Starting phenix.real_space_refine (version: dev) on Sun Feb 26 05:36:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jq0_9872/02_2023/6jq0_9872_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jq0_9872/02_2023/6jq0_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jq0_9872/02_2023/6jq0_9872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jq0_9872/02_2023/6jq0_9872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jq0_9872/02_2023/6jq0_9872_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jq0_9872/02_2023/6jq0_9872_neut_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A GLU 290": "OE1" <-> "OE2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "B ASP 579": "OD1" <-> "OD2" Residue "B ASP 585": "OD1" <-> "OD2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B ASP 670": "OD1" <-> "OD2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 763": "NH1" <-> "NH2" Residue "B ARG 764": "NH1" <-> "NH2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "B ASP 1129": "OD1" <-> "OD2" Residue "B TYR 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1167": "OE1" <-> "OE2" Residue "B ASP 1175": "OD1" <-> "OD2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 340": "OD1" <-> "OD2" Residue "C ARG 351": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C ARG 425": "NH1" <-> "NH2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C GLU 574": "OE1" <-> "OE2" Residue "C GLU 575": "OE1" <-> "OE2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 697": "OD1" <-> "OD2" Residue "C GLU 711": "OE1" <-> "OE2" Residue "C GLU 746": "OE1" <-> "OE2" Residue "C ARG 761": "NH1" <-> "NH2" Residue "C ARG 764": "NH1" <-> "NH2" Residue "C ASP 1148": "OD1" <-> "OD2" Residue "D PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 351": "NH1" <-> "NH2" Residue "D ARG 354": "NH1" <-> "NH2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D ASP 431": "OD1" <-> "OD2" Residue "D GLU 485": "OE1" <-> "OE2" Residue "D TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ASP 508": "OD1" <-> "OD2" Residue "D GLU 574": "OE1" <-> "OE2" Residue "D ASP 579": "OD1" <-> "OD2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D GLU 596": "OE1" <-> "OE2" Residue "D ASP 670": "OD1" <-> "OD2" Residue "D ASP 672": "OD1" <-> "OD2" Residue "D ASP 697": "OD1" <-> "OD2" Residue "D ARG 761": "NH1" <-> "NH2" Residue "D ARG 764": "NH1" <-> "NH2" Residue "E ASP 260": "OD1" <-> "OD2" Residue "E ARG 294": "NH1" <-> "NH2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 340": "OD1" <-> "OD2" Residue "E ARG 351": "NH1" <-> "NH2" Residue "E ARG 354": "NH1" <-> "NH2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E ARG 425": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E ASP 456": "OD1" <-> "OD2" Residue "E ARG 500": "NH1" <-> "NH2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "E GLU 531": "OE1" <-> "OE2" Residue "E GLU 557": "OE1" <-> "OE2" Residue "E GLU 574": "OE1" <-> "OE2" Residue "E ASP 580": "OD1" <-> "OD2" Residue "E ASP 585": "OD1" <-> "OD2" Residue "E PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 591": "NH1" <-> "NH2" Residue "E GLU 593": "OE1" <-> "OE2" Residue "E TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 648": "OE1" <-> "OE2" Residue "E GLU 746": "OE1" <-> "OE2" Residue "E ARG 761": "NH1" <-> "NH2" Residue "E ARG 764": "NH1" <-> "NH2" Residue "E GLU 1183": "OE1" <-> "OE2" Residue "F ASP 272": "OD1" <-> "OD2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F GLU 327": "OE1" <-> "OE2" Residue "F PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 340": "OD1" <-> "OD2" Residue "F ARG 351": "NH1" <-> "NH2" Residue "F ARG 354": "NH1" <-> "NH2" Residue "F ASP 374": "OD1" <-> "OD2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F ARG 426": "NH1" <-> "NH2" Residue "F ASP 431": "OD1" <-> "OD2" Residue "F GLU 461": "OE1" <-> "OE2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "F GLU 544": "OE1" <-> "OE2" Residue "F GLU 551": "OE1" <-> "OE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "F ASP 670": "OD1" <-> "OD2" Residue "F GLU 718": "OE1" <-> "OE2" Residue "F PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 761": "NH1" <-> "NH2" Residue "F ARG 763": "NH1" <-> "NH2" Residue "F ARG 764": "NH1" <-> "NH2" Residue "F GLU 768": "OE1" <-> "OE2" Residue "F ASP 1148": "OD1" <-> "OD2" Residue "F GLU 1176": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: 14.78, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 10.11 Conformation dependent library (CDL) restraints added in 4.0 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... running ksdssp... Secondary structure from input PDB file: 160 helices and 14 sheets defined 36.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.057A pdb=" N GLN A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.786A pdb=" N ARG A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 361 Processing helix chain 'A' and resid 373 through 376 No H-bonds generated for 'chain 'A' and resid 373 through 376' Processing helix chain 'A' and resid 386 through 399 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) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 441 through 452 removed outlier: 3.816A pdb=" N GLU A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N HIS A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 464 No H-bonds generated for 'chain 'A' and resid 461 through 464' Processing helix chain 'A' and resid 466 through 469 No H-bonds generated for 'chain 'A' and resid 466 through 469' Processing helix chain 'A' and resid 476 through 491 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) removed outlier: 4.119A pdb=" N ILE A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 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) removed outlier: 3.600A pdb=" N ARG A 525 " --> pdb=" O MET A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 removed outlier: 3.584A pdb=" N GLN