Starting phenix.real_space_refine on Fri Mar 6 02:02:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jq0_9872/03_2026/6jq0_9872_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jq0_9872/03_2026/6jq0_9872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jq0_9872/03_2026/6jq0_9872_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jq0_9872/03_2026/6jq0_9872_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jq0_9872/03_2026/6jq0_9872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jq0_9872/03_2026/6jq0_9872.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.030 sd= 1.233 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: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 131 5.16 5 C 17184 2.51 5 N 4600 2.21 5 O 4985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26917 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4144 Classifications: {'peptide': 516} Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 481} Chain breaks: 3 Chain: "B" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4587 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 41, 'TRANS': 529} Chain breaks: 1 Chain: "C" Number of atoms: 4574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4574 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 41, 'TRANS': 527} Chain breaks: 1 Chain: "D" Number of atoms: 4547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4547 Classifications: {'peptide': 566} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 524} Chain breaks: 1 Chain: "E" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4628 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "F" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4185 Classifications: {'peptide': 524} Link IDs: {'CIS': 2, 'PTRANS': 38, 'TRANS': 483} Chain breaks: 3 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.29, per 1000 atoms: 0.23 Number of scatterers: 26917 At special positions: 0 Unit cell: (157.92, 153.44, 128.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 17 15.00 O 4985 8.00 N 4600 7.00 C 17184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=23, symmetry=0 Number of additional bonds: simple=23, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6388 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 14 sheets defined 44.4% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.057A pdb=" N GLN A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.742A pdb=" N LEU A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 322 removed outlier: 3.786A pdb=" N ARG A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 removed outlier: 3.567A pdb=" N ARG A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.126A pdb=" N LEU A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.596A pdb=" N ALA A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.530A pdb=" N ARG A 425 " --> pdb=" O PRO A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 450 removed outlier: 3.816A pdb=" N GLU A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 465 through 470 removed outlier: 4.111A pdb=" N GLU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 465 through 470' Processing helix chain 'A' and resid 475 through 490 removed outlier: 3.537A pdb=" N ARG A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 removed outlier: 4.072A pdb=" N PHE A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 520 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 558 removed outlier: 3.808A pdb=" N PHE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 removed outlier: 3.888A pdb=" N MET A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.801A pdb=" N GLU A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 571 through 576' Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.626A pdb=" N ALA A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 623 through 626 removed outlier: 4.102A pdb=" N TYR A 626 " --> pdb=" O LEU A 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 623 through 626' Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.742A pdb=" N LEU A 639 " --> pdb=" O MET A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 removed outlier: 3.831A pdb=" N ILE A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 657 " --> pdb=" O HIS A 653 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 678 removed outlier: 3.669A pdb=" N VAL A 677 " --> pdb=" O ASN A 673 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 678 " --> pdb=" O TRP A 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 678' Processing helix chain 'A' and resid 679 through 692 removed outlier: 4.011A pdb=" N MET A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 690 " --> pdb=" O PHE A 686 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.934A pdb=" N ARG A 717 " --> pdb=" O HIS A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 1147 through 1152 removed outlier: 3.867A pdb=" N LEU A1151 " --> pdb=" O ASP A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1183 removed outlier: 4.686A pdb=" N ARG A1179 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A1180 " --> pdb=" O GLU A1176 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A1181 " --> pdb=" O CYS A1177 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A1182 " --> pdb=" O GLU A1178 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A1183 " --> pdb=" O ARG A1179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1175 through 1183' Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.580A pdb=" N ASN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 removed outlier: 3.896A pdb=" N LEU B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 removed outlier: 4.257A pdb=" N PHE B 292 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 288 through 293' Processing helix chain 'B' and resid 314 through 324 removed outlier: 4.163A pdb=" N ARG B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 363 removed outlier: 3.586A pdb=" N LEU B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 385 through 399 removed outlier: 3.751A pdb=" N ALA B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 392 " --> pdb=" O HIS B 388 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 removed outlier: 3.721A pdb=" N ARG B 425 " --> pdb=" O PRO B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.708A pdb=" N CYS B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 removed outlier: 3.633A pdb=" N CYS B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.763A pdb=" N ARG B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 499 removed outlier: 4.177A pdb=" N TYR B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 515 through 524 removed outlier: 3.639A pdb=" N PHE B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 524 " --> pdb=" O VAL B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 545 through 550 removed outlier: 4.190A pdb=" N LEU B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.554A pdb=" N GLN B 554 " --> pdb=" O ASN B 550 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.601A pdb=" N GLU B 575 " --> pdb=" O ASN B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.596A pdb=" N LEU B 639 " --> pdb=" O MET B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 660 removed outlier: 3.755A pdb=" N SER B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 651 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 657 " --> pdb=" O HIS B 653 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 removed outlier: 3.555A pdb=" N TRP B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 688 removed outlier: 3.595A pdb=" N PHE B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 712 removed outlier: 3.905A pdb=" N LEU B 712 " --> pdb=" O LEU B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 720 removed outlier: 3.698A pdb=" N TRP B 719 " --> pdb=" O GLN B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 741 removed outlier: 3.822A pdb=" N PHE B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 741 " --> pdb=" O ILE B 737 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 736 through 741' Processing helix chain 'B' and resid 741 through 748 Processing helix chain 'B' and resid 1130 through 1141 removed outlier: 4.278A pdb=" N LEU B1134 " --> pdb=" O ARG B1130 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP B1140 " --> pdb=" O GLN B1136 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER B1141 " --> pdb=" O LEU B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1151 removed outlier: 3.558A pdb=" N LEU B1151 " --> pdb=" O VAL B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 Processing helix chain 'B' and resid 1157 through 1162 removed outlier: 3.698A pdb=" N ILE B1161 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP B1162 " --> pdb=" O TYR B1158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1157 through 1162' Processing helix chain 'B' and resid 1170 through 1175 Processing helix chain 'B' and resid 1176 through 1183 removed outlier: 3.598A pdb=" N VAL B1181 " --> pdb=" O CYS B1177 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.826A pdb=" N ASN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.825A pdb=" N ARG C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 326 removed outlier: 3.914A pdb=" N MET C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 362 removed outlier: 3.811A pdb=" N PHE C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 376 Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.730A pdb=" N ALA C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 392 " --> pdb=" O HIS C 388 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 425 removed outlier: 3.585A pdb=" N ARG C 425 " --> pdb=" O PRO C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 451 removed outlier: 3.542A pdb=" N ILE C 448 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 470 removed outlier: 4.023A pdb=" N ALA C 468 " --> pdb=" O CYS C 464 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 495 removed outlier: 4.277A pdb=" N ALA C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 499 removed outlier: 3.715A pdb=" N TYR C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 499' Processing helix chain 'C' and resid 508 through 512 removed outlier: 3.679A pdb=" N THR C 511 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 508 through 512' Processing helix chain 'C' and resid 515 through 524 removed outlier: 3.949A pdb=" N PHE C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 522 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS C 524 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 549 removed outlier: 3.638A pdb=" N LEU C 548 " --> pdb=" O LEU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 562 removed outlier: 3.535A pdb=" N GLN C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 576 Processing helix chain 'C' and resid 589 through 595 removed outlier: 3.692A pdb=" N THR C 594 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE C 595 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 617 Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 646 through 659 removed outlier: 3.516A pdb=" N SER C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 654 " --> pdb=" O SER C 650 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU C 657 " --> pdb=" O HIS C 653 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 679 through 693 removed outlier: 3.617A pdb=" N THR C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR C 685 " --> pdb=" O THR C 681 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 690 " --> pdb=" O PHE C 686 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 693 " --> pdb=" O MET C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 720 removed outlier: 3.536A pdb=" N TRP C 719 " --> pdb=" O GLN C 715 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 720 " --> pdb=" O LEU C 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 715 through 720' Processing helix chain 'C' and resid 722 through 724 No H-bonds generated for 'chain 'C' and resid 722 through 724' Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.974A pdb=" N ILE C 738 " --> pdb=" O ARG C 734 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 739 " --> pdb=" O ASP C 735 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE C 741 " --> pdb=" O ILE C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 749 removed outlier: 3.872A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 747 " --> pdb=" O PRO C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 1131 through 1141 removed outlier: 3.575A pdb=" N ASP C1140 " --> pdb=" O GLN C1136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C1141 " --> pdb=" O LEU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1146 through 1165 removed outlier: 3.738A pdb=" N LEU C1151 " --> pdb=" O VAL C1147 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N HIS C1152 " --> pdb=" O ASP C1148 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C1153 " --> pdb=" O GLN C1149 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS C1154 " --> pdb=" O LEU C1150 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C1158 " --> pdb=" O HIS C1154 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C1159 " --> pdb=" O SER C1155 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C1164 " --> pdb=" O ILE C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1169 