REVERT: B 470 ASN cc_start: 0.6828 (p0) cc_final: 0.6548 (p0) REVERT: B 621 MET cc_start: 0.6764 (mmm) cc_final: 0.5969 (mmm) REVERT: C 264 MET cc_start: 0.7435 (tpp) cc_final: 0.6761 (tpt) REVERT: C 301 GLU cc_start: 0.8384 (pp20) cc_final: 0.8176 (pp20) REVERT: C 348 ARG cc_start: 0.6906 (tpp80) cc_final: 0.6695 (tpp80) REVERT: C 459 MET cc_start: 0.7481 (mmm) cc_final: 0.6929 (tpp) REVERT: C 615 LEU cc_start: 0.9450 (mt) cc_final: 0.9045 (mt) REVERT: A 271 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: A 288 MET cc_start: 0.4393 (mpp) cc_final: 0.3021 (tmm) REVERT: A 342 MET cc_start: 0.8495 (ptm) cc_final: 0.7868 (ppp) REVERT: A 407 GLU cc_start: 0.7659 (tp30) cc_final: 0.7383 (pm20) REVERT: A 427 GLU cc_start: 0.7281 (tp30) cc_final: 0.6887 (pt0) REVERT: A 459 MET cc_start: 0.7073 (tpt) cc_final: 0.6848 (tpp) REVERT: A 537 LEU cc_start: 0.7920 (tp) cc_final: 0.7521 (mt) REVERT: A 587 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: A 659 ASP cc_start: 0.6334 (p0) cc_final: 0.5996 (p0) outliers start: 58 outliers final: 36 residues processed: 326 average time/residue: 0.2932 time to fit residues: 149.1075 Evaluate side-chains 302 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 261 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain B residue 239 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 417 VAL Chi-restraints excluded: chain B residue 425 CYS 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 556 GLU 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 330 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 472 SER 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 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 587 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 20.0000 chunk 137 optimal weight: 0.9980 chunk 3 optimal weight: 0.0670 chunk 180 optimal weight: 0.0980 chunk 100 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 217 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 306 ASN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20014 Z= 0.168 Angle : 0.702 10.274 27114 Z= 0.318 Chirality : 0.045 0.171 3061 Planarity : 0.004 0.054 3543 Dihedral : 12.079 179.715 2849 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.04 % Favored : 92.88 % Rotamer: Outliers : 2.92 % Allowed : 17.88 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.16), residues: 2513 helix: -1.23 (0.17), residues: 940 sheet: -0.74 (0.32), residues: 253 loop : -2.11 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 486 HIS 0.004 0.001 HIS C 394 PHE 0.013 0.001 PHE D 275 TYR 0.020 0.001 TYR A 254 ARG 0.008 0.000 ARG D 369 *********************** 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 346 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 286 time to evaluate : 2.327 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 264 MET cc_start: 0.7159 (mtt) cc_final: 0.6685 (mtt) REVERT: D 283 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6675 (mt-10) REVERT: D 316 ILE cc_start: 0.7781 (mm) cc_final: 0.7331 (mm) REVERT: D 513 TYR cc_start: 0.8715 (m-80) cc_final: 0.8437 (m-10) REVERT: D 532 THR cc_start: 0.8491 (p) cc_final: 0.8146 (t) REVERT: D 762 MET cc_start: 0.5075 (mmp) cc_final: 0.4781 (ptp) REVERT: E 572 ILE cc_start: 0.8474 (tp) cc_final: 0.8245 (tp) REVERT: B 232 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8388 (mm) REVERT: B 364 ASP cc_start: 0.6057 (OUTLIER) cc_final: 0.5827 (t0) REVERT: B 402 ASP cc_start: 0.6930 (p0) cc_final: 0.6436 (p0) REVERT: B 424 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8943 (tp) REVERT: B 439 LEU cc_start: 0.3273 (OUTLIER) cc_final: 0.2767 (tp) REVERT: B 470 ASN cc_start: 0.6779 (p0) cc_final: 0.6532 (p0) REVERT: C 264 MET cc_start: 0.7545 (tpp) cc_final: 0.6891 (tpt) REVERT: C 301 GLU cc_start: 0.8360 (pp20) cc_final: 0.8115 (pp20) REVERT: C 348 ARG cc_start: 0.6916 (tpp80) cc_final: 0.6667 (tpp80) REVERT: C 459 MET cc_start: 0.7502 (mmm) cc_final: 0.6915 (tpp) REVERT: C 615 LEU cc_start: 0.9497 (mt) cc_final: 0.9099 (mt) REVERT: A 271 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: A 288 MET cc_start: 0.4534 (mpp) cc_final: 0.3154 (tmm) REVERT: A 342 MET cc_start: 0.8647 (ptm) cc_final: 0.7954 (ppp) REVERT: A 407 GLU cc_start: 0.7735 (tp30) cc_final: 0.7489 (pm20) REVERT: A 427 GLU cc_start: 0.7295 (tp30) cc_final: 0.6912 (pt0) REVERT: A 537 LEU cc_start: 0.7967 (tp) cc_final: 0.7585 (mt) REVERT: A 587 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: A 659 ASP cc_start: 0.6215 (p0) cc_final: 0.5827 (p0) outliers start: 60 outliers final: 39 residues processed: 327 average time/residue: 0.2888 time to fit residues: 148.4069 Evaluate side-chains 309 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 264 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 611 VAL 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 378 ASP Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 670 GLN Chi-restraints excluded: chain B residue 232 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 391 LEU Chi-restraints excluded: chain B residue 424 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 556 GLU 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 377 VAL Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 583 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 Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 587 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 4.9990 chunk 218 optimal weight: 0.1980 chunk 47 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 242 optimal weight: 0.2980 chunk 201 optimal weight: 0.9980 chunk 112 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS A 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20014 Z= 0.161 Angle : 0.695 9.374 27114 Z= 0.314 Chirality : 0.044 0.157 3061 Planarity : 0.004 0.057 3543 Dihedral : 11.861 169.771 2848 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.00 % Favored : 92.96 % Rotamer: Outliers : 2.73 % Allowed : 19.01 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.16), residues: 2513 helix: -0.94 (0.17), residues: 933 sheet: -0.73 (0.32), residues: 258 loop : -2.02 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 486 HIS 0.004 0.001 HIS C 394 PHE 0.010 0.001 PHE A 549 TYR 0.016 0.001 TYR A 254 ARG 0.007 0.000 ARG D 369 *********************** 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 330 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 274 time to evaluate : 2.249 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 283 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6705 (mt-10) REVERT: D 316 ILE cc_start: 0.7793 (mm) cc_final: 0.7359 (mm) REVERT: D 513 TYR cc_start: 0.8742 (m-80) cc_final: 0.8489 (m-10) REVERT: D 532 THR cc_start: 0.8435 (p) cc_final: 0.8222 (t) REVERT: D 590 ASP cc_start: 0.5998 (t0) cc_final: 0.5626 (t0) REVERT: E 505 TYR cc_start: 0.8467 (m-80) cc_final: 0.8121 (m-80) REVERT: E 572 ILE cc_start: 0.8403 (tp) cc_final: 0.8198 (tp) REVERT: B 232 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8316 (mm) REVERT: B 293 GLU cc_start: 0.6532 (mp0) cc_final: 0.5487 (mp0) REVERT: B 402 ASP cc_start: 0.6971 (p0) cc_final: 0.6500 (p0) REVERT: B 424 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8903 (tp) REVERT: B 439 LEU cc_start: 0.3069 (OUTLIER) cc_final: 0.2443 (tp) REVERT: B 470 ASN cc_start: 0.6893 (p0) cc_final: 0.6616 (p0) REVERT: B 557 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8649 (pp) REVERT: B 569 ILE cc_start: 0.8576 (pp) cc_final: 0.8358 (pp) REVERT: C 264 MET cc_start: 0.7355 (tpp) cc_final: 0.6702 (tpt) REVERT: C 301 GLU cc_start: 0.8352 (pp20) cc_final: 0.8145 (pp20) REVERT: C 348 ARG cc_start: 0.6969 (tpp80) cc_final: 0.6746 (tpp80) REVERT: C 459 MET cc_start: 0.7239 (mmm) cc_final: 0.6767 (tpp) REVERT: C 560 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7055 (ppp) REVERT: C 615 LEU cc_start: 0.9483 (mt) cc_final: 0.9088 (mt) REVERT: A 271 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: A 288 MET cc_start: 0.4528 (mpp) cc_final: 0.3391 (tmm) REVERT: A 407 GLU cc_start: 0.7728 (tp30) cc_final: 0.7471 (pm20) REVERT: A 427 GLU cc_start: 0.7333 (tp30) cc_final: 0.6959 (pt0) REVERT: A 430 MET cc_start: 0.8160 (mmm) cc_final: 0.7801 (mmm) REVERT: A 437 MET cc_start: 0.7688 (mmm) cc_final: 0.7152 (tpp) REVERT: A 537 LEU cc_start: 0.7991 (tp) cc_final: 0.7706 (mt) REVERT: A 587 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8144 (m-30) REVERT: A 659 ASP cc_start: 0.6282 (p0) cc_final: 0.5919 (p0) outliers start: 56 outliers final: 34 residues processed: 312 average time/residue: 0.2877 time to fit residues: 141.5147 Evaluate side-chains 297 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 256 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 664 LEU 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 E residue 537 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 670 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 263 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 477 THR 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 278 LEU 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 472 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 583 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 Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 587 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 241 optimal weight: 0.6980 chunk 151 optimal weight: 0.0970 chunk 147 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- 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 394 HIS ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 GLN C 782 GLN A 236 HIS A 337 GLN A 414 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20014 Z= 0.293 Angle : 0.828 13.173 27114 Z= 0.384 Chirality : 0.048 0.194 3061 Planarity : 0.005 0.061 3543 Dihedral : 12.071 169.261 2848 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.71 % Favored : 91.25 % Rotamer: Outliers : 3.51 % Allowed : 19.40 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2513 helix: -0.98 (0.17), residues: 951 sheet: -0.95 (0.30), residues: 268 loop : -1.90 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 486 HIS 0.020 0.002 HIS C 394 PHE 0.018 0.002 PHE D 373 TYR 0.041 0.002 TYR A 505 ARG 0.011 0.001 ARG D 369 *********************** 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 350 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 278 time to evaluate : 2.392 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: 0.7820 (m-30) cc_final: 0.7431 (t0) REVERT: D 216 ILE cc_start: 0.8619 (tp) cc_final: 0.8194 (tp) REVERT: D 283 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7093 (mt-10) REVERT: D 513 TYR cc_start: 0.8872 (m-80) cc_final: 0.8604 (m-10) REVERT: D 532 THR cc_start: 0.8798 (p) cc_final: 0.8538 (t) REVERT: D 560 MET cc_start: 0.8062 (ptp) cc_final: 0.7564 (ptp) REVERT: D 621 MET cc_start: 0.8704 (tpp) cc_final: 0.8501 (tpp) REVERT: E 505 TYR cc_start: 0.8508 (m-80) cc_final: 0.8150 (m-80) REVERT: E 513 TYR cc_start: 0.8762 (m-80) cc_final: 0.7985 (m-80) REVERT: E 572 ILE cc_start: 0.8477 (tp) cc_final: 0.8266 (tp) REVERT: B 232 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8485 (mm) REVERT: B 253 MET cc_start: 0.8388 (mtp) cc_final: 0.8079 (mtt) REVERT: B 293 GLU cc_start: 0.7753 (mp0) cc_final: 0.6838 (mp0) REVERT: B 323 ARG cc_start: 0.5644 (mmm160) cc_final: 0.4676 (tpp80) REVERT: B 402 ASP cc_start: 0.7003 (p0) cc_final: 0.6577 (p0) REVERT: C 301 GLU cc_start: 0.8432 (pp20) cc_final: 0.8190 (pp20) REVERT: C 348 ARG cc_start: 0.7002 (tpp80) cc_final: 0.6702 (tpp80) REVERT: C 459 MET cc_start: 0.7638 (mmm) cc_final: 0.7309 (tpp) REVERT: C 474 LEU cc_start: 0.8237 (pt) cc_final: 0.7976 (pp) REVERT: A 271 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: A 288 MET cc_start: 0.4838 (mpp) cc_final: 0.3924 (tmm) REVERT: A 407 GLU cc_start: 0.7749 (tp30) cc_final: 0.7493 (pm20) REVERT: A 430 MET cc_start: 0.8516 (mmm) cc_final: 0.8074 (mmm) REVERT: A 437 MET cc_start: 0.7937 (mmm) cc_final: 0.7575 (tpp) REVERT: A 527 TYR cc_start: 0.7098 (p90) cc_final: 0.6852 (p90) REVERT: A 537 LEU cc_start: 0.8138 (tp) cc_final: 0.7905 (mt) REVERT: A 659 ASP cc_start: 0.7013 (p0) cc_final: 0.6659 (p0) outliers start: 72 outliers final: 39 residues processed: 329 average time/residue: 0.3022 time to fit residues: 153.8132 Evaluate side-chains 285 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 244 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 486 TRP Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 335 VAL 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 E residue 495 