A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.989A pdb=" N VAL A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 577' Processing helix chain 'A' and resid 618 through 625 removed outlier: 4.018A pdb=" N ILE A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN A 624 " --> pdb=" O PRO A 620 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 625' Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 649 through 660 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) Processing helix chain 'A' and resid 674 through 677 No H-bonds generated for 'chain 'A' and resid 674 through 677' Processing helix chain 'A' and resid 680 through 690 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) Processing helix chain 'A' and resid 714 through 717 No H-bonds generated for 'chain 'A' and resid 714 through 717' Processing helix chain 'A' and resid 742 through 745 No H-bonds generated for 'chain 'A' and resid 742 through 745' Processing helix chain 'A' and resid 1148 through 1151 removed outlier: 3.867A pdb=" N LEU A1151 " --> pdb=" O ASP A1148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1148 through 1151' Processing helix chain 'A' and resid 1176 through 1182 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) No H-bonds generated for 'chain 'A' and resid 1176 through 1182' Processing helix chain 'B' and resid 273 through 280 removed outlier: 3.804A pdb=" N GLU B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 No H-bonds generated for 'chain 'B' and resid 284 through 287' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.923A pdb=" N GLN B 293 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG B 294 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.573A pdb=" N CYS B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 362 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 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 386 through 399 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 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 442 through 449 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.594A pdb=" N GLU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 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 488 through 494 removed outlier: 3.572A pdb=" N ILE B 491 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 493 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.678A pdb=" N SER B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 549 removed outlier: 3.532A pdb=" N LYS B 546 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Proline residue: B 547 - end of helix No H-bonds generated for 'chain 'B' and resid 543 through 549' Processing helix chain 'B' and resid 551 through 561 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) Processing helix chain 'B' and resid 572 through 577 removed outlier: 4.689A pdb=" N MET B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 647 through 659 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) Processing helix chain 'B' and resid 671 through 676 removed outlier: 4.310A pdb=" N ASN B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.595A pdb=" N PHE B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 711 No H-bonds generated for 'chain 'B' and resid 709 through 711' Processing helix chain 'B' and resid 716 through 719 No H-bonds generated for 'chain 'B' and resid 716 through 719' Processing helix chain 'B' and resid 737 through 740 No H-bonds generated for 'chain 'B' and resid 737 through 740' Processing helix chain 'B' and resid 742 through 747 Processing helix chain 'B' and resid 1129 through 1142 removed outlier: 4.035A pdb=" N THR B1132 " --> pdb=" O ASP B1129 " (cutoff:3.500A) Proline residue: B1133 - end of helix removed outlier: 3.552A pdb=" N LEU B1137 " --> pdb=" O LEU B1134 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B1139 " --> pdb=" O GLN B1136 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP B1140 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER B1141 " --> pdb=" O LEU B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1151 removed outlier: 3.558A pdb=" N LEU B1151 " --> pdb=" O VAL B1147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1147 through 1151' Processing helix chain 'B' and resid 1153 through 1156 No H-bonds generated for 'chain 'B' and resid 1153 through 1156' Processing helix chain 'B' and resid 1158 through 1161 No H-bonds generated for 'chain 'B' and resid 1158 through 1161' Processing helix chain 'B' and resid 1171 through 1174 No H-bonds generated for 'chain 'B' and resid 1171 through 1174' Processing helix chain 'B' and resid 1177 through 1182 removed outlier: 3.598A pdb=" N VAL B1181 " --> pdb=" O CYS B1177 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 282 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 290 through 295 removed outlier: 3.825A pdb=" N ARG C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 295' Processing helix chain 'C' and resid 313 through 325 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 349 through 361 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 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 386 through 399 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) Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 443 through 450 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) Processing helix chain 'C' and resid 461 through 469 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) Processing helix chain 'C' and resid 478 through 494 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 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 509 through 511 No H-bonds generated for 'chain 'C' and resid 509 through 511' Processing helix chain 'C' and resid 516 through 523 removed outlier: 3.511A pdb=" N SER C 522 " --> pdb=" O ASP C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 548 No H-bonds generated for 'chain 'C' and resid 546 through 548' Processing