through 1173 removed outlier: 3.605A pdb=" N SER C1172 " --> pdb=" O ASN C1169 " (cutoff:3.500A) Processing helix chain 'C' and resid 1174 through 1179 removed outlier: 3.597A pdb=" N GLU C1178 " --> pdb=" O VAL C1174 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG C1179 " --> pdb=" O ASP C1175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1174 through 1179' Processing helix chain 'D' and resid 272 through 279 removed outlier: 3.794A pdb=" N ASN D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 313 through 323 removed outlier: 3.916A pdb=" N ALA D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.939A pdb=" N ASN D 328 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 362 removed outlier: 3.667A pdb=" N ARG D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 386 through 398 removed outlier: 3.870A pdb=" N VAL D 392 " --> pdb=" O HIS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 425 Processing helix chain 'D' and resid 442 through 451 removed outlier: 3.598A pdb=" N GLU D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 471 removed outlier: 3.924A pdb=" N CYS D 464 " --> pdb=" O PRO D 460 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU D 469 " --> pdb=" O SER D 465 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 470 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER D 471 " --> pdb=" O LEU D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 495 removed outlier: 3.580A pdb=" N LEU D 488 " --> pdb=" O THR D 484 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 491 " --> pdb=" O ALA D 487 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 493 " --> pdb=" O ASN D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 removed outlier: 3.675A pdb=" N TYR D 499 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER D 501 " --> pdb=" O LEU D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 525 removed outlier: 3.817A pdb=" N PHE D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG D 525 " --> pdb=" O MET D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 545 through 564 removed outlier: 3.790A pdb=" N LEU D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLU D 551 " --> pdb=" O PRO D 547 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE D 556 " --> pdb=" O ALA D 552 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS D 562 " --> pdb=" O LYS D 558 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 563 " --> pdb=" O THR D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 575 Processing helix chain 'D' and resid 591 through 596 removed outlier: 3.667A pdb=" N PHE D 595 " --> pdb=" O ARG D 591 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 591 through 596' Processing helix chain 'D' and resid 614 through 617 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 646 through 659 removed outlier: 3.568A pdb=" N SER D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 654 " --> pdb=" O SER D 650 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D 657 " --> pdb=" O HIS D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 removed outlier: 3.550A pdb=" N TRP D 674 " --> pdb=" O ASP D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 removed outlier: 3.546A pdb=" N THR D 684 " --> pdb=" O LEU D 680 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR D 685 " --> pdb=" O THR D 681 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 690 " --> pdb=" O PHE D 686 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU D 693 " --> pdb=" O MET D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 741 removed outlier: 3.579A pdb=" N PHE D 740 " --> pdb=" O SER D 736 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 741 " --> pdb=" O ILE D 737 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 736 through 741' Processing helix chain 'D' and resid 741 through 749 removed outlier: 3.505A pdb=" N LYS D 749 " --> pdb=" O LEU D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1138 removed outlier: 3.727A pdb=" N GLN D1136 " --> pdb=" O THR D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1146 through 1155 removed outlier: 4.589A pdb=" N HIS D1152 " --> pdb=" O ASP D1148 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D1153 " --> pdb=" O GLN D1149 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS D1154 " --> pdb=" O LEU D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1156 through 1164 removed outlier: 3.969A pdb=" N ILE D1160 " --> pdb=" O PHE D1156 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP D1162 " --> pdb=" O TYR D1158 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D1164 " --> pdb=" O ILE D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1172 through 1180 removed outlier: 3.548A pdb=" N GLU D1176 " --> pdb=" O SER D1172 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU D1178 " --> pdb=" O VAL D1174 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 283 removed outlier: 3.676A pdb=" N ASN E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N MET E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 292 removed outlier: 3.728A pdb=" N ILE E 291 " --> pdb=" O TYR E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 326 removed outlier: 3.540A pdb=" N ALA E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 362 removed outlier: 3.503A pdb=" N GLU E 358 " --> pdb=" O ARG E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 387 through 400 removed outlier: 3.677A pdb=" N VAL E 392 " --> pdb=" O HIS E 388 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER E 393 " --> pdb=" O ALA E 389 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 395 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 451 removed outlier: 3.928A pdb=" N LYS E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS E 451 " --> pdb=" O ILE E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 464 removed outlier: 3.758A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 471 Processing helix chain 'E' and resid 477 through 495 removed outlier: 3.867A pdb=" N ALA E 481 " --> pdb=" O ALA E 477 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS E 483 " --> pdb=" O LEU E 479 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 491 " --> pdb=" O ALA E 487 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS E 492 " --> pdb=" O LEU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 499 removed outlier: 3.917A pdb=" N TYR E 499 " --> pdb=" O PRO E 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 496 through 499' Processing helix chain 'E' and resid 516 through 526 removed outlier: 3.707A pdb=" N VAL E 520 " --> pdb=" O VAL E 516 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS E 524 " --> pdb=" O VAL E 520 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG E 525 " --> pdb=" O MET E 521 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET E 526 " --> pdb=" O SER E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 564 removed outlier: 3.767A pdb=" N LEU E 549 " --> pdb=" O LEU E 545 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU E 551 " --> pdb=" O PRO E 547 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP E 555 " --> pdb=" O GLU E 551 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS E 562 " --> pdb=" O LYS E 558 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU E 563 " --> pdb=" O THR E 559 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET E 564 " --> pdb=" O LEU E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 576 removed outlier: 3.526A pdb=" N GLU E 575 " --> pdb=" O ASN E 571 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 576 " --> pdb=" O PRO E 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 571 through 576' Processing helix chain 'E' and resid 589 through 595 Processing helix chain 'E' and resid 618 through 622 removed outlier: 3.700A pdb=" N ALA E 621 " --> pdb=" O LEU E 618 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE E 622 " --> pdb=" O GLY E 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 618 through 622' Processing helix chain 'E' and resid 635 through 640 Processing helix chain 'E' and resid 646 through 659 removed outlier: 3.720A pdb=" N SER E 650 " --> pdb=" O SER E 646 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE E 651 " --> pdb=" O ILE E 647 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE E 655 " --> pdb=" O ILE E 651 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU E 657 " --> pdb=" O HIS E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 688 removed outlier: 3.500A pdb=" N ILE E 683 " --> pdb=" O PRO E 679 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR E 685 " --> pdb=" O THR E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 715 through 720 removed outlier: 3.880A pdb=" N TRP E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE E 720 " --> pdb=" O LEU E 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 715 through 720' Processing helix chain 'E' and resid 722 through 726 removed outlier: 4.121A pdb=" N VAL E 726 " --> pdb=" O LYS E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.666A pdb=" N ILE E 737 " --> pdb=" O THR E 733 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE E 738 " --> pdb=" O ARG E 734 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA E 739 " --> pdb=" O ASP E 735 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 740 " --> pdb=" O SER E 736 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE E 741 " --> pdb=" O ILE E 737 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 733 through 741' Processing helix chain 'E' and resid 741 through 748 Processing helix chain 'E' and resid 1130 through 1139 removed outlier: 3.575A pdb=" N LEU E1134 " --> pdb=" O ARG E1130 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE E1139 " --> pdb=" O LYS E1135 " (cutoff:3.500A) Processing helix chain 'E' and resid 1146 through 1157 removed outlier: 3.697A pdb=" N LEU E1151 " --> pdb=" O VAL E1147 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS E1152 " --> pdb=" O ASP E1148 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E1153 " --> pdb=" O GLN E1149 " (cutoff:3.500A) Processing helix chain 'E' and resid 1157 through 1164 removed outlier: 3.522A pdb=" N ASN E1163 " --> pdb=" O GLN E1159 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR E1164 " --> pdb=" O ILE E1160 " (cutoff:3.500A) Processing helix chain 'E' and resid 1176 through 1185 removed outlier: 3.543A pdb=" N GLU E1183 " --> pdb=" O ARG E1179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E1184 " --> pdb=" O ALA E1180 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N MET E1185 " --> pdb=" O VAL E1181 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 removed outlier: 3.878A pdb=" N LEU F 278 " --> pdb=" O TYR F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 325 removed outlier: 4.137A pdb=" N MET F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 362 removed outlier: 3.543A pdb=" N LEU F 356 " --> pdb=" O GLN F 352 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU F 358 " --> pdb=" O ARG F 354 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 394 Processing helix chain 'F' and resid 394 through 399 removed outlier: 3.903A pdb=" N LEU F 398 " --> pdb=" O THR F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 removed outlier: 3.962A pdb=" N ARG F 426 " --> pdb=" O ALA F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 448 removed outlier: 4.007A pdb=" N LYS F 446 " --> pdb=" O ASP F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 471 removed outlier: 4.379A pdb=" N GLU F 469 " --> pdb=" O SER F 465 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS F 470 " --> pdb=" O MET F 466 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 495 removed outlier: 3.572A pdb=" N ALA F 481 " --> pdb=" O ALA F 477 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE F 491 " --> pdb=" O ALA F 487 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS F 492 " --> pdb=" O LEU F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 523 removed outlier: 3.611A pdb=" N VAL F 520 " --> pdb=" O VAL F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 549 removed outlier: 3.932A pdb=" N LEU F 548 " --> pdb=" O LEU F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 564 Processing helix chain 'F' and resid 614 through 617 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 646 through 659 removed outlier: 3.636A pdb=" N SER F 650 " --> pdb=" O SER F 646 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 654 " --> pdb=" O SER F 650 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 659 " --> pdb=" O PHE F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 678 removed outlier: 3.815A pdb=" N ASN F 676 " --> pdb=" O ASP F 672 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 677 " --> pdb=" O ASN F 673 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU F 678 " --> pdb=" O TRP F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 688 removed outlier: 3.519A pdb=" N THR F 684 " --> pdb=" O LEU F 680 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER F 687 " --> pdb=" O ILE F 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 722 through 726 removed outlier: 4.150A pdb=" N VAL F 726 " --> pdb=" O LYS F 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 747 Processing helix chain 'F' and resid 1131 through 1141 removed