ILE Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain B residue 232 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 424 LEU Chi-restraints excluded: chain B residue 541 VAL 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 278 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 377 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 701 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 164 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 ASN B 414 HIS A 236 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20014 Z= 0.191 Angle : 0.751 10.880 27114 Z= 0.344 Chirality : 0.046 0.164 3061 Planarity : 0.004 0.050 3543 Dihedral : 11.938 170.215 2848 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.96 % Favored : 93.00 % Rotamer: Outliers : 2.05 % Allowed : 21.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2513 helix: -0.78 (0.17), residues: 953 sheet: -0.84 (0.31), residues: 259 loop : -1.85 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 486 HIS 0.004 0.001 HIS C 394 PHE 0.009 0.001 PHE A 549 TYR 0.026 0.001 TYR B 254 ARG 0.012 0.000 ARG D 369 *********************** 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 301 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 259 time to evaluate : 2.799 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 215 ASP cc_start: 0.7966 (m-30) cc_final: 0.7475 (t0) REVERT: D 216 ILE cc_start: 0.8535 (tp) cc_final: 0.8064 (tp) REVERT: D 280 ASN cc_start: 0.7602 (m110) cc_final: 0.6381 (m-40) REVERT: D 345 MET cc_start: 0.6570 (mmt) cc_final: 0.6338 (tpp) REVERT: D 513 TYR cc_start: 0.8753 (m-80) cc_final: 0.8439 (m-10) REVERT: D 532 THR cc_start: 0.8578 (p) cc_final: 0.8304 (t) REVERT: D 560 MET cc_start: 0.7993 (ptp) cc_final: 0.7479 (ptp) REVERT: D 621 MET cc_start: 0.8699 (tpp) cc_final: 0.8493 (tpp) REVERT: E 505 TYR cc_start: 0.8457 (m-80) cc_final: 0.8156 (m-80) REVERT: E 513 TYR cc_start: 0.8723 (m-80) cc_final: 0.7869 (m-80) REVERT: E 572 ILE cc_start: 0.8371 (tp) cc_final: 0.8157 (tp) REVERT: E 657 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5913 (mm) REVERT: B 232 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 323 ARG cc_start: 0.5365 (mmm160) cc_final: 0.4497 (tpp80) REVERT: B 402 ASP cc_start: 0.7183 (p0) cc_final: 0.6772 (p0) REVERT: C 249 ARG cc_start: 0.7179 (mmp80) cc_final: 0.6573 (tpp-160) REVERT: C 301 GLU cc_start: 0.8298 (pp20) cc_final: 0.8062 (pp20) REVERT: C 345 MET cc_start: 0.7505 (tpp) cc_final: 0.7203 (tpt) REVERT: C 348 ARG cc_start: 0.7119 (tpp80) cc_final: 0.6775 (tpp80) REVERT: C 615 LEU cc_start: 0.9585 (mt) cc_final: 0.9255 (mt) REVERT: A 223 MET cc_start: 0.2408 (mmm) cc_final: 0.2134 (tpt) REVERT: A 271 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: A 288 MET cc_start: 0.4575 (mpp) cc_final: 0.4032 (tmm) REVERT: A 407 GLU cc_start: 0.7751 (tp30) cc_final: 0.7479 (pm20) REVERT: A 427 GLU cc_start: 0.7643 (tp30) cc_final: 0.7110 (pt0) REVERT: A 430 MET cc_start: 0.8547 (mmm) cc_final: 0.8025 (mmm) REVERT: A 574 ASP cc_start: 0.7100 (t0) cc_final: 0.6770 (m-30) REVERT: A 587 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: A 659 ASP cc_start: 0.6963 (p0) cc_final: 0.6709 (p0) outliers start: 42 outliers final: 29 residues processed: 292 average time/residue: 0.3022 time to fit residues: 136.6379 Evaluate side-chains 275 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 242 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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 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 E residue 537 LEU Chi-restraints excluded: chain E residue 588 GLU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 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 753 ILE 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 541 VAL Chi-restraints excluded: chain A residue 587 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 0.0770 chunk 231 optimal weight: 6.9990 chunk 211 optimal weight: 0.3980 chunk 225 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 chunk 224 optimal weight: 0.1980 overall best weight: 1.5342 ------------------------------------------------------------------------------- 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** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS A 236 HIS A 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20014 Z= 0.236 Angle : 0.790 11.708 27114 Z= 0.364 Chirality : 0.048 0.429 3061 Planarity : 0.004 0.065 3543 Dihedral : 11.993 178.155 2848 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.79 % Favored : 91.17 % Rotamer: Outliers : 2.24 % Allowed : 22.22 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2513 helix: -0.69 (0.17), residues: 949 sheet: -0.87 (0.31), residues: 261 loop : -1.78 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 486 HIS 0.017 0.001 HIS C 394 PHE 0.019 0.001 PHE C 462 TYR 0.017 0.001 TYR A 505 ARG 0.010 0.001 ARG D 369 *********************** 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 294 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 248 time to evaluate : 2.354 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 215 ASP cc_start: 0.7923 (m-30) cc_final: 0.7420 (t0) REVERT: D 216 ILE cc_start: 0.8690 (tp) cc_final: 0.8161 (tp) REVERT: D 345 MET cc_start: 0.6529 (mmt) cc_final: 0.6325 (tpp) REVERT: D 513 TYR cc_start: 0.8774 (m-80) cc_final: 0.8452 (m-10) REVERT: D 532 THR cc_start: 0.8600 (p) cc_final: 0.8380 (t) REVERT: D 560 MET cc_start: 0.8049 (ptp) cc_final: 0.7550 (ptp) REVERT: D 615 LEU cc_start: 0.9142 (mt) cc_final: 0.8823 (mp) REVERT: D 621 MET cc_start: 0.8684 (tpp) cc_final: 0.8469 (tpp) REVERT: E 513 TYR cc_start: 0.8784 (m-80) cc_final: 0.7996 (m-80) REVERT: E 572 ILE cc_start: 0.8419 (tp) cc_final: 0.8192 (tp) REVERT: E 657 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6113 (mm) REVERT: B 232 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8423 (mm) REVERT: B 323 ARG cc_start: 0.5708 (mmm160) cc_final: 0.4770 (tpp80) REVERT: B 402 ASP cc_start: 0.7213 (p0) cc_final: 0.6880 (p0) REVERT: C 301 GLU cc_start: 0.8244 (pp20) cc_final: 0.8019 (pp20) REVERT: C 345 MET cc_start: 0.7788 (tpp) cc_final: 0.7377 (tpt) REVERT: C 378 ASP cc_start: 0.6888 (t70) cc_final: 0.6660 (t0) REVERT: C 615 LEU cc_start: 0.9617 (mt) cc_final: 0.9362 (mt) REVERT: A 223 MET cc_start: 0.3170 (mmm) cc_final: 0.2854 (tpt) REVERT: A 271 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: A 288 MET cc_start: 0.4601 (mpp) cc_final: 0.4062 (tmm) REVERT: A 407 GLU cc_start: 0.7854 (tp30) cc_final: 0.7604 (pm20) REVERT: A 430 MET cc_start: 0.8702 (mmm) cc_final: 0.8264 (mmm) REVERT: A 574 ASP cc_start: 0.7120 (t0) cc_final: 0.6835 (m-30) REVERT: A 587 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: A 696 ASP cc_start: 0.4359 (m-30) cc_final: 0.3745 (t70) outliers start: 46 outliers final: 31 residues processed: 281 average time/residue: 0.3068 time to fit residues: 133.0179 Evaluate side-chains 273 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 238 time to evaluate : 2.138 ------------------------------------------------------------------------------- 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 367 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 624 LYS Chi-restraints excluded: chain D residue 664 LEU 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 E residue 588 GLU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain B residue 232 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 541 VAL Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 417 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 753 ILE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 587 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 145 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 165 optimal weight: 0.0570 chunk 250 optimal weight: 20.0000 chunk 230 optimal weight: 4.9990 chunk 199 optimal weight: 0.0070 chunk 20 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 ASN ** 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 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20014 Z= 0.176 Angle : 0.753 11.943 27114 Z= 0.345 Chirality : 0.046 0.217 3061 Planarity : 0.004 0.060 3543 Dihedral : 11.954 179.407 2848 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.20 % Favored : 92.76 % Rotamer: Outliers : 2.00 % Allowed : 22.51 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.17), residues: 2513 helix: -0.58 (0.17), residues: 