helix chain 'C' and resid 554 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 572 through 577 removed outlier: 4.364A pdb=" N MET C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.692A pdb=" N THR C 594 " --> pdb=" O ARG C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 619 through 622 No H-bonds generated for 'chain 'C' and resid 619 through 622' Processing helix chain 'C' and resid 647 through 658 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) Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 680 through 692 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) Processing helix chain 'C' and resid 716 through 719 No H-bonds generated for 'chain 'C' and resid 716 through 719' Processing helix chain 'C' and resid 723 through 725 No H-bonds generated for 'chain 'C' and resid 723 through 725' Processing helix chain 'C' and resid 734 through 740 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) Processing helix chain 'C' and resid 742 through 748 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 1132 through 1142 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) removed outlier: 3.967A pdb=" N THR C1142 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1164 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 1170 through 1172 No H-bonds generated for 'chain 'C' and resid 1170 through 1172' Processing helix chain 'C' and resid 1174 through 1178 removed outlier: 3.873A pdb=" N GLU C1178 " --> pdb=" O ASP C1175 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 280 removed outlier: 3.535A pdb=" N GLN D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 314 through 322 removed outlier: 4.013A pdb=" N ALA D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 351 through 361 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) Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 387 through 395 removed outlier: 3.870A pdb=" N VAL D 392 " --> pdb=" O HIS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 443 through 450 removed outlier: 3.598A pdb=" N GLU D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 470 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) Processing helix chain 'D' and resid 479 through 494 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 500 removed outlier: 3.675A pdb=" N TYR D 499 " --> pdb=" O PRO D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 523 removed outlier: 3.724A pdb=" N SER D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 563 Proline residue: D 547 - end of helix removed outlier: 6.241A pdb=" N ASN D 550 " --> pdb=" O PRO D 547 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU D 551 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN D 554 " --> pdb=" O GLU D 551 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP D 555 " --> pdb=" O ALA D 552 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS D 558 " --> pdb=" O ASP D 555 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU D 560 " --> pdb=" O GLU D 557 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D 561 " --> pdb=" O LYS D 558 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 574 No H-bonds generated for 'chain 'D' and resid 572 through 574' Processing helix chain 'D' and resid 592 through 595 No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 615 through 617 No H-bonds generated for 'chain 'D' and resid 615 through 617' Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 647 through 658 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 671 through 675 Processing helix chain 'D' and resid 680 through 692 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) Processing helix chain 'D' and resid 734 through 740 removed outlier: 5.944A pdb=" N ILE D 738 " --> pdb=" O ASP D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 748 Processing helix chain 'D' and resid 1132 through 1137 removed outlier: 3.727A pdb=" N GLN D1136 " --> pdb=" O THR D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1154 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 1157 through 1163 removed outlier: 3.593A pdb=" N TRP D1162 " --> pdb=" O TYR D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1173 through 1179 removed outlier: 3.908A pdb=" N GLU D1178 " --> pdb=" O VAL D1174 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 282 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) Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 317 through 325 removed outlier: 3.540A pdb=" N ALA E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 361 removed outlier: 3.503A pdb=" N GLU E 358 " --> pdb=" O ARG E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 388 through 399 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) Processing helix chain 'E' and resid 443 through 450 removed outlier: 3.577A pdb=" N GLU E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 463 No H-bonds generated for 'chain 'E' and resid 461 through 463' Processing helix chain 'E' and resid 467 through 470 No H-bonds generated for 'chain 'E' and resid 467 through 470' Processing helix chain 'E' and resid 476 through 494 removed outlier: 4.281A pdb=" N ARG E 480 " --> pdb=" O GLY E 476 " (cutoff:3.500A) 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 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 517 through 525 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) Processing helix chain 'E' and resid 546 through 563 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) Processing helix chain 'E' and resid 572 through 576 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 572 through 576' Processing helix chain 'E' and resid 590 through 594 Processing helix chain 'E' and resid 619 through 625 removed outlier: 3.842A pdb=" N ILE E 622 " --> pdb=" O GLY E 619 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU E 623 " --> pdb=" O PRO E 620 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN E 625 