outlier: 3.705A pdb=" N GLN F1136 " --> pdb=" O THR F1132 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE F1139 " --> pdb=" O LYS F1135 " (cutoff:3.500A) Processing helix chain 'F' and resid 1146 through 1163 removed outlier: 3.572A pdb=" N LEU F1151 " --> pdb=" O VAL F1147 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N HIS F1152 " --> pdb=" O ASP F1148 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU F1153 " --> pdb=" O GLN F1149 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS F1154 " --> pdb=" O LEU F1150 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F1157 " --> pdb=" O LEU F1153 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN F1159 " --> pdb=" O SER F1155 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE F1160 " --> pdb=" O PHE F1156 " (cutoff:3.500A) Processing helix chain 'F' and resid 1173 through 1186 removed outlier: 3.533A pdb=" N CYS F1177 " --> pdb=" O VAL F1173 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS F1182 " --> pdb=" O GLU F1178 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET F1185 " --> pdb=" O VAL F1181 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE F1186 " --> pdb=" O LYS F1182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.885A pdb=" N TYR A 334 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 303 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR A 414 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 305 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE A 434 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 304 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 630 through 633 removed outlier: 7.249A pdb=" N HIS A 630 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N TYR A 667 " --> pdb=" O HIS A 630 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN A 632 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 703 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N TYR A 727 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 606 " --> pdb=" O TYR A 727 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 332 through 335 removed outlier: 6.261A pdb=" N SER B 332 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE B 369 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR B 334 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 413 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N PHE B 434 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 304 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 604 through 607 removed outlier: 3.591A pdb=" N ALA B 703 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER B 664 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 702 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 332 through 336 removed outlier: 3.506A pdb=" N ASP C 371 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 413 " --> pdb=" O PHE C 370 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE C 434 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 304 " --> pdb=" O PHE C 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 630 through 633 removed outlier: 6.544A pdb=" N HIS C 630 " --> pdb=" O ILE C 665 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR C 667 " --> pdb=" O HIS C 630 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN C 632 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU C 702 " --> pdb=" O SER C 664 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 666 " --> pdb=" O LEU C 702 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LEU C 704 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE C 668 " --> pdb=" O LEU C 704 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 606 " --> pdb=" O TYR C 727 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 305 through 306 removed outlier: 6.216A pdb=" N PHE D 305 " --> pdb=" O THR D 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 332 through 334 removed outlier: 7.026A pdb=" N SER D 332 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE D 369 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR D 334 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 630 through 631 removed outlier: 6.903A pdb=" N HIS D 630 " --> pdb=" O ILE D 665 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N TYR D 667 " --> pdb=" O HIS D 630 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER D 664 " --> pdb=" O LEU D 700 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU D 702 " --> pdb=" O SER D 664 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE D 666 " --> pdb=" O LEU D 702 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LEU D 704 " --> pdb=" O ILE D 666 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE D 668 " --> pdb=" O LEU D 704 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 332 through 334 removed outlier: 6.574A pdb=" N SER E 332 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE E 369 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYR E 334 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL E 303 " --> pdb=" O GLY E 412 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR E 414 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE E 305 " --> pdb=" O THR E 414 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU E 304 " --> pdb=" O PHE E 434 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 607 through 608 Processing sheet with id=AB3, first strand: chain 'E' and resid 630 through 633 removed outlier: 6.894A pdb=" N HIS E 630 " --> pdb=" O ILE E 665 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR E 667 " --> pdb=" O HIS E 630 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN E 632 " --> pdb=" O TYR E 667 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER E 664 " --> pdb=" O LEU E 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 332 through 334 removed outlier: 3.686A pdb=" N ILE F 367 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER F 366 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE F 411 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE F 368 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA F 413 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE F 370 " --> pdb=" O ALA F 413 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY F 302 " --> pdb=" O PHE F 430 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG F 432 " --> pdb=" O GLY F 302 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 605 through 606 removed outlier: 3.820A pdb=" N PHE F 605 " --> pdb=" O PHE F 701 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 703 " --> pdb=" O PHE F 605 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU F 700 " --> pdb=" O SER F 664 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.07 Time building geometry restraints manager: 3.06 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: 8517 1.34 - 1.46: 4891 1.46 - 1.57: 13868 1.57 - 1.69: 29 1.69 - 1.81: 226 Bond restraints: 27531 Sorted by residual: bond pdb=" C4 ATP C1201 " pdb=" C5 ATP C1201 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.11e+01 bond pdb=" C4 ATP D1201 " pdb=" C5 ATP D1201 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.11e+01 bond pdb=" C4 ATP F1201 " pdb=" C5 ATP F1201 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.10e+01 bond pdb=" C4 ATP B1201 " pdb=" C5 ATP B1201 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.10e+01 bond pdb=" C4 ATP E1201 " pdb=" C5 ATP E1201 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.00e+01 ... (remaining 27526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 36832 4.36 - 8.72: 424 8.72 - 13.07: 43 13.07 - 17.43: 8 17.43 - 21.79: 6 Bond angle restraints: 37313 Sorted by residual: angle pdb=" PB ATP D1201 " pdb=" O3B ATP D1201 " pdb=" PG ATP D1201 " ideal model delta sigma weight residual 139.87 118.08 21.79 1.00e+00 1.00e+00 4.75e+02 angle pdb=" PB ATP E1201 " pdb=" O3B ATP E1201 " pdb=" PG ATP E1201 " ideal model delta sigma weight residual 139.87 118.08 21.79 1.00e+00 1.00e+00 4.75e+02 angle pdb=" PB ATP B1201 " pdb=" O3B ATP B1201 " pdb=" PG ATP B1201 " ideal model delta sigma weight residual 139.87 118.08 21.79 1.00e+00 1.00e+00 4.75e+02 angle pdb=" PB ATP F1201 " pdb=" O3B ATP F1201 " pdb=" PG ATP F1201 " ideal model delta sigma weight residual 139.87 118.09 21.78 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PB ATP C1201 " pdb=" O3B ATP C1201 " pdb=" PG ATP C1201 " ideal model delta sigma weight residual 139.87 118.11 21.76 1.00e+00 1.00e+00 4.74e+02 ... (remaining 37308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14693 17.99 - 35.98: 1962 35.98 - 53.96: 333 53.96 - 71.95: 61 71.95 - 89.94: 28 Dihedral angle restraints: 17077 sinusoidal: 7284 harmonic: 9793 Sorted by residual: dihedral pdb=" CA THR B 662 " pdb=" C THR B 662 " pdb=" N PRO B 663 " pdb=" CA PRO B 663 " ideal model delta harmonic sigma weight residual -180.00 -116.63 -63.37 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA ARG E 453 " pdb=" C ARG E 453 " pdb=" N ASN E 454 " pdb=" CA ASN E 454 " ideal model delta harmonic sigma weight residual -180.00 -117.22 -62.78 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CA ILE B 507 " pdb=" C ILE B 507 " pdb=" N ASP B 508 " pdb=" CA ASP B 508 " ideal model delta harmonic sigma weight residual 180.00 118.40 61.60 0 5.00e+00 4.00e-02 1.52e+02 ... (remaining 17074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3377 0.074 - 0.149: 675 0.149 - 0.223: 94 0.223 - 0.298: 21 0.298 - 0.372: 4 Chirality restraints: 4171 Sorted by residual: chirality pdb=" CB VAL D 566 " pdb=" CA VAL D 566 " pdb=" CG1 VAL D 566 " pdb=" CG2 VAL D 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE B 748 " pdb=" CA ILE B 748 " pdb=" CG1 ILE B 748 " pdb=" CG2 ILE B 748 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CB VAL B 566 " pdb=" CA VAL B 566 " pdb=" CG1 VAL B 566 " pdb=" CG2 VAL B 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 4168 not shown) Planarity restraints: 4759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 662 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO B 663 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO B 663 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 663 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 751 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 752 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 752 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 752 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 662 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO A 663 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 663 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 663 " 0.058 5.00e-02 4.00e+02 ... (remaining 4756 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5935 2.77 - 3.30: 23300 3.30 - 3.83: 39906 3.83 - 4.37: 44034 4.37 - 4.90: 75000 Nonbonded interactions: 188175 Sorted by model distance: nonbonded pdb=" N LYS B 313 " pdb=" O1A ATP B1201 " model vdw 2.235 3.120 nonbonded pdb=" OG1 THR E1146 " pdb=" OE1 GLN E1149 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR E 314 " pdb=" O2A ATP E1201 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR D 314 " pdb=" O2A ATP D1201 " model vdw 2.289 3.040 nonbonded pdb=" O PHE D 519 " pdb=" OG SER D 522 " model vdw 2.291 3.040 ... (remaining 188170 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 265 through 285 or resid 294 through 567 or resid 601 thro \ ugh 1186)) selection = (chain 'B' and (resid 265 through 285 or resid 294 through 492 or resid 512 thro \ ugh 526 or resid 536 through 567 or resid 601 through 748 or resid 1131 through \ 1186)) selection = (chain 'C' and (resid 265 through 285 or resid 294 through 492 or resid 512 thro \ ugh 526 or resid 536 through 567 or resid 601 through 748 or resid 1131 through \ 1186)) selection = (chain 'D' and (resid 265 through 285 or resid 294 through 492 or resid 512 thro \ ugh 526 or resid 536 through 567 or resid 601 through 748 or resid 1131 through \ 1186)) selection = (chain 'E' and (resid 265 through 285 or resid 294 through 492 or resid 512 thro \ ugh 526 or resid 536 through 567 or resid 601 through 748 or resid 1131 through \ 1186)) selection = (chain 'F' and (resid 265 through 492 or resid 512 through 526 or resid 536 thro \ ugh 748 or resid 1131 through 1186)) } 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: 2.640 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.360 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.007 0.092 27554 Z= 0.375 Angle : 1.212 21.791 37313 Z= 0.709 Chirality : 0.063 0.372 4171 Planarity : 0.009 0.116 4759 Dihedral : 16.300 89.941 10689 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.97 % Favored : 86.48 % Rotamer: Outliers : 0.63 % Allowed : 13.56 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 6.36 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.59 (0.11), residues: 3291 helix: -4.61 (0.06), residues: 1139 sheet: -2.50 (0.26), residues: 324 loop : -3.41 (0.12), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 429 TYR 0.026 0.002 TYR E 626 PHE 0.020 0.002 PHE D 605 TRP 0.022 0.002 TRP E 674 HIS 0.009 0.002 HIS F 713 Details of bonding type rmsd covalent geometry : bond 0.00738 (27531) covalent geometry : angle 1.21168 (37313) hydrogen bonds : bond 0.34966 ( 579) hydrogen bonds : angle 9.25863 ( 1620) Misc. bond : bond 0.00715 ( 23) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 644 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ILE cc_start: 0.9501 (tt) cc_final: 0.9274 (tp) REVERT: A 336 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.7657 (ttm110) REVERT: A 352 GLN cc_start: 0.9260 (tt0) cc_final: 0.8998 (mt0) REVERT: A 524 LYS cc_start: 0.7051 (mmmt) cc_final: 0.6358 (mtmt) REVERT: A 558 LYS cc_start: 0.9141 (pttm) cc_final: 0.8825 (pttt) REVERT: A 563 LEU cc_start: 0.7908 (mm) cc_final: 0.7554 (mm) REVERT: A 590 GLN cc_start: 0.9290 (mm-40) cc_final: 0.9074 (mm110) REVERT: A 636 MET cc_start: 0.8828 (mmm) cc_final: 0.8093 (mpp) REVERT: A 657 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8644 (mm-30) REVERT: A 702 LEU cc_start: 0.8230 (mt) cc_final: 0.8023 (mt) REVERT: A 1169 ASN cc_start: 0.4629 (m-40) cc_final: 0.4214 (m-40) REVERT: B 361 LYS cc_start: 0.9550 (tttt) cc_final: 0.9341 (tttp) REVERT: B 382 SER cc_start: 0.9285 (m) cc_final: 0.8754 (t) REVERT: B 503 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8510 (mmmm) REVERT: B 600 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8671 (mt) REVERT: B 641 GLN cc_start: 0.9071 (pp30) cc_final: 0.8328 (pp30) REVERT: B 735 ASP cc_start: 0.9101 (t0) cc_final: 0.8722 (t0) REVERT: B 1145 PHE cc_start: 0.9092 (m-10) cc_final: 0.8857 (m-80) REVERT: B 1159 GLN cc_start: 0.8978 (pt0) cc_final: 0.8668 (pt0) REVERT: C 431 ASP cc_start: 0.8049 (t0) cc_final: 0.7759 (t0) REVERT: C 546 LYS cc_start: 0.8889 (tttp) cc_final: 0.8512 (ttpt) REVERT: C 718 GLU cc_start: 0.8689 (tp30) cc_final: 0.8469 (tp30) REVERT: D 329 LYS cc_start: 0.7652 (mmmm) cc_final: 0.7421 (mmmt) REVERT: D 575 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8804 (tm-30) REVERT: D 580 ASP cc_start: 0.8616 (p0) cc_final: 0.8028 (p0) REVERT: D 607 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8282 (mm) REVERT: E 369 PHE cc_start: 0.8324 (m-80) cc_final: 0.8104 (m-10) REVERT: E 400 ASP cc_start: 0.9031 (t70) cc_final: 0.8650 (t0) REVERT: E 642 ASP cc_start: 0.8899 (t0) cc_final: 0.8511 (t0) REVERT: E 689 MET cc_start: 0.9070 (mmm) cc_final: 0.8838 (mmm) REVERT: E 695 PHE cc_start: 0.8968 (p90) cc_final: 0.8675 (p90) REVERT: F 277 GLN cc_start: 0.8278 (tt0) cc_final: 0.8011 (tm-30) REVERT: F 278 LEU cc_start: 0.8577 (pp) cc_final: 0.8143 (pp) REVERT: F 279 LYS cc_start: 0.8871 (ptmt) cc_final: 0.8503 (ttpp) REVERT: F 281 MET cc_start: 0.8719 (ppp) cc_final: 0.8266 (ppp) REVERT: F 359 GLU cc_start: 0.8322 (tt0) cc_final: 0.8091 (tp30) REVERT: F 380 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7543 (mtm180) REVERT: F 403 GLU cc_start: 0.6198 (pm20) cc_final: 0.5695 (pm20) REVERT: F 407 GLN cc_start: 0.6388 (mm-40) cc_final: 0.5953 (mp10) REVERT: F 492 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8773 (ttmt) REVERT: F 506 GLN cc_start: 0.7939 (pm20) cc_final: 0.7438 (pm20) REVERT: F 636 MET cc_start: 0.8549 (mtm) cc_final: 0.8247 (mtt) REVERT: F 672 ASP cc_start: 0.8811 (m-30) cc_final: 0.8527 (m-30) REVERT: F 689 MET cc_start: 0.8211 (ppp) cc_final: 0.7943 (ppp) REVERT: F 727 TYR cc_start: 0.8369 (t80) cc_final: 0.7640 (t80) REVERT: F 1148 ASP cc_start: 0.8523 (t0) cc_final: 0.8097 (t0) outliers start: 19 outliers final: 5 residues processed: 658 average time/residue: 0.1855 time to fit residues: 188.3403 Evaluate side-chains 495 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 488 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 1142 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 589 GLN ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A1149 GLN B 673 ASN B1149 GLN C 415 ASN C 454 ASN C 584 ASN C 715 GLN C1149 GLN D 328 ASN D 352 GLN D 364 GLN D 415 ASN D 489 ASN D 589 GLN D 653 HIS D 676 ASN D 713 HIS D1149 GLN E 386 GLN E 407 GLN E 415 ASN E 653 HIS E 676 ASN E 715 GLN E1152 HIS F 296 ASN F 561 GLN ** F 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 GLN F 713 HIS F1149 GLN F1163 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096563 restraints weight = 49635.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099867 restraints weight = 24214.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102038 restraints weight = 14865.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.103474 restraints weight = 10580.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104392 restraints weight = 8392.870| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27554 Z= 0.137 Angle : 0.783 16.765 37313 Z= 0.390 Chirality : 0.047 0.230 4171 Planarity : 0.007 0.107 4759 Dihedral : 8.940 87.664 3808 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.15 % Favored : 87.57 % Rotamer: Outliers : 2.76 % Allowed : 17.95 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 5.08 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.12), residues: 3291 helix: -3.13 (0.11), residues: 1168 sheet: -2.23 (0.26), residues: 345 loop : -2.91 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 444 TYR 0.019 0.001 TYR A1158 PHE 0.017 0.001 PHE C 695 TRP 0.016 0.001 TRP E 455 HIS 0.003 0.001 HIS F 713 Details of bonding type rmsd covalent geometry : bond 0.00309 (27531) covalent geometry : angle 0.78251 (37313) hydrogen bonds : bond 0.05066 ( 579) hydrogen bonds : angle 5.07306 ( 1620) Misc. bond : bond 0.00315 ( 23) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 580 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 291 ILE cc_start: 0.9427 (tt) cc_final: 0.9210 (tp) REVERT: A 336 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.7805 (tpp80) REVERT: A 402 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7995 (ttp) REVERT: A 408 VAL cc_start: 0.9185 (t) cc_final: 0.8896 (m) REVERT: A 524 LYS cc_start: 0.6993 (mmmt) cc_final: 0.6382 (mtmt) REVERT: A 563 LEU cc_start: 0.7940 (mm) cc_final: 0.7689 (mm) REVERT: A 574 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7079 (tp30) REVERT: A 590 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8964 (mm110) REVERT: A 636 MET cc_start: 0.8591 (mmm) cc_final: 0.8071 (mpp) REVERT: B 371 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6989 (t70) REVERT: B 382 SER cc_start: 0.9402 (m) cc_final: 0.8866 (t) REVERT: B 441 ARG cc_start: 0.7946 (ttt180) cc_final: 0.7709 (ttt180) REVERT: B 503 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8332 (mmmm) REVERT: B 577 MET cc_start: 0.8691 (mmt) cc_final: 0.8465 (mmt) REVERT: B 600 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8463 (mt) REVERT: B 678 LEU cc_start: 0.8550 (pp) cc_final: 0.8227 (pp) REVERT: B 735 ASP cc_start: 0.9260 (t0) cc_final: 0.8978 (t0) REVERT: B 1145 PHE cc_start: 0.9112 (m-10) cc_final: 0.8855 (m-80) REVERT: B 1159 GLN cc_start: 0.8898 (pt0) cc_final: 0.8578 (pt0) REVERT: B 1179 ARG cc_start: 0.9086 (mtp-110) cc_final: 0.8578 (ptp-110) REVERT: C 431 ASP cc_start: 0.8076 (t0) cc_final: 0.7749 (t0) REVERT: C 478 ASP cc_start: 0.8221 (m-30) cc_final: 0.7932 (m-30) REVERT: C 546 LYS cc_start: 0.8731 (tttp) cc_final: 0.8414 (ttmt) REVERT: C 575 GLU cc_start: 0.9152 (tp30) cc_final: 0.8883 (tp30) REVERT: C 704 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7954 (pp) REVERT: C 718 GLU cc_start: 0.8741 (tp30) cc_final: 0.8509 (tp30) REVERT: C 1178 GLU cc_start: 0.9426 (mp0) cc_final: 0.9150 (mp0) REVERT: D 266 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7516 (tm-30) REVERT: D 348 GLU cc_start: 0.8545 (tp30) cc_final: 0.8079 (tp30) REVERT: D 418 ASP cc_start: 0.9072 (t0) cc_final: 0.8860 (m-30) REVERT: D 489 ASN cc_start: 0.9166 (OUTLIER) cc_final: 0.8938 (t0) REVERT: D 575 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8836 (tm-30) REVERT: D 1157 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7597 (pp) REVERT: E 366 SER cc_start: 0.9158 (t) cc_final: 0.8955 (m) REVERT: E 399 MET cc_start: 0.8552 (mtt) cc_final: 0.8250 (mtt) REVERT: E 400 ASP cc_start: 0.9003 (t70) cc_final: 0.8620 (t0) REVERT: E 642 ASP cc_start: 0.8989 (t0) cc_final: 0.8322 (t0) REVERT: E 695 PHE cc_start: 0.9000 (p90) cc_final: 0.8662 (p90) REVERT: E 1184 PHE cc_start: 0.8463 (m-80) cc_final: 0.7830 (m-80) REVERT: F 278 LEU cc_start: 0.8585 (pp) cc_final: 0.8225 (pp) REVERT: F 279 LYS cc_start: 0.8856 (ptmt) cc_final: 0.8483 (ttpp) REVERT: F 281 MET cc_start: 0.8625 (ppp) cc_final: 0.7690 (ppp) REVERT: F 354 ARG cc_start: 0.8513 (mmt90) cc_final: 0.8278 (ttm110) REVERT: F 380 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7514 (mtm180) REVERT: F 403 GLU cc_start: 0.5994 (pm20) cc_final: 0.5537 (pm20) REVERT: F 472 LYS cc_start: 0.9045 (tppt) cc_final: 0.8768 (tptp) REVERT: F 492 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8469 (ttmm) REVERT: F 506 GLN cc_start: 0.7639 (pm20) cc_final: 0.7138 (pm20) REVERT: F 636 MET cc_start: 0.8550 (mtm) cc_final: 0.8166 (mtt) REVERT: F 670 ASP cc_start: 0.7023 (t0) cc_final: 0.6812 (t0) REVERT: F 672 ASP cc_start: 0.8803 (m-30) cc_final: 0.8438 (m-30) REVERT: F 727 TYR cc_start: 0.8137 (t80) cc_final: 0.7366 (t80) REVERT: F 729 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7998 (mm) REVERT: F 1148 ASP cc_start: 0.8722 (t0) cc_final: 0.8238 (t0) REVERT: F 1179 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7621 (ptp-170) outliers start: 83 outliers final: 37 residues processed: 631 average time/residue: 0.1607 time to fit residues: 164.7658 Evaluate side-chains 534 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 490 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1149 GLN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 1132 THR Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 674 TRP Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 713 HIS Chi-restraints excluded: chain F residue 720 PHE Chi-restraints excluded: chain F residue 729 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 1174 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 242 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 296 optimal weight: 8.9990 chunk 317 optimal weight: 9.9990 chunk 53 optimal weight: 0.0070 chunk 75 optimal weight: 5.9990 chunk 153 optimal weight: 0.1980 chunk 217 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 224 optimal weight: 7.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1149 GLN A1152 HIS C1163 ASN E 386 GLN E 407 GLN E 415 ASN E1152 HIS F 277 GLN F 550 ASN F 632 GLN F 645 GLN F 713 HIS F1154 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.097244 restraints weight = 50017.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100537 restraints weight = 24340.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102698 restraints weight = 14960.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104154 restraints weight = 10640.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105028 restraints weight = 8423.360| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27554 Z= 0.125 Angle : 0.743 17.463 37313 Z= 0.366 Chirality : 0.047 0.219 4171 Planarity : 0.006 0.104 4759 Dihedral : 8.397 79.700 3804 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.06 % Favored : 87.72 % Rotamer: Outliers : 3.20 % Allowed : 19.92 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 3.39 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.13), residues: 3291 helix: -2.20 (0.13), residues: 1183 sheet: -2.06 (0.26), residues: 355 loop : -2.68 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 444 TYR 0.020 0.001 TYR A 588 PHE 0.033 0.001 PHE A 595 TRP 0.012 0.001 TRP A 674 HIS 0.005 0.001 HIS F 451 Details of bonding type rmsd covalent geometry : bond 0.00293 (27531) covalent geometry : angle 0.74348 (37313) hydrogen bonds : bond 0.04177 ( 579) hydrogen bonds : angle 4.50511 ( 1620) Misc. bond : bond 0.00212 ( 23) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 539 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 291 ILE cc_start: 0.9434 (tt) cc_final: 0.9203 (tp) REVERT: A 336 ARG cc_start: 0.8015 (tpp-160) cc_final: 0.7739 (tpp80) REVERT: A 359 GLU cc_start: 0.8968 (tt0) cc_final: 0.8303 (tm-30) REVERT: A 524 LYS cc_start: 0.7008 (mmmt) cc_final: 0.6398 (mtmt) REVERT: A 563 LEU cc_start: 0.7948 (mm) cc_final: 0.7735 (mm) REVERT: A 590 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8968 (mm110) REVERT: A 636 MET cc_start: 0.8521 (mmm) cc_final: 0.8080 (mpp) REVERT: B 382 SER cc_start: 0.9408 (m) cc_final: 0.8893 (t) REVERT: B 484 THR cc_start: 0.9264 (t) cc_final: 0.8955 (t) REVERT: B 503 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8326 (mmmm) REVERT: B 561 GLN cc_start: 0.8967 (tm-30) cc_final: 0.7934 (tm-30) REVERT: B 577 MET cc_start: 0.8643 (mmt) cc_final: 0.8418 (mmt) REVERT: B 600 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8352 (mt) REVERT: B 678 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8072 (pp) REVERT: B 693 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8367 (pp) REVERT: B 735 ASP cc_start: 0.9288 (t0) cc_final: 0.9020 (t0) REVERT: B 1159 GLN cc_start: 0.8872 (pt0) cc_final: 0.8541 (pt0) REVERT: B 1179 ARG cc_start: 0.9126 (mtp-110) cc_final: 0.8583 (ptp-110) REVERT: C 355 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8572 (tt) REVERT: C 358 GLU cc_start: 0.8096 (pm20) cc_final: 0.7763 (pm20) REVERT: C 359 GLU cc_start: 0.8044 (pm20) cc_final: 0.7682 (pm20) REVERT: C 431 ASP cc_start: 0.8115 (t0) cc_final: 0.7778 (t0) REVERT: C 478 ASP cc_start: 0.8506 (m-30) cc_final: 0.8197 (m-30) REVERT: C 546 LYS cc_start: 