952 sheet: -0.76 (0.32), residues: 261 loop : -1.77 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 486 HIS 0.011 0.001 HIS C 394 PHE 0.011 0.001 PHE C 277 TYR 0.034 0.001 TYR D 416 ARG 0.009 0.000 ARG C 249 ********************** 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 297 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 256 time to evaluate : 2.179 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 215 ASP cc_start: 0.7996 (m-30) cc_final: 0.7470 (t0) REVERT: D 216 ILE cc_start: 0.8563 (tp) cc_final: 0.8062 (tp) REVERT: D 280 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.6696 (m-40) REVERT: D 345 MET cc_start: 0.6426 (mmt) cc_final: 0.6164 (tpp) REVERT: D 513 TYR cc_start: 0.8722 (m-80) cc_final: 0.8342 (m-10) REVERT: D 532 THR cc_start: 0.8417 (p) cc_final: 0.8179 (t) REVERT: D 560 MET cc_start: 0.7961 (ptp) cc_final: 0.7606 (ptp) REVERT: D 615 LEU cc_start: 0.9140 (mt) cc_final: 0.8831 (mp) REVERT: D 621 MET cc_start: 0.8639 (tpp) cc_final: 0.8410 (tpp) REVERT: E 505 TYR cc_start: 0.8400 (m-80) cc_final: 0.8193 (m-80) REVERT: E 513 TYR cc_start: 0.8708 (m-80) cc_final: 0.7891 (m-80) REVERT: E 657 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6028 (mm) REVERT: B 232 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8427 (mm) REVERT: B 323 ARG cc_start: 0.5542 (mmm160) cc_final: 0.4662 (tpp80) REVERT: B 402 ASP cc_start: 0.7069 (p0) cc_final: 0.6733 (p0) REVERT: C 301 GLU cc_start: 0.8167 (pp20) cc_final: 0.7938 (pp20) REVERT: C 348 ARG cc_start: 0.7211 (tpp80) cc_final: 0.6825 (tpp80) REVERT: C 459 MET cc_start: 0.7687 (mmm) cc_final: 0.7356 (tpp) REVERT: C 615 LEU cc_start: 0.9577 (mt) cc_final: 0.9236 (mt) REVERT: A 223 MET cc_start: 0.3103 (mmm) cc_final: 0.2790 (tpt) REVERT: A 271 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 288 MET cc_start: 0.4495 (mpp) cc_final: 0.3969 (tmm) REVERT: A 407 GLU cc_start: 0.7776 (tp30) cc_final: 0.7538 (pm20) REVERT: A 430 MET cc_start: 0.8705 (mmm) cc_final: 0.8189 (mmm) REVERT: A 564 GLU cc_start: 0.8094 (mp0) cc_final: 0.7877 (mm-30) REVERT: A 574 ASP cc_start: 0.7133 (t0) cc_final: 0.6835 (m-30) REVERT: A 587 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: A 659 ASP cc_start: 0.7028 (p0) cc_final: 0.6644 (p0) REVERT: A 696 ASP cc_start: 0.4262 (m-30) cc_final: 0.3629 (t70) outliers start: 41 outliers final: 28 residues processed: 285 average time/residue: 0.3003 time to fit residues: 133.0389 Evaluate side-chains 273 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 240 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 367 LEU 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 E residue 492 LEU Chi-restraints excluded: chain E residue 588 GLU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 377 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 753 ILE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 587 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 0.0000 chunk 212 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 199 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 461 ASN C 358 ASN C 702 GLN ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.129804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102199 restraints weight = 47122.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.105096 restraints weight = 25377.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.106955 restraints weight = 17018.555| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 20014 Z= 0.180 Angle : 0.756 13.069 27114 Z= 0.345 Chirality : 0.046 0.190 3061 Planarity : 0.005 0.113 3543 Dihedral : 11.921 176.034 2848 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.95 % Allowed : 22.81 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.57 % Cis-general : 0.13 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2513 helix: -0.51 (0.17), residues: 946 sheet: -0.75 (0.32), residues: 264 loop : -1.71 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 486 HIS 0.011 0.001 HIS C 394 PHE 0.011 0.001 PHE C 277 TYR 0.030 0.001 TYR A 505 ARG 0.008 0.000 ARG D 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4040.03 seconds wall clock time: 72 minutes 38.45 seconds (4358.45 seconds total)