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 639 No H-bonds generated for 'chain 'E' and resid 636 through 639' Processing helix chain 'E' and resid 647 through 658 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 680 through 688 removed outlier: 3.792A pdb=" N THR E 685 " --> pdb=" O THR E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 719 No H-bonds generated for 'chain 'E' and resid 716 through 719' Processing helix chain 'E' and resid 723 through 725 No H-bonds generated for 'chain 'E' and resid 723 through 725' Processing helix chain 'E' and resid 734 through 740 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) No H-bonds generated for 'chain 'E' and resid 734 through 740' Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 1131 through 1138 Processing helix chain 'E' and resid 1147 through 1156 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 1158 through 1163 removed outlier: 3.522A pdb=" N ASN E1163 " --> pdb=" O GLN E1159 " (cutoff:3.500A) Processing helix chain 'E' and resid 1177 through 1183 removed outlier: 3.543A pdb=" N GLU E1183 " --> pdb=" O ARG E1179 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 277 No H-bonds generated for 'chain 'F' and resid 274 through 277' Processing helix chain 'F' and resid 313 through 324 removed outlier: 3.524A pdb=" N ALA F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 361 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) Processing helix chain 'F' and resid 386 through 398 removed outlier: 3.820A pdb=" N LEU F 395 " --> pdb=" O ILE F 391 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU F 396 " --> pdb=" O VAL F 392 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU F 398 " --> pdb=" O THR F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 425 Processing helix chain 'F' and resid 442 through 447 removed outlier: 4.007A pdb=" N LYS F 446 " --> pdb=" O ASP F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 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) Processing helix chain 'F' and resid 478 through 494 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 517 through 522 Processing helix chain 'F' and resid 546 through 548 No H-bonds generated for 'chain 'F' and resid 546 through 548' Processing helix chain 'F' and resid 554 through 563 Processing helix chain 'F' and resid 615 through 617 No H-bonds generated for 'chain 'F' and resid 615 through 617' Processing helix chain 'F' and resid 619 through 623 Processing helix chain 'F' and resid 647 through 658 removed outlier: 3.565A pdb=" N LEU F 654 " --> pdb=" O SER F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 677 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) Processing helix chain 'F' and resid 680 through 687 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 723 through 725 No H-bonds generated for 'chain 'F' and resid 723 through 725' Processing helix chain 'F' and resid 742 through 748 removed outlier: 4.001A pdb=" N ILE F 748 " --> pdb=" O ILE F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 1132 through 1140 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 1147 through 1164 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 1174 through 1185 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) Processing sheet with id= A, first strand: chain 'A' and resid 433 through 435 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) removed outlier: 8.618A pdb=" N VAL A 303 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 410 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N PHE A 305 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY A 412 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N SER A 366 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ILE A 411 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 368 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ALA A 413 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 334 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 726 through 728 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) removed outlier: 3.557A pdb=" N ALA A 703 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER A 664 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU A 702 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE A 666 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LEU A 704 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE A 668 " --> pdb=" O LEU A 704 " (cutoff:3.500A) 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) Processing sheet with id= C, first strand: chain 'B' and resid 433 through 435 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) removed outlier: 8.966A pdb=" N VAL B 303 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 410 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE B 305 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY B 412 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER B 366 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ILE B 411 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 368 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA B 413 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE B 370 " --> pdb=" O ALA B 413 " (cutoff:3.500A) 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) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 604 through 607 removed outlier: 6.184A pdb=" N PHE B 701 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE B 607 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA B 703 " --> pdb=" O ILE B 607 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 433 through 435 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) removed outlier: 8.633A pdb=" N VAL C 303 " --> pdb=" O VAL C 408 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 410 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE C 305 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY C 412 " --> pdb=" O PHE C 305 