0.8704 (tttp) cc_final: 0.8348 (ttmt) REVERT: C 575 GLU cc_start: 0.9145 (tp30) cc_final: 0.8888 (tp30) REVERT: C 704 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7883 (pp) REVERT: C 718 GLU cc_start: 0.8732 (tp30) cc_final: 0.8474 (tp30) REVERT: C 1178 GLU cc_start: 0.9431 (mp0) cc_final: 0.9139 (mp0) REVERT: D 266 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 329 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7335 (mmmm) REVERT: D 348 GLU cc_start: 0.8546 (tp30) cc_final: 0.7763 (tp30) REVERT: D 352 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8571 (mm-40) REVERT: D 418 ASP cc_start: 0.9094 (t0) cc_final: 0.8877 (m-30) REVERT: D 431 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8088 (p0) REVERT: D 440 ASP cc_start: 0.8641 (p0) cc_final: 0.8214 (p0) REVERT: D 575 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8780 (tm-30) REVERT: D 693 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8300 (pp) REVERT: E 399 MET cc_start: 0.8544 (mtt) cc_final: 0.8202 (mtt) REVERT: E 400 ASP cc_start: 0.9038 (t70) cc_final: 0.8661 (t0) REVERT: E 407 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7702 (tp40) REVERT: E 630 HIS cc_start: 0.8322 (t70) cc_final: 0.7820 (t70) REVERT: E 642 ASP cc_start: 0.9000 (t0) cc_final: 0.8347 (t0) REVERT: E 695 PHE cc_start: 0.9040 (p90) cc_final: 0.8735 (p90) REVERT: E 1184 PHE cc_start: 0.8476 (m-80) cc_final: 0.7763 (m-80) REVERT: F 278 LEU cc_start: 0.8618 (pp) cc_final: 0.8149 (pp) REVERT: F 279 LYS cc_start: 0.8852 (ptmt) cc_final: 0.8498 (ttpp) REVERT: F 281 MET cc_start: 0.8647 (ppp) cc_final: 0.7717 (ppp) REVERT: F 354 ARG cc_start: 0.8388 (mmt90) cc_final: 0.8100 (ttm110) REVERT: F 364 GLN cc_start: 0.7418 (tp40) cc_final: 0.6642 (tp-100) REVERT: F 380 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7582 (mtm180) REVERT: F 403 GLU cc_start: 0.5842 (pm20) cc_final: 0.5380 (pm20) REVERT: F 466 MET cc_start: 0.8761 (ttm) cc_final: 0.8553 (ttp) REVERT: F 472 LYS cc_start: 0.9087 (tppt) cc_final: 0.8734 (tppt) REVERT: F 492 LYS cc_start: 0.8731 (ttpp) cc_final: 0.8455 (ttmm) REVERT: F 506 GLN cc_start: 0.7268 (pm20) cc_final: 0.6760 (pm20) REVERT: F 636 MET cc_start: 0.8327 (mtm) cc_final: 0.7972 (mtt) REVERT: F 670 ASP cc_start: 0.7133 (t0) cc_final: 0.6854 (t0) REVERT: F 672 ASP cc_start: 0.8857 (m-30) cc_final: 0.8483 (m-30) REVERT: F 727 TYR cc_start: 0.8195 (t80) cc_final: 0.7427 (t80) REVERT: F 729 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7986 (mm) REVERT: F 1148 ASP cc_start: 0.8732 (t0) cc_final: 0.8205 (t0) REVERT: F 1179 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7662 (ptp-170) outliers start: 96 outliers final: 49 residues processed: 594 average time/residue: 0.1662 time to fit residues: 160.2579 Evaluate side-chains 556 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 498 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 1149 GLN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 724 GLN Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 333 PHE Chi-restraints excluded: chain E residue 407 GLN Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 674 TRP Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 1152 HIS Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 631 VAL Chi-restraints excluded: chain F residue 713 HIS Chi-restraints excluded: chain F residue 720 PHE Chi-restraints excluded: chain F residue 729 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 1142 THR Chi-restraints excluded: chain F residue 1174 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 179 optimal weight: 0.0060 chunk 235 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 229 optimal weight: 0.0170 chunk 245 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 238 optimal weight: 0.5980 chunk 301 optimal weight: 1.9990 overall best weight: 0.7036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 713 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098508 restraints weight = 49538.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101854 restraints weight = 24082.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104045 restraints weight = 14716.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105467 restraints weight = 10433.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106351 restraints weight = 8259.821| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27554 Z= 0.117 Angle : 0.720 17.177 37313 Z= 0.353 Chirality : 0.046 0.224 4171 Planarity : 0.006 0.101 4759 Dihedral : 8.018 75.015 3804 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.91 % Favored : 87.91 % Rotamer: Outliers : 3.16 % Allowed : 20.92 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.97 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.14), residues: 3291 helix: -1.62 (0.14), residues: 1186 sheet: -1.87 (0.26), residues: 357 loop : -2.54 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 761 TYR 0.028 0.001 TYR F 626 PHE 0.048 0.001 PHE A 595 TRP 0.014 0.001 TRP E 455 HIS 0.024 0.001 HIS E1152 Details of bonding type rmsd covalent geometry : bond 0.00273 (27531) covalent geometry : angle 0.71973 (37313) hydrogen bonds : bond 0.03519 ( 579) hydrogen bonds : angle 4.22865 ( 1620) Misc. bond : bond 0.00208 ( 23) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 533 time to evaluate : 1.069 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: A 280 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8787 (tm-30) REVERT: A 291 ILE cc_start: 0.9433 (tt) cc_final: 0.9197 (tp) REVERT: A 336 ARG cc_start: 0.8061 (tpp-160) cc_final: 0.7824 (tpp80) REVERT: A 359 GLU cc_start: 0.9037 (tt0) cc_final: 0.8752 (tt0) REVERT: A 524 LYS cc_start: 0.7088 (mmmt) cc_final: 0.6394 (mtmt) REVERT: A 563 LEU cc_start: 0.7956 (mm) cc_final: 0.7744 (mm) REVERT: A 590 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8954 (mm110) REVERT: A 636 MET cc_start: 0.8500 (mmm) cc_final: 0.8070 (mpp) REVERT: A 692 ARG cc_start: 0.8345 (mtm110) cc_final: 0.8038 (mtm-85) REVERT: B 503 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8295 (mmmm) REVERT: B 561 GLN cc_start: 0.8864 (tm-30) cc_final: 0.7822 (tm-30) REVERT: B 577 MET cc_start: 0.8647 (mmt) cc_final: 0.8429 (mmt) REVERT: B 596 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8274 (mm-30) REVERT: B 693 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8317 (pp) REVERT: B 694 ASP cc_start: 0.8653 (p0) cc_final: 0.8437 (p0) REVERT: B 735 ASP cc_start: 0.9288 (t0) cc_final: 0.9038 (t0) REVERT: B 1159 GLN cc_start: 0.8849 (pt0) cc_final: 0.8500 (pt0) REVERT: B 1179 ARG cc_start: 0.9115 (mtp-110) cc_final: 0.8389 (ptp-170) REVERT: C 327 GLU cc_start: 0.8550 (mp0) cc_final: 0.8331 (mp0) REVERT: C 355 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8689 (tt) REVERT: C 431 ASP cc_start: 0.8023 (t0) cc_final: 0.7651 (t0) REVERT: C 478 ASP cc_start: 0.8471 (m-30) cc_final: 0.8161 (m-30) REVERT: C 546 LYS cc_start: 0.8635 (tttp) cc_final: 0.8252 (ttmt) REVERT: C 575 GLU cc_start: 0.9084 (tp30) cc_final: 0.8837 (tp30) REVERT: C 704 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7826 (pp) REVERT: C 718 GLU cc_start: 0.8705 (tp30) cc_final: 0.8386 (tp30) REVERT: C 1178 GLU cc_start: 0.9417 (mp0) cc_final: 0.9127 (mp0) REVERT: D 266 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7558 (tm-30) REVERT: D 348 GLU cc_start: 0.8497 (tp30) cc_final: 0.7598 (tp30) REVERT: D 352 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8445 (mm-40) REVERT: D 358 GLU cc_start: 0.9013 (tp30) cc_final: 0.8796 (tp30) REVERT: D 418 ASP cc_start: 0.9106 (t0) cc_final: 0.8885 (m-30) REVERT: D 431 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8130 (p0) REVERT: D 440 ASP cc_start: 0.8565 (p0) cc_final: 0.8214 (p0) REVERT: D 570 LEU cc_start: 0.7693 (mp) cc_final: 0.7367 (tp) REVERT: D 575 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8822 (tm-30) REVERT: D 580 ASP cc_start: 0.8292 (p0) cc_final: 0.7538 (p0) REVERT: D 693 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8218 (pp) REVERT: D 1157 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7818 (pp) REVERT: E 283 MET cc_start: 0.8196 (tmm) cc_final: 0.7991 (tmm) REVERT: E 295 PHE cc_start: 0.8204 (m-80) cc_final: 0.7716 (m-80) REVERT: E 400 ASP cc_start: 0.9027 (t70) cc_final: 0.8641 (t0) REVERT: E 407 GLN cc_start: 0.8491 (tt0) cc_final: 0.7847 (tp40) REVERT: E 630 HIS cc_start: 0.8356 (t70) cc_final: 0.7855 (t70) REVERT: E 642 ASP cc_start: 0.8921 (t0) cc_final: 0.8304 (t0) REVERT: E 695 PHE cc_start: 0.9043 (p90) cc_final: 0.8729 (p90) REVERT: E 1184 PHE cc_start: 0.8414 (m-80) cc_final: 0.7670 (m-80) REVERT: F 278 LEU cc_start: 0.8653 (pp) cc_final: 0.8136 (pp) REVERT: F 279 LYS cc_start: 0.8826 (ptmt) cc_final: 0.8471 (ttpp) REVERT: F 281 MET cc_start: 0.8643 (ppp) cc_final: 0.7760 (ppp) REVERT: F 354 ARG cc_start: 0.8403 (mmt90) cc_final: 0.8084 (ttm110) REVERT: F 364 GLN cc_start: 0.7224 (tp40) cc_final: 0.6537 (tp-100) REVERT: F 380 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7568 (mtm180) REVERT: F 399 MET cc_start: 0.9224 (tmm) cc_final: 0.8981 (tmm) REVERT: F 403 GLU cc_start: 0.5708 (pm20) cc_final: 0.5288 (pm20) REVERT: F 466 MET cc_start: 0.8800 (ttm) cc_final: 0.8585 (ttp) REVERT: F 472 LYS cc_start: 0.9052 (tppt) cc_final: 0.8755 (tppt) REVERT: F 492 LYS cc_start: 0.8713 (ttpp) cc_final: 0.8448 (ttmm) REVERT: F 506 GLN cc_start: 0.7124 (pm20) cc_final: 0.6581 (pm20) REVERT: F 670 ASP cc_start: 0.7268 (t0) cc_final: 0.7001 (t0) REVERT: F 672 ASP cc_start: 0.8889 (m-30) cc_final: 0.8520 (m-30) REVERT: F 1148 ASP cc_start: 0.8718 (t0) cc_final: 0.8170 (t0) REVERT: F 1179 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7626 (ptp-170) outliers start: 95 outliers final: 62 residues processed: 590 average time/residue: 0.1654 time to fit residues: 157.8400 Evaluate side-chains 572 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 504 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 724 GLN Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1146 THR Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 333 PHE Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 674 TRP Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 1152 HIS Chi-restraints excluded: chain E residue 1161 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 464 CYS Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 631 VAL Chi-restraints excluded: chain F residue 720 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 1142 THR Chi-restraints excluded: chain F residue 1174 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 84 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 274 optimal weight: 0.3980 chunk 191 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 GLN B1152 HIS C 454 ASN E 407 GLN E1136 GLN E1152 HIS F 415 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093903 restraints weight = 50308.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.097124 restraints weight = 24656.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099225 restraints weight = 15156.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100607 restraints weight = 10827.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101524 restraints weight = 8604.155| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 27554 Z= 0.194 Angle : 0.774 16.773 37313 Z= 0.381 Chirality : 0.049 0.293 4171 Planarity : 0.006 0.118 4759 Dihedral : 8.189 79.178 3802 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.76 % Favored : 86.96 % Rotamer: Outliers : 4.56 % Allowed : 21.29 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 3.39 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.14), residues: 3291 helix: -1.26 (0.15), residues: 1201 sheet: -1.76 (0.27), residues: 359 loop : -2.47 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 444 TYR 0.027 0.001 TYR E 626 PHE 0.027 0.001 PHE A 595 TRP 0.011 0.001 TRP A 674 HIS 0.006 0.001 HIS F 451 Details of bonding type rmsd covalent geometry : bond 0.00462 (27531) covalent geometry : angle 0.77413 (37313) hydrogen bonds : bond 0.04176 ( 579) hydrogen bonds : angle 4.43633 ( 1620) Misc. bond : bond 0.00266 ( 23) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 501 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8769 (tm-30) REVERT: A 291 ILE cc_start: 0.9434 (tt) cc_final: 0.9188 (tp) REVERT: A 336 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7747 (tpp80) REVERT: A 402 MET cc_start: 0.8643 (ttp) cc_final: 0.8301 (ttp) REVERT: A 408 VAL cc_start: 0.9081 (t) cc_final: 0.8816 (m) REVERT: A 524 LYS cc_start: 0.7201 (mmmt) cc_final: 0.6510 (mtmt) REVERT: A 558 LYS cc_start: 0.8902 (pttm) cc_final: 0.8700 (pttm) REVERT: A 563 LEU cc_start: 0.7899 (mm) cc_final: 0.7688 (mm) REVERT: A 590 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8953 (mm110) REVERT: A 636 MET cc_start: 0.8569 (mmm) cc_final: 0.8059 (mpp) REVERT: B 469 GLU cc_start: 0.8744 (tp30) cc_final: 0.8378 (tp30) REVERT: B 503 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8356 (mmmm) REVERT: B 596 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 693 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8411 (pp) REVERT: B 694 ASP cc_start: 0.8635 (p0) cc_final: 0.8351 (p0) REVERT: B 735 ASP cc_start: 0.9328 (t0) cc_final: 0.9091 (t0) REVERT: B 1159 GLN cc_start: 0.8921 (pt0) cc_final: 0.8567 (pt0) REVERT: B 1168 TRP cc_start: 0.7063 (m-10) cc_final: 0.5512 (t60) REVERT: B 1179 ARG cc_start: 0.9162 (mtp-110) cc_final: 0.8561 (ptp-110) REVERT: C 327 GLU cc_start: 0.8606 (mp0) cc_final: 0.8333 (mp0) REVERT: C 335 MET cc_start: 0.7290 (mmt) cc_final: 0.7015 (mmt) REVERT: C 355 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8810 (tt) REVERT: C 431 ASP cc_start: 0.8102 (t0) cc_final: 0.7851 (t0) REVERT: C 478 ASP cc_start: 0.8577 (m-30) cc_final: 0.8234 (m-30) REVERT: C 546 LYS cc_start: 0.8739 (tttp) cc_final: 0.8328 (ttpt) REVERT: C 575 GLU cc_start: 0.9126 (tp30) cc_final: 0.8884 (tp30) REVERT: C 704 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7969 (pp) REVERT: C 718 GLU cc_start: 0.8725 (tp30) cc_final: 0.8414 (tp30) REVERT: C 1178 GLU cc_start: 0.9401 (mp0) cc_final: 0.9034 (mp0) REVERT: D 266 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7709 (tm-30) REVERT: D 348 GLU cc_start: 0.8543 (tp30) cc_final: 0.8179 (tp30) REVERT: D 352 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8684 (mm110) REVERT: D 431 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8192 (p0) REVERT: D 440 ASP cc_start: 0.8736 (p0) cc_final: 0.8303 (p0) REVERT: D 570 LEU cc_start: 0.7633 (mp) cc_final: 0.7329 (tp) REVERT: D 575 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8744 (tm-30) REVERT: D 580 ASP cc_start: 0.8303 (p0) cc_final: 0.7746 (p0) REVERT: D 670 ASP cc_start: 0.7907 (t70) cc_final: 0.7577 (t0) REVERT: D 1157 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7923 (pp) REVERT: D 1178 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8178 (pp20) REVERT: E 283 MET cc_start: 0.8039 (tmm) cc_final: 0.7791 (tmm) REVERT: E 295 PHE cc_start: 0.8313 (m-80) cc_final: 0.7926 (m-80) REVERT: E 400 ASP cc_start: 0.9063 (t70) cc_final: 0.8717 (t0) REVERT: E 407 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7911 (tp40) REVERT: E 610 ARG cc_start: 0.8021 (tpp80) cc_final: 0.7555 (ttp80) REVERT: E 642 ASP cc_start: 0.8952 (t0) cc_final: 0.8296 (t0) REVERT: E 695 PHE cc_start: 0.9038 (p90) cc_final: 0.8726 (p90) REVERT: F 278 LEU cc_start: 0.8651 (pp) cc_final: 0.8174 (pp) REVERT: F 279 LYS cc_start: 0.8846 (ptmt) cc_final: 0.8507 (ttpp) REVERT: F 281 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7629 (ppp) REVERT: F 354 ARG cc_start: 0.8462 (mmt90) cc_final: 0.8120 (ttm110) REVERT: F 380 ARG cc_start: 0.7977 (mtm180) cc_final: 0.7520 (mtm180) REVERT: F 403 GLU cc_start: 0.5831 (pm20) cc_final: 0.5376 (pm20) REVERT: F 466 MET cc_start: 0.8834 (ttm) cc_final: 0.8605 (ttp) REVERT: F 472 LYS cc_start: 0.9077 (tppt) cc_final: 0.8774 (tppt) REVERT: F 639 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8451 (pp) REVERT: F 670 ASP cc_start: 0.7501 (t0) cc_final: 0.7265 (t0) REVERT: F 672 ASP cc_start: 0.8922 (m-30) cc_final: 0.8562 (m-30) REVERT: F 729 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7912 (mm) REVERT: F 1148 ASP cc_start: 0.8792 (t0) cc_final: 0.8253 (t0) REVERT: F 1179 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7705 (ptp-170) outliers start: 137 outliers final: 94 residues processed: 591 average time/residue: 0.1649 time to fit residues: 158.3001 Evaluate side-chains 590 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 486 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 724 GLN Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 1132 THR Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1146 THR Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain D residue 1178 GLU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 333 PHE Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 407 GLN Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 674 TRP Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 733 THR Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 1152 HIS Chi-restraints excluded: chain E residue 1161 ILE Chi-restraints excluded: chain E residue 1186 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 631 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 720 PHE Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 729 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 1142 THR Chi-restraints excluded: chain F residue 1173 VAL Chi-restraints excluded: chain F residue 1174 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 288 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 313 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 133 optimal weight: 0.3980 chunk 315 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B1152 HIS C 454 ASN ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1152 HIS F 415 ASN F1154 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096218 restraints weight = 49981.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099493 restraints weight = 24377.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101682 restraints weight = 14940.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103080 restraints weight = 10601.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104017 restraints weight = 8409.649| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27554 Z= 0.130 Angle : 0.737 17.122 37313 Z= 0.360 Chirality : 0.047 0.214 4171 Planarity : 0.006 0.107 4759 Dihedral : 7.984 84.669 3802 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.03 % Favored : 87.75 % Rotamer: Outliers : 4.26 % Allowed : 22.05 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.54 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.15), residues: 3291 helix: -0.92 (0.15), residues: 1189 sheet: -1.69 (0.27), residues: 361 loop : -2.40 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 444 TYR 0.024 0.001 TYR F 626 PHE 0.028 0.001 PHE A 595 TRP 0.013 0.001 TRP A 674 HIS 0.009 0.001 HIS E1152 Details of bonding type rmsd covalent geometry : bond 0.00309 (27531) covalent geometry : angle 0.73668 (37313) hydrogen bonds : bond 0.03567 ( 579) hydrogen bonds : angle 4.18612 ( 1620) Misc. bond : bond 0.00219 ( 23) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 510 time to evaluate : 0.973 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: A 280 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8825 (tm-30) REVERT: A 291 ILE cc_start: 0.9482 (tt) cc_final: 0.9245 (tp) REVERT: A 336 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.7855 (tpp80) REVERT: A 402 MET cc_start: 0.8684 (ttp) cc_final: 0.8340 (ttp) REVERT: A 524 LYS cc_start: 0.7193 (mmmt) cc_final: 0.6484 (mtmt) REVERT: A 636 MET cc_start: 0.8593 (mmm) cc_final: 0.8108 (mpp) REVERT: B 441 ARG cc_start: 0.8433 (tpt-90) cc_final: 0.7979 (tpp80) REVERT: B 469 GLU cc_start: 0.8750 (tp30) cc_final: 0.8293 (mm-30) REVERT: B 503 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8351 (mmmm) REVERT: B 596 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 693 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8509 (pp) REVERT: B 735 ASP cc_start: 0.9210 (t0) cc_final: 0.8984 (t0) REVERT: B 1159 GLN cc_start: 0.8854 (pt0) cc_final: 0.8551 (pt0) REVERT: B 1179 ARG cc_start: 0.9118 (mtp-110) cc_final: 0.8391 (ptp-170) REVERT: C 355 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8776 (tt) REVERT: C 431 ASP cc_start: 0.7874 (t0) cc_final: 0.7567 (t0) REVERT: C 478 ASP cc_start: 0.8374 (m-30) cc_final: 0.8070 (m-30) REVERT: C 546 LYS cc_start: 0.8778 (tttp) cc_final: 0.8380 (ttpt) REVERT: C 575 GLU cc_start: 0.9115 (tp30) cc_final: 0.8900 (tp30) REVERT: C 704 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8012 (pp) REVERT: C 718 GLU cc_start: 0.8630 (tp30) cc_final: 0.8344 (tp30) REVERT: C 1178 GLU cc_start: 0.9367 (mp0) cc_final: 0.9053 (mp0) REVERT: D 266 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 298 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7566 (mm110) REVERT: D 348 GLU cc_start: 0.8416 (tp30) cc_final: 0.8028 (tp30) REVERT: D 352 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8597 (mm110) REVERT: D 431 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8192 (p0) REVERT: D 440 ASP cc_start: 0.8652 (p0) cc_final: 0.8236 (p0) REVERT: D 570 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7286 (tp) REVERT: D 575 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8796 (tm-30) REVERT: D 580 ASP cc_start: 0.8222 (p0) cc_final: 0.7690 (p0) REVERT: D 670 ASP cc_start: 0.7879 (t70) cc_final: 0.7612 (t0) REVERT: D 1157 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7953 (pp) REVERT: E 283 MET cc_start: 0.8154 (tmm) cc_final: 0.7751 (tmm) REVERT: E 295 PHE cc_start: 0.8296 (m-80) cc_final: 0.7833 (m-80) REVERT: E 400 ASP cc_start: 0.9071 (t70) cc_final: 0.8738 (t0) REVERT: E 407 GLN cc_start: 0.8434 (tt0) cc_final: 0.7977 (tp40) REVERT: E 630 HIS cc_start: 0.8317 (t70) cc_final: 0.7750 (t70) REVERT: E 642 ASP cc_start: 0.8923 (t0) cc_final: 0.8299 (t0) REVERT: E 695 PHE cc_start: 0.9024 (p90) cc_final: 0.8722 (p90) REVERT: F 278 LEU cc_start: 0.8671 (pp) cc_final: 0.8192 (pp) REVERT: F 279 LYS cc_start: 0.8857 (ptmt) cc_final: 0.8514 (ttpp) REVERT: F 281 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7624 (ppp) REVERT: F 354 ARG cc_start: 0.8517 (mmt90) cc_final: 0.8155 (ttm110) REVERT: F 380 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7546 (mtm180) REVERT: F 403 GLU cc_start: 0.5805 (pm20) cc_final: 0.5344 (pm20) REVERT: F 466 MET cc_start: 0.8789 (ttm) cc_final: 0.8518 (ttp) REVERT: F 472 LYS cc_start: 0.9045 (tppt) cc_final: 0.8736 (tppt) REVERT: F 639 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8364 (pp) REVERT: F 670 ASP cc_start: 0.7751 (t0) cc_final: 0.7505 (t0) REVERT: F 672 ASP cc_start: 0.8881 (m-30) cc_final: 0.8576 (m-30) REVERT: F 1148 ASP cc_start: 0.8706 (t0) cc_final: 0.8159 (t0) REVERT: F 1179 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7643 (ptp-170) outliers start: 128 outliers final: 96 residues processed: 588 average time/residue: 0.1548 time to fit residues: 148.5398 Evaluate side-chains 592 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 487 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 724 GLN Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 1132 THR Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1146 THR Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 333 PHE Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 674 TRP Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 1152 HIS Chi-restraints excluded: chain E residue 1161 ILE Chi-restraints excluded: chain E residue 1186 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 464 CYS Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 631 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 720 PHE Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 1142 THR Chi-restraints excluded: chain F residue 1158 TYR Chi-restraints excluded: chain F residue 1174 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 52 optimal weight: 4.9990 chunk 329 optimal weight: 20.0000 chunk 279 optimal weight: 0.9990 chunk 252 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 320 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 243 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B1152 HIS C 454 ASN ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1152 HIS ** F 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1154 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095193 restraints weight = 49717.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098418 restraints weight = 24307.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100528 restraints weight = 14949.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101916 restraints weight = 10650.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102849 restraints weight = 8465.062| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 27554 Z= 0.157 Angle : 0.755 17.184 37313 Z= 0.369 Chirality : 0.048 0.243 4171 Planarity : 0.006 0.105 4759 Dihedral : 8.019 87.345 3802 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.67 % Favored : 87.12 % Rotamer: Outliers : 4.56 % Allowed : 22.32 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.97 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.15), residues: 3291 helix: -0.75 (0.15), residues: 1194 sheet: -1.68 (0.27), residues: 361 loop : -2.38 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 525 TYR 0.023 0.001 TYR F 626 PHE 0.021 0.001 PHE C 695 TRP 0.012 0.001 TRP A 674 HIS 0.010 0.001 HIS E1152 Details of bonding type rmsd covalent geometry : bond 0.00374 (27531) covalent geometry : angle 0.75496 (37313) hydrogen bonds : bond 0.03731 ( 579) hydrogen bonds : angle 4.23388 ( 1620) Misc. bond : bond 0.00249 ( 23) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 496 time to evaluate : 1.060 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: A 291 ILE cc_start: 0.9451 (tt) cc_final: 0.9205 (tp) REVERT: A 336 ARG cc_start: 0.8094 (tpp-160) cc_final: 0.7798 (tpp80) REVERT: A 402 MET cc_start: 0.8716 (ttp) cc_final: 0.8361 (ttp) REVERT: A 524 LYS cc_start: 0.7174 (mmmt) cc_final: 0.6466 (mtmt) REVERT: A 563 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7457 (mm) REVERT: A 636 MET cc_start: 0.8573 (mmm) cc_final: 0.8017 (mpp) REVERT: B 441 ARG cc_start: 0.8485 (tpt-90) cc_final: 0.8007 (tpp80) REVERT: B 469 GLU cc_start: 0.8764 (tp30) cc_final: 0.8288 (mm-30) REVERT: B 503 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8309 (mmmm) REVERT: B 596 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8324 (mm-30) REVERT: B 693 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8449 (pp) REVERT: B 735 ASP cc_start: 0.9281 (t0) cc_final: 0.9062 (t0) REVERT: B 1153 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8860 (mp) REVERT: B 1159 GLN cc_start: 0.8859 (pt0) cc_final: 0.8563 (pt0) REVERT: B 1168 TRP cc_start: 0.6965 (m-10) cc_final: 0.5464 (t60) REVERT: B 1179 ARG cc_start: 0.9154 (mtp-110) cc_final: 0.8398 (ptp-170) REVERT: C 355 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8771 (tt) REVERT: C 431 ASP cc_start: 0.8007 (t0) cc_final: 0.7761 (t0) REVERT: C 478 ASP cc_start: 0.8516 (m-30) cc_final: 0.8169 (m-30) REVERT: C 546 LYS cc_start: 0.8768 (tttp) cc_final: 0.8348 (ttpt) REVERT: C 575 GLU cc_start: 0.9138 (tp30) cc_final: 0.8916 (tp30) REVERT: C 626 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7533 (p90) REVERT: C 704 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7941 (pp) REVERT: C 718 GLU cc_start: 0.8677 (tp30) cc_final: 0.8391 (tp30) REVERT: C 1178 GLU cc_start: 0.9391 (mp0) cc_final: 0.9045 (mp0) REVERT: D 266 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 283 MET cc_start: 0.8545 (tmm) cc_final: 0.8332 (tmm) REVERT: D 298 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7625 (mm110) REVERT: D 330 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7975 (mmtm) REVERT: D 348 GLU cc_start: 0.8478 (tp30) cc_final: 0.8023 (tp30) REVERT: D 352 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8628 (mm110) REVERT: D 431 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8197 (p0) REVERT: D 440 ASP cc_start: 0.8729 (p0) cc_final: 0.8296 (p0) REVERT: D 526 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8570 (ttm) REVERT: D 570 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7286 (tp) REVERT: D 575 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8771 (tm-30) REVERT: D 580 ASP cc_start: 0.8277 (p0) cc_final: 0.7740 (p0) REVERT: D 607 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8346 (mm) REVERT: D 670 ASP cc_start: 0.7848 (t70) cc_final: 0.7599 (t0) REVERT: E 283 MET cc_start: 0.8202 (tmm) cc_final: 0.7911 (tmm) REVERT: E 295 PHE cc_start: 0.8310 (m-80) cc_final: 0.7915 (m-80) REVERT: E 359 GLU cc_start: 0.8933 (tt0) cc_final: 0.8304 (tt0) REVERT: E 400 ASP cc_start: 0.9061 (t70) cc_final: 0.8713 (t0) REVERT: E 407 GLN cc_start: 0.8538 (tt0) cc_final: 0.8012 (tp40) REVERT: E 630 HIS cc_start: 0.8294 (t70) cc_final: 0.7673 (t70) REVERT: E 642 ASP cc_start: 0.8939 (t0) cc_final: 0.8268 (t0) REVERT: E 695 PHE cc_start: 0.9005 (p90) cc_final: 0.8675 (p90) REVERT: E 748 ILE cc_start: 0.9263 (tp) cc_final: 0.9016 (tp) REVERT: F 278 LEU cc_start: 0.8667 (pp) cc_final: 0.8209 (pp) REVERT: F 279 LYS cc_start: 0.8888 (ptmt) cc_final: 0.8559 (ttpp) REVERT: F 281 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7611 (ppp) REVERT: F 354 ARG cc_start: 0.8476 (mmt90) cc_final: 0.8132 (ttm110) REVERT: F 380 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7517 (mtm180) REVERT: F 402 MET cc_start: 0.6885 (mmm) cc_final: 0.6509 (mmm) REVERT: F 403 GLU cc_start: 0.5835 (pm20) cc_final: 0.5367 (pm20) REVERT: F 472 LYS cc_start: 0.9056 (tppt) cc_final: 0.8760 (tppt) REVERT: F 639 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8443 (pp) REVERT: F 670 ASP cc_start: 0.7764 (t0) cc_final: 0.7512 (t0) REVERT: F 672 ASP cc_start: 0.8886 (m-30) cc_final: 0.8574 (m-30) REVERT: F 727 TYR cc_start: 0.8177 (t80) cc_final: 0.7451 (t80) REVERT: F 1148 ASP cc_start: 0.8749 (t0) cc_final: 0.8208 (t0) REVERT: F 1179 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7635 (ptp-170) outliers start: 137 outliers final: 110 residues processed: 583 average time/residue: 0.1582 time to fit residues: 151.3887 Evaluate side-chains 602 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 479 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 626 TYR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 724 GLN Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 1132 THR Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1146 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 333 PHE Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 674 TRP Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 733 THR Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 1161 ILE Chi-restraints excluded: chain E residue 1186 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 529 SER Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 631 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 720 PHE Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 1142 THR Chi-restraints excluded: chain F residue 1158 TYR Chi-restraints excluded: chain F residue 1174 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 209 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 317 optimal weight: 0.2980 chunk 188 optimal weight: 8.9990 chunk 250 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 97 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B1152 HIS C 454 ASN ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.097625 restraints weight = 49636.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100942 restraints weight = 24159.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103107 restraints weight = 14767.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104513 restraints weight = 10474.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105481 restraints weight = 8290.040| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27554 Z= 0.123 Angle : 0.741 17.644 37313 Z= 0.358 Chirality : 0.047 0.273 4171 Planarity : 0.006 0.103 4759 Dihedral : 7.852 89.570 3802 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.03 % Favored : 87.78 % Rotamer: Outliers : 4.23 % Allowed : 22.98 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.12 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.15), residues: 3291 helix: -0.54 (0.16), residues: 1184 sheet: -1.58 (0.27), residues: 362 loop : -2.33 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 525 TYR 0.024 0.001 TYR A 588 PHE 0.030 0.001 PHE A 595 TRP 0.015 0.001 TRP F 719 HIS 0.005 0.001 HIS B1152 Details of bonding type rmsd covalent geometry : bond 0.00290 (27531) covalent geometry : angle 0.74083 (37313) hydrogen bonds : bond 0.03311 ( 579) hydrogen bonds : angle 4.04419 ( 1620) Misc. bond : bond 0.00257 ( 23) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 515 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ILE cc_start: 0.9402 (tt) cc_final: 0.9164 (tp) REVERT: A 336 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7812 (tpp80) REVERT: A 402 MET cc_start: 0.8632 (ttp) cc_final: 0.8398 (ttp) REVERT: A 524 LYS cc_start: 0.7120 (mmmt) cc_final: 0.6442 (mtmt) REVERT: A 563 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7389 (mm) REVERT: A 636 MET cc_start: 0.8541 (mmm) cc_final: 0.8008 (mpp) REVERT: B 441 ARG cc_start: 0.8452 (tpt-90) cc_final: 0.8151 (tpp80) REVERT: B 469 GLU cc_start: 0.8817 (tp30) cc_final: 0.8489 (mm-30) REVERT: B 503 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8323 (mmmm) REVERT: B 517 LYS cc_start: 0.8284 (tttt) cc_final: 0.8030 (tmtt) REVERT: B 596 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8304 (mm-30) REVERT: B 693 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8384 (pp) REVERT: B 735 ASP cc_start: 0.9299 (t0) cc_final: 0.9077 (t0) REVERT: B 1153 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8735 (mp) REVERT: B 1159 GLN cc_start: 0.8714 (pt0) cc_final: 0.8512 (pt0) REVERT: B 1179 ARG cc_start: 0.9137 (mtp-110) cc_final: 0.8443 (ptp-170) REVERT: C 355 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8735 (tt) REVERT: C 431 ASP cc_start: 0.7876 (t0) cc_final: 0.7572 (t0) REVERT: C 449 GLU cc_start: 0.8947 (pp20) cc_final: 0.8442 (pp20) REVERT: C 478 ASP cc_start: 0.8438 (m-30) cc_final: 0.8120 (m-30) REVERT: C 546 LYS cc_start: 0.8702 (tttp) cc_final: 0.8286 (ttpt) REVERT: C 704 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7850 (pp) REVERT: C 718 GLU cc_start: 0.8661 (tp30) cc_final: 0.8385 (tp30) REVERT: C 1178 GLU cc_start: 0.9392 (mp0) cc_final: 0.9052 (mp0) REVERT: D 266 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7673 (tm-30) REVERT: D 298 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7531 (mm110) REVERT: D 330 LYS cc_start: 0.8270 (mmtm) cc_final: 0.8020 (mmtm) REVERT: D 348 GLU cc_start: 0.8460 (tp30) cc_final: 0.7915 (tp30) REVERT: D 352 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8599 (mm110) REVERT: D 431 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8158 (p0) REVERT: D 440 ASP cc_start: 0.8624 (p0) cc_final: 0.8242 (p0) REVERT: D 526 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8425 (ttm) REVERT: D 570 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7322 (tp) REVERT: D 575 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8776 (tm-30) REVERT: D 580 ASP cc_start: 0.8281 (p0) cc_final: 0.7742 (p0) REVERT: D 607 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8269 (mm) REVERT: E 295 PHE cc_start: 0.8293 (m-80) cc_final: 0.7830 (m-80) REVERT: E 359 GLU cc_start: 0.8926 (tt0) cc_final: 0.8271 (tt0) REVERT: E 400 ASP cc_start: 0.9035 (t70) cc_final: 0.8726 (t0) REVERT: E 407 GLN cc_start: 0.8504 (tt0) cc_final: 0.7966 (tp40) REVERT: E 426 ARG cc_start: 0.8695 (tmm160) cc_final: 0.7726 (tmm-80) REVERT: E 630 HIS cc_start: 0.8316 (t70) cc_final: 0.7728 (t70) REVERT: E 642 ASP cc_start: 0.8922 (t0) cc_final: 0.8367 (t0) REVERT: E 695 PHE cc_start: 0.8994 (p90) cc_final: 0.8664 (p90) REVERT: E 748 ILE cc_start: 0.9227 (tp) cc_final: 0.9005 (tp) REVERT: F 278 LEU cc_start: 0.8685 (pp) cc_final: 0.8161 (pp) REVERT: F 279 LYS cc_start: 0.8984 (ptmt) cc_final: 0.8661 (ttpp) REVERT: F 281 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.7652 (ppp) REVERT: F 380 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7494 (mtm180) REVERT: F 402 MET cc_start: 0.6807 (mmm) cc_final: 0.6438 (mmm) REVERT: F 403 GLU cc_start: 0.5765 (pm20) cc_final: 0.5292 (pm20) REVERT: F 472 LYS cc_start: 0.9010 (tppt) cc_final: 0.8745 (tppt) REVERT: F 639 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8397 (pp) REVERT: F 670 ASP cc_start: 0.7686 (t0) cc_final: 0.7320 (t0) REVERT: F 672 ASP cc_start: 0.8891 (m-30) cc_final: 0.8575 (m-30) REVERT: F 727 TYR cc_start: 0.8135 (t80) cc_final: 0.7520 (t80) REVERT: F 747 LEU cc_start: 0.9362 (mt) cc_final: 0.9085 (tt) REVERT: F 1148 ASP cc_start: 0.8707 (t0) cc_final: 0.8165 (t0) REVERT: F 1179 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7600 (ptp-170) outliers start: 127 outliers final: 95 residues processed: 585 average time/residue: 0.1551 time to fit residues: 148.5409 Evaluate side-chains 606 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 499 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 724 GLN Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 731 TYR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1146 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 333 PHE Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 674 TRP Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 LEU Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 1186 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 464 CYS Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 631 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 720 PHE Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 1142 THR Chi-restraints excluded: chain F residue 1158 TYR Chi-restraints excluded: chain F residue 1174 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 5.9990 chunk 84 optimal weight: 0.0170 chunk 68 optimal weight: 6.9990 chunk 223 optimal weight: 0.0770 chunk 271 optimal weight: 0.0070 chunk 219 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 328 optimal weight: 10.0000 chunk 286 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B1152 HIS C 454 ASN E 384 GLN E 713 HIS E1149 GLN F1154 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098347 restraints weight = 49671.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101694 restraints weight = 24136.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103873 restraints weight = 14704.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.105294 restraints weight = 10409.