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER C 366 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE C 411 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 368 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ALA C 413 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE C 370 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER C 332 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N PHE C 369 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR C 334 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP C 371 " --> pdb=" O TYR C 334 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG C 336 " --> pdb=" O ASP C 371 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 702 through 704 removed outlier: 7.038A pdb=" N PHE C 605 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 727 " --> pdb=" O LEU C 606 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 630 through 633 removed outlier: 4.014A pdb=" N GLN C 632 " --> pdb=" O ILE C 665 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 667 " --> pdb=" O GLN C 632 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 332 through 335 removed outlier: 3.752A pdb=" N PHE D 369 " --> pdb=" O TYR D 334 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 664 through 669 Processing sheet with id= J, first strand: chain 'E' and resid 433 through 436 removed outlier: 6.665A pdb=" N LEU E 304 " --> pdb=" O PHE E 434 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE E 436 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N HIS E 306 " --> pdb=" O PHE E 436 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 307 " --> pdb=" O THR E 414 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER E 366 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ILE E 411 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE E 368 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA E 413 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE E 370 " --> pdb=" O ALA E 413 " (cutoff:3.500A) 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) Processing sheet with id= K, first strand: chain 'E' and resid 630 through 633 removed outlier: 3.907A pdb=" N GLN E 632 " --> pdb=" O ILE E 665 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR E 667 " --> pdb=" O GLN E 632 " (cutoff:3.500A) Processing sheet with id= L, 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: 3.811A pdb=" N ILE F 409 " --> pdb=" O SER F 366 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 630 through 633 removed outlier: 3.628A pdb=" N LEU F 700 " --> pdb=" O SER F 664 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 302 through 304 removed outlier: 3.853A pdb=" N ASP F 431 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU F 304 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU F 433 " --> pdb=" O LEU F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= N 419 hydrogen bonds defined for protein. 1188 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: 7.56 Time building geometry restraints manager: 10.90 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: 98.93 - 106.44: 1169 106.44 - 113.96: 15588 113.96 - 121.47: 14169 121.47 - 128.99: 6154 128.99 - 136.50: 233 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: 14593 17.99 - 35.98: 1912 35.98 - 53.96: 328 53.96 - 71.95: 61 71.95 - 89.94: 28 Dihedral angle restraints: 16922 sinusoidal: 7129 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 16919 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: 5946 2.77 - 3.30: 23402 3.30 - 3.83: 40056 3.83 - 4.37: 44329 4.37 - 4.90: 75082 Nonbonded interactions: 188815 Sorted by model distance: nonbonded pdb=" N LYS B 313 " pdb=" O1A ATP B1201 " model vdw 2.235 2.520 nonbonded pdb=" OG1 THR E1146 " pdb=" OE1 GLN E1149 " model vdw 2.258 2.440 nonbonded pdb=" OG1 THR E 314 " pdb=" O2A ATP E1201 " model vdw 2.258 2.440 nonbonded pdb=" OG1 THR D 314 " pdb=" O2A ATP D1201 " model vdw 2.289 2.440 nonbonded pdb=" O PHE D 519 " pdb=" OG SER D 522 " model vdw 2.291 2.440 ... (remaining 188810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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. 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: 2.450 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: 10.820 Check model and map are aligned: 0.390 Process input model: 64.050 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 27531 Z= 0.478 Angle : 1.211 21.791 37313 Z= 0.708 Chirality : 0.063 0.372 4171 Planarity : 0.009 0.116 4759 Dihedral : 16.267 89.941 10534 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.97 % Favored : 86.48 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 6.36 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.59 (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 *********************** 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 fitting. rotamer outliers: 19 poor density : 644 time to evaluate : 3.257 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 outliers start: 19 outliers final: 5 residues processed: 658 average time/residue: 0.4202 time to fit residues: 424.3816 Evaluate side-chains 476 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 471 time to evaluate : 3.200 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2316 time to fit residues: 6.8380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 168 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 258 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 673 ASN B 673 ASN B1149 GLN B1152 HIS B1159 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 454 ASN D 489 ASN D 589 GLN 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 277 GLN 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 27531 Z= 0.210 Angle : 0.773 16.297 37313 Z= 0.382 Chirality : 0.047 0.217 4171 Planarity : 0.007 0.107 4759 Dihedral : 8.146 89.391 3642 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.37 % Favored : 87.33 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 4.66 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.12), residues: 3291 helix: -3.21 (0.11), residues: 1134 sheet: -2.24 (0.26), residues: 351 loop : -2.95 (0.14), residues: 1806 *********************** 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 621 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 532 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 42 residues processed: 581 average time/residue: 0.3759 time to fit residues: 351.2117 Evaluate side-chains 505 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 463 time to evaluate : 3.189 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2422 time to fit residues: 23.5050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 324 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 297 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 240 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 ASN D 653 HIS E 384 GLN E 386 GLN E 407 GLN E1152 HIS ** F 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 27531 Z= 0.288 Angle : 0.778 17.326 37313 Z= 0.382 Chirality : 0.049 0.223 4171 Planarity : 0.006 0.107 4759 Dihedral : 7.823 78.436 3642 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.28 % Favored : 86.33 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 4.66 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.14), residues: 3291 helix: -2.28 (0.13), residues: 1162 sheet: -1.94 (0.27), residues: 353 loop : -2.76 (0.14), residues: 1776 *********************** 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 588 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 492 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 45 residues processed: 558 average time/residue: 0.3609 time to fit residues: 325.8391 Evaluate side-chains 502 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 457 time to evaluate : 3.131 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2341 time to fit residues: 24.2325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 285 optimal weight: 7.9990 chunk 85 optimal weight: 0.2980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 GLN C 454 ASN E 384 GLN F 415 ASN F 645 GLN F1154 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 27531 Z= 0.244 Angle : 0.750 16.474 37313 Z= 0.366 Chirality : 0.048 0.230 4171 Planarity : 0.006 0.102 4759 Dihedral : 7.506 76.787 3642 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.46 % Favored : 87.27 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 3.81 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.14), residues: 3291 helix: -1.71 (0.14), residues: 1173 sheet: -1.85 (0.27), residues: 365 loop : -2.63 (0.15), residues: 1753 *********************** 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 588 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 512 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 45 residues processed: 558 average time/residue: 0.3675 time to fit residues: 330.2453 Evaluate side-chains 514 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 469 time to evaluate : 3.543 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2562 time to fit residues: 26.0651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 chunk 237 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 220 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 384 GLN E 407 GLN F1154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 27531 Z= 0.181 Angle : 0.714 16.821 37313 Z= 0.344 Chirality : 0.046 0.231 4171 Planarity : 0.006 0.098 4759 Dihedral : 7.125 75.503 3642 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.31 % Favored : 87.45 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 3.39 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.15), residues: 3291 helix: -1.22 (0.15), residues: 1163 sheet: -1.63 (0.27), residues: 365 loop : -2.45 (0.15), residues: 1763 *********************** 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 582 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 523 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 26 residues processed: 559 average time/residue: 0.3694 time to fit residues: 337.2582 Evaluate side-chains 506 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 480 time to evaluate : 3.524 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.2618 time to fit residues: 17.5074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.0670 chunk 287 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 454 ASN E 384 GLN F1154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 27531 Z= 0.266 Angle : 0.754 19.137 37313 Z= 0.363 Chirality : 0.048 0.248 4171 Planarity : 0.006 0.104 4759 Dihedral : 7.163 76.851 3642 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.70 % Favored : 86.99 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.97 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.15), residues: 3291 helix: -1.14 (0.15), residues: 1195 sheet: -1.63 (0.28), residues: 366 loop : -2.48 (0.15), residues: 1730 *********************** 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 558 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 494 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 43 residues processed: 531 average time/residue: 0.3628 time to fit residues: 315.2193 Evaluate side-chains 520 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 477 time to evaluate : 3.227 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 43 outliers final: 1 residues processed: 43 average time/residue: 0.2374 time to fit residues: 23.8944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 181 optimal weight: 0.0170 chunk 233 optimal weight: 0.0170 chunk 180 optimal weight: 0.8980 chunk 268 optimal weight: 0.0470 chunk 178 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 199 optimal weight: 0.1980 chunk 193 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 