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106250 restraints weight = 8227.673| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27554 Z= 0.122 Angle : 0.742 17.770 37313 Z= 0.358 Chirality : 0.046 0.214 4171 Planarity : 0.006 0.102 4759 Dihedral : 7.759 89.451 3802 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.97 % Favored : 87.85 % Rotamer: Outliers : 3.93 % Allowed : 23.65 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.12 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.15), residues: 3291 helix: -0.39 (0.16), residues: 1180 sheet: -1.51 (0.27), residues: 377 loop : -2.26 (0.16), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 426 TYR 0.021 0.001 TYR A 588 PHE 0.020 0.001 PHE B 333 TRP 0.026 0.001 TRP F 462 HIS 0.007 0.001 HIS B1152 Details of bonding type rmsd covalent geometry : bond 0.00291 (27531) covalent geometry : angle 0.74151 (37313) hydrogen bonds : bond 0.03163 ( 579) hydrogen bonds : angle 3.96027 ( 1620) Misc. bond : bond 0.00221 ( 23) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 512 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ILE cc_start: 0.9453 (tt) cc_final: 0.9209 (tp) REVERT: A 336 ARG cc_start: 0.8099 (tpp-160) cc_final: 0.7843 (tpp80) REVERT: A 402 MET cc_start: 0.8636 (ttp) cc_final: 0.8292 (ttp) REVERT: A 524 LYS cc_start: 0.7138 (mmmt) cc_final: 0.6442 (mtmt) REVERT: A 563 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7566 (mm) REVERT: A 583 GLU cc_start: 0.8279 (pm20) cc_final: 0.8076 (pm20) REVERT: A 636 MET cc_start: 0.8581 (mmm) cc_final: 0.8121 (mpp) REVERT: B 329 LYS cc_start: 0.7902 (tppt) cc_final: 0.7285 (tppt) REVERT: B 441 ARG cc_start: 0.8475 (tpt-90) cc_final: 0.8187 (tpp80) REVERT: B 469 GLU cc_start: 0.8774 (tp30) cc_final: 0.8472 (mm-30) REVERT: B 503 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8355 (mmmm) REVERT: B 517 LYS cc_start: 0.8367 (tttt) cc_final: 0.8106 (tmtt) REVERT: B 693 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8413 (pp) REVERT: B 735 ASP cc_start: 0.9224 (t0) cc_final: 0.9014 (t0) REVERT: B 1179 ARG cc_start: 0.9059 (mtp-110) cc_final: 0.8379 (ptp-170) REVERT: C 431 ASP cc_start: 0.7811 (t0) cc_final: 0.7511 (t0) REVERT: C 449 GLU cc_start: 0.8984 (pp20) cc_final: 0.8440 (pp20) REVERT: C 478 ASP cc_start: 0.8378 (m-30) cc_final: 0.8087 (m-30) REVERT: C 526 MET cc_start: 0.8150 (ttp) cc_final: 0.7905 (ttp) REVERT: C 546 LYS cc_start: 0.8766 (tttp) cc_final: 0.8353 (ttpt) REVERT: C 704 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7956 (pp) REVERT: C 718 GLU cc_start: 0.8556 (tp30) cc_final: 0.8306 (tp30) REVERT: C 761 ARG cc_start: 0.8427 (ptt-90) cc_final: 0.8219 (ptt90) REVERT: C 1178 GLU cc_start: 0.9367 (mp0) cc_final: 0.9057 (mp0) REVERT: D 298 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7380 (mm110) REVERT: D 348 GLU cc_start: 0.8396 (tp30) cc_final: 0.7868 (tp30) REVERT: D 352 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8545 (mm110) REVERT: D 431 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8162 (p0) REVERT: D 440 ASP cc_start: 0.8554 (p0) cc_final: 0.8257 (p0) REVERT: D 526 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8338 (ttm) REVERT: D 580 ASP cc_start: 0.8193 (p0) cc_final: 0.7708 (p0) REVERT: D 585 ASP cc_start: 0.8594 (p0) cc_final: 0.8085 (p0) REVERT: D 607 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8358 (mm) REVERT: E 295 PHE cc_start: 0.8325 (m-80) cc_final: 0.7853 (m-80) REVERT: E 359 GLU cc_start: 0.8897 (tt0) cc_final: 0.8204 (tt0) REVERT: E 400 ASP cc_start: 0.9067 (t70) cc_final: 0.8743 (t0) REVERT: E 407 GLN cc_start: 0.8524 (tt0) cc_final: 0.7949 (tp40) REVERT: E 426 ARG cc_start: 0.8703 (tmm160) cc_final: 0.7712 (tmm-80) REVERT: E 630 HIS cc_start: 0.8207 (t70) cc_final: 0.7720 (t70) REVERT: E 642 ASP cc_start: 0.8896 (t0) cc_final: 0.8379 (t0) REVERT: E 695 PHE cc_start: 0.8994 (p90) cc_final: 0.8696 (p90) REVERT: E 748 ILE cc_start: 0.9257 (tp) cc_final: 0.9047 (tp) REVERT: E 1145 PHE cc_start: 0.8887 (m-80) cc_final: 0.8626 (m-80) REVERT: F 278 LEU cc_start: 0.8667 (pp) cc_final: 0.8164 (pp) REVERT: F 279 LYS cc_start: 0.8997 (ptmt) cc_final: 0.8653 (ttpp) REVERT: F 281 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7593 (ppp) REVERT: F 380 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7555 (mtm180) REVERT: F 399 MET cc_start: 0.9005 (tmm) cc_final: 0.8780 (tmm) REVERT: F 402 MET cc_start: 0.6847 (mmm) cc_final: 0.6474 (mmm) REVERT: F 403 GLU cc_start: 0.5784 (pm20) cc_final: 0.5273 (pm20) REVERT: F 472 LYS cc_start: 0.8976 (tppt) cc_final: 0.8690 (tppt) REVERT: F 630 HIS cc_start: 0.8401 (t-90) cc_final: 0.8113 (t-170) REVERT: F 639 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8375 (pp) REVERT: F 670 ASP cc_start: 0.7717 (t0) cc_final: 0.7375 (t0) REVERT: F 747 LEU cc_start: 0.9361 (mt) cc_final: 0.9069 (tt) REVERT: F 1179 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7601 (ptp-170) outliers start: 118 outliers final: 92 residues processed: 580 average time/residue: 0.1511 time to fit residues: 143.4976 Evaluate side-chains 596 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 495 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 731 TYR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 1132 THR Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1146 THR Chi-restraints excluded: chain D residue 1158 TYR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 333 PHE Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 674 TRP Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 1186 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 631 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 720 PHE Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 1142 THR Chi-restraints excluded: chain F residue 1158 TYR Chi-restraints excluded: chain F residue 1174 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 146 optimal weight: 0.0770 chunk 130 optimal weight: 0.7980 chunk 228 optimal weight: 9.9990 chunk 301 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 324 optimal weight: 6.9990 chunk 321 optimal weight: 0.0670 chunk 211 optimal weight: 0.7980 chunk 262 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1152 HIS B1159 GLN C 454 ASN E 384 GLN E 713 HIS E1149 GLN F1154 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097598 restraints weight = 49767.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.100922 restraints weight = 24241.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103080 restraints weight = 14772.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104503 restraints weight = 10482.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105452 restraints weight = 8278.215| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27554 Z= 0.135 Angle : 0.765 17.963 37313 Z= 0.367 Chirality : 0.048 0.433 4171 Planarity : 0.006 0.125 4759 Dihedral : 7.790 89.730 3802 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.70 % Favored : 88.12 % Rotamer: Outliers : 3.66 % Allowed : 23.85 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.12 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.15), residues: 3291 helix: -0.34 (0.16), residues: 1196 sheet: -1.49 (0.27), residues: 376 loop : -2.26 (0.16), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 426 TYR 0.022 0.001 TYR F 626 PHE 0.029 0.001 PHE A 595 TRP 0.022 0.001 TRP F 462 HIS 0.003 0.001 HIS F 451 Details of bonding type rmsd covalent geometry : bond 0.00326 (27531) covalent geometry : angle 0.76517 (37313) hydrogen bonds : bond 0.03323 ( 579) hydrogen bonds : angle 3.99112 ( 1620) Misc. bond : bond 0.00269 ( 23) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 496 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ILE cc_start: 0.9491 (tt) cc_final: 0.9277 (tp) REVERT: A 336 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7812 (tpp80) REVERT: A 402 MET cc_start: 0.8665 (ttp) cc_final: 0.8334 (ttp) REVERT: A 524 LYS cc_start: 0.7138 (mmmt) cc_final: 0.6439 (mtmt) REVERT: A 563 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7434 (mm) REVERT: A 577 MET cc_start: 0.8739 (mtt) cc_final: 0.8485 (mtp) REVERT: A 636 MET cc_start: 0.8576 (mmm) cc_final: 0.8105 (mpp) REVERT: B 329 LYS cc_start: 0.7903 (tppt) cc_final: 0.7409 (tppt) REVERT: B 441 ARG cc_start: 0.8473 (tpt-90) cc_final: 0.8173 (tpp80) REVERT: B 469 GLU cc_start: 0.8761 (tp30) cc_final: 0.8389 (mm-30) REVERT: B 503 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8336 (mmmm) REVERT: B 693 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8417 (pp) REVERT: B 735 ASP cc_start: 0.9231 (t0) cc_final: 0.9024 (t0) REVERT: B 1153 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8643 (mp) REVERT: B 1179 ARG cc_start: 0.9064 (mtp-110) cc_final: 0.8374 (ptp-170) REVERT: C 431 ASP cc_start: 0.7830 (t0) cc_final: 0.7538 (t0) REVERT: C 449 GLU cc_start: 0.8996 (pp20) cc_final: 0.8400 (pp20) REVERT: C 478 ASP cc_start: 0.8415 (m-30) cc_final: 0.8106 (m-30) REVERT: C 526 MET cc_start: 0.8220 (ttp) cc_final: 0.7980 (ttp) REVERT: C 546 LYS cc_start: 0.8788 (tttp) cc_final: 0.8358 (ttpt) REVERT: C 704 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8012 (pp) REVERT: C 718 GLU cc_start: 0.8555 (tp30) cc_final: 0.8310 (tp30) REVERT: C 1178 GLU cc_start: 0.9362 (mp0) cc_final: 0.9046 (mp0) REVERT: D 298 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7386 (mm110) REVERT: D 348 GLU cc_start: 0.8349 (tp30) cc_final: 0.7811 (tp30) REVERT: D 352 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8534 (mm110) REVERT: D 431 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8180 (p0) REVERT: D 440 ASP cc_start: 0.8555 (p0) cc_final: 0.8229 (p0) REVERT: D 526 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8323 (ttm) REVERT: D 580 ASP cc_start: 0.8216 (p0) cc_final: 0.7721 (p0) REVERT: D 585 ASP cc_start: 0.8603 (p0) cc_final: 0.8113 (p0) REVERT: E 295 PHE cc_start: 0.8331 (m-80) cc_final: 0.7898 (m-80) REVERT: E 359 GLU cc_start: 0.8884 (tt0) cc_final: 0.8183 (tt0) REVERT: E 400 ASP cc_start: 0.9078 (t70) cc_final: 0.8760 (t0) REVERT: E 407 GLN cc_start: 0.8534 (tt0) cc_final: 0.7998 (tp40) REVERT: E 426 ARG cc_start: 0.8692 (tmm160) cc_final: 0.7624 (tmm-80) REVERT: E 630 HIS cc_start: 0.8257 (t70) cc_final: 0.7720 (t70) REVERT: E 642 ASP cc_start: 0.8904 (t0) cc_final: 0.8381 (t0) REVERT: E 695 PHE cc_start: 0.8836 (p90) cc_final: 0.8509 (p90) REVERT: E 1145 PHE cc_start: 0.8845 (m-80) cc_final: 0.8540 (m-80) REVERT: E 1149 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8343 (pm20) REVERT: F 278 LEU cc_start: 0.8624 (pp) cc_final: 0.8128 (pp) REVERT: F 279 LYS cc_start: 0.8997 (ptmt) cc_final: 0.8655 (ttpp) REVERT: F 281 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7597 (ppp) REVERT: F 380 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7551 (mtm180) REVERT: F 399 MET cc_start: 0.9011 (tmm) cc_final: 0.8774 (tmm) REVERT: F 402 MET cc_start: 0.6823 (mmm) cc_final: 0.6452 (mmm) REVERT: F 403 GLU cc_start: 0.5893 (pm20) cc_final: 0.5343 (pm20) REVERT: F 472 LYS cc_start: 0.8968 (tppt) cc_final: 0.8710 (tppt) REVERT: F 630 HIS cc_start: 0.8433 (t-90) cc_final: 0.8170 (t-170) REVERT: F 639 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8388 (pp) REVERT: F 670 ASP cc_start: 0.7679 (t0) cc_final: 0.7355 (t0) REVERT: F 747 LEU cc_start: 0.9361 (mt) cc_final: 0.9075 (tt) REVERT: F 1179 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7626 (ptp-170) outliers start: 110 outliers final: 93 residues processed: 561 average time/residue: 0.1508 time to fit residues: 138.5233 Evaluate side-chains 587 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 484 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain B residue 1159 GLN Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 724 GLN Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 731 TYR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 1132 THR Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1146 THR Chi-restraints excluded: chain D residue 1158 TYR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 333 PHE Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 674 TRP Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 1149 GLN Chi-restraints excluded: chain E residue 1152 HIS Chi-restraints excluded: chain E residue 1186 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 343 SER Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 631 VAL Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 720 PHE Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 1142 THR Chi-restraints excluded: chain F residue 1158 TYR Chi-restraints excluded: chain F residue 1174 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 132 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 265 optimal weight: 0.3980 chunk 276 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 384 GLN E 713 HIS E1149 GLN F1154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097448 restraints weight = 49600.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100720 restraints weight = 24186.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102864 restraints weight = 14846.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104300 restraints weight = 10555.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.105252 restraints weight = 8325.140| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 27554 Z= 0.190 Angle : 0.913 59.194 37313 Z= 0.488 Chirality : 0.050 0.821 4171 Planarity : 0.006 0.124 4759 Dihedral : 7.810 89.711 3802 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.76 % Favored : 88.06 % Rotamer: Outliers : 3.56 % Allowed : 24.25 % Favored : 72.19 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.12 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.15), residues: 3291 helix: -0.33 (0.16), residues: 1196 sheet: -1.48 (0.27), residues: 376 loop : -2.27 (0.16), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 444 TYR 0.068 0.002 TYR B 578 PHE 0.020 0.001 PHE C 695 TRP 0.015 0.001 TRP F 462 HIS 0.081 0.002 HIS B1152 Details of bonding type rmsd covalent geometry : bond 0.00431 (27531) covalent geometry : angle 0.91327 (37313) hydrogen bonds : bond 0.03324 ( 579) hydrogen bonds : angle 3.99168 ( 1620) Misc. bond : bond 0.00421 ( 23) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5083.24 seconds wall clock time: 88 minutes 6.32 seconds (5286.32 seconds total)