384 GLN E 415 ASN ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 27531 Z= 0.174 Angle : 0.733 19.473 37313 Z= 0.347 Chirality : 0.046 0.185 4171 Planarity : 0.005 0.103 4759 Dihedral : 6.798 78.062 3642 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.36 % Favored : 88.45 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.12 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.15), residues: 3291 helix: -0.85 (0.16), residues: 1152 sheet: -1.45 (0.28), residues: 365 loop : -2.30 (0.15), residues: 1774 *********************** 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 569 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 541 time to evaluate : 3.368 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 outliers start: 28 outliers final: 14 residues processed: 556 average time/residue: 0.3826 time to fit residues: 342.4688 Evaluate side-chains 497 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 483 time to evaluate : 3.352 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2619 time to fit residues: 11.5500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.0870 chunk 127 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 0.0670 chunk 61 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 454 ASN D 296 ASN E 384 GLN E 386 GLN ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 27531 Z= 0.178 Angle : 0.731 18.733 37313 Z= 0.345 Chirality : 0.046 0.206 4171 Planarity : 0.006 0.119 4759 Dihedral : 6.672 78.137 3642 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.61 % Favored : 88.21 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.12 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.15), residues: 3291 helix: -0.72 (0.16), residues: 1170 sheet: -1.31 (0.28), residues: 362 loop : -2.26 (0.15), residues: 1759 *********************** 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 549 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 513 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 531 average time/residue: 0.3780 time to fit residues: 325.1679 Evaluate side-chains 498 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 479 time to evaluate : 3.226 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.2541 time to fit residues: 13.7537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 9.9990 chunk 304 optimal weight: 8.9990 chunk 278 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 232 optimal weight: 0.0270 chunk 90 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN E 384 GLN ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 27531 Z= 0.235 Angle : 0.764 18.538 37313 Z= 0.364 Chirality : 0.047 0.211 4171 Planarity : 0.006 0.126 4759 Dihedral : 6.773 80.801 3642 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.22 % Favored : 87.51 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.12 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.15), residues: 3291 helix: -0.61 (0.16), residues: 1185 sheet: -1.44 (0.28), residues: 375 loop : -2.26 (0.16), residues: 1731 *********************** 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 510 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 484 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 494 average time/residue: 0.3880 time to fit residues: 312.9768 Evaluate side-chains 485 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 467 time to evaluate : 3.213 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.2499 time to fit residues: 12.8292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 8.9990 chunk 313 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 328 optimal weight: 20.0000 chunk 302 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN C 454 ASN E 384 GLN ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 ASN F 630 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 27531 Z= 0.202 Angle : 0.760 18.931 37313 Z= 0.358 Chirality : 0.046 0.201 4171 Planarity : 0.006 0.125 4759 Dihedral : 6.724 83.513 3642 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.94 % Favored : 87.88 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.12 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.15), residues: 3291 helix: -0.46 (0.16), residues: 1186 sheet: -1.37 (0.28), residues: 375 loop : -2.26 (0.16), residues: 1730 ********************** 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 495 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 480 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 485 average time/residue: 0.3872 time to fit residues: 304.1486 Evaluate side-chains 477 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 466 time to evaluate : 3.532 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2865 time to fit residues: 10.4731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 0.0980 chunk 278 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 262 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 48 optimal weight: 8.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094037 restraints weight = 50400.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097178 restraints weight = 25003.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.099225 restraints weight = 15503.102| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 27531 Z= 0.305 Angle : 0.812 18.871 37313 Z= 0.388 Chirality : 0.049 0.228 4171 Planarity : 0.006 0.130 4759 Dihedral : 7.026 86.797 3642 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.40 % Favored : 86.30 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.16 % Twisted Proline : 2.54 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 3291 helix: -0.52 (0.16), residues: 1192 sheet: -1.47 (0.28), residues: 367 loop : -2.29 (0.16), residues: 1732 =============================================================================== Job complete usr+sys time: 6136.05 seconds wall clock time: 112 minutes 10.13 seconds (6730.13 seconds total)