Starting phenix.real_space_refine on Sun Sep 29 21:22:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/09_2024/5vc7_8658_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/09_2024/5vc7_8658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/09_2024/5vc7_8658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/09_2024/5vc7_8658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/09_2024/5vc7_8658_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/09_2024/5vc7_8658_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 60 5.16 5 C 14760 2.51 5 N 4050 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23298 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 3821 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 275 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, E, D, G, F Time building chain proxies: 10.75, per 1000 atoms: 0.46 Number of scatterers: 23298 At special positions: 0 Unit cell: (146.45, 137.75, 97.15, 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 60 16.00 P 36 15.00 O 4392 8.00 N 4050 7.00 C 14760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.81 Conformation dependent library (CDL) restraints added in 3.6 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 18 sheets defined 56.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 195 through 212 Proline residue: A 209 - end of helix removed outlier: 3.671A pdb=" N HIS A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.558A pdb=" N LEU A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.759A pdb=" N ALA A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.113A pdb=" N MET A 261 " --> pdb=" O GLY A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 261' Processing helix chain 'A' and resid 267 through 282 removed outlier: 3.592A pdb=" N ILE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 321 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.672A pdb=" N LYS A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.541A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 418 removed outlier: 3.921A pdb=" N ARG A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 422 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.636A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 472 through 489 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 513 through 525 removed outlier: 3.764A pdb=" N LYS A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.625A pdb=" N LEU A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.569A pdb=" N PHE A 553 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.504A pdb=" N ILE A 572 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.661A pdb=" N THR A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.726A pdb=" N THR A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 637 through 650 removed outlier: 4.245A pdb=" N SER A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.749A pdb=" N ALA A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 690 removed outlier: 3.603A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.717A pdb=" N ALA A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 removed outlier: 3.766A pdb=" N LYS A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 195 through 212 Proline residue: C 209 - end of helix removed outlier: 3.672A pdb=" N HIS C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 219 removed outlier: 3.558A pdb=" N LEU C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 removed outlier: 3.760A pdb=" N ALA C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 removed outlier: 4.113A pdb=" N MET C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 257 through 261' Processing helix chain 'C' and resid 267 through 282 removed outlier: 3.593A pdb=" N ILE C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 321 Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.672A pdb=" N LYS C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 393 removed outlier: 3.540A pdb=" N ALA C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 418 removed outlier: 3.921A pdb=" N ARG C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 422 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.636A pdb=" N PHE C 442 " --> pdb=" O THR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 472 through 489 Proline residue: C 486 - end of helix Processing helix chain 'C' and resid 489 through 495 Processing helix chain 'C' and resid 513 through 525 removed outlier: 3.763A pdb=" N LYS C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 540 removed outlier: 3.624A pdb=" N LEU C 538 " --> pdb=" O GLY C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 3.569A pdb=" N PHE C 553 " --> pdb=" O ILE C 549 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 573 removed outlier: 3.505A pdb=" N ILE C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 586 removed outlier: 3.661A pdb=" N THR C 585 " --> pdb=" O ASP C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.726A pdb=" N THR C 594 " --> pdb=" O ASN C 590 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 637 through 650 removed outlier: 4.246A pdb=" N SER C 643 " --> pdb=" O GLU C 639 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS C 648 " --> pdb=" O ILE C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 667 removed outlier: 3.750A pdb=" N ALA C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 690 removed outlier: 3.602A pdb=" N LEU C 675 " --> pdb=" O VAL C 671 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C 684 " --> pdb=" O ARG C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 706 removed outlier: 3.716A pdb=" N ALA C 704 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 724 removed outlier: 3.766A pdb=" N LYS C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 195 through 212 Proline residue: D 209 - end of helix removed outlier: 3.671A pdb=" N HIS D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 219 removed outlier: 3.558A pdb=" N LEU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 249 removed outlier: 3.759A pdb=" N ALA D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 261 removed outlier: 4.113A pdb=" N MET D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 257 through 261' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.592A pdb=" N ILE D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 321 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 359 through 371 removed outlier: 3.672A pdb=" N LYS D 364 " --> pdb=" O ARG D 360 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU D 365 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 393 removed outlier: 3.541A pdb=" N ALA D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 392 " --> pdb=" O GLU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 418 removed outlier: 3.921A pdb=" N ARG D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 422 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.636A pdb=" N PHE D 442 " --> pdb=" O THR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 472 through 489 Proline residue: D 486 - end of helix Processing helix chain 'D' and resid 489 through 495 Processing helix chain 'D' and resid 513 through 525 removed outlier: 3.764A pdb=" N LYS D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.625A pdb=" N LEU D 538 " --> pdb=" O GLY D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 560 removed outlier: 3.569A pdb=" N PHE D 553 " --> pdb=" O ILE D 549 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 554 " --> pdb=" O ARG D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 573 removed outlier: 3.505A pdb=" N ILE D 572 " --> pdb=" O GLU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 removed outlier: 3.661A pdb=" N THR D 585 " --> pdb=" O ASP D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.726A pdb=" N THR D 594 " --> pdb=" O ASN D 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 637 through 650 removed outlier: 4.245A pdb=" N SER D 643 " --> pdb=" O GLU D 639 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS D 648 " --> pdb=" O ILE D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 667 removed outlier: 3.750A pdb=" N ALA D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 690 removed outlier: 3.603A pdb=" N LEU D 675 " --> pdb=" O VAL D 671 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET D 684 " --> pdb=" O ARG D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 706 removed outlier: 3.717A pdb=" N ALA D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 724 removed outlier: 3.766A pdb=" N LYS D 718 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 192 Processing helix chain 'E' and resid 195 through 212 Proline residue: E 209 - end of helix removed outlier: 3.672A pdb=" N HIS E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 219 removed outlier: 3.559A pdb=" N LEU E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 249 removed outlier: 3.760A pdb=" N ALA E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG E 242 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 261 removed outlier: 4.113A pdb=" N MET E 261 " --> pdb=" O GLY E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 257 through 261' Processing helix chain 'E' and resid 267 through 282 removed outlier: 3.592A pdb=" N ILE E 275 " --> pdb=" O LYS E 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE E 276 " --> pdb=" O LEU E 272 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 321 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 359 through 371 removed outlier: 3.672A pdb=" N LYS E 364 " --> pdb=" O ARG E 360 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU E 365 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 393 removed outlier: 3.540A pdb=" N ALA E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP E 392 " --> pdb=" O GLU E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 418 removed outlier: 3.921A pdb=" N ARG E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG E 416 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR E 417 " --> pdb=" O ALA E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 422 Processing helix chain 'E' and resid 438 through 446 removed outlier: 3.636A pdb=" N PHE E 442 " --> pdb=" O THR E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 469 Processing helix chain 'E' and resid 472 through 489 Proline residue: E 486 - end of helix Processing helix chain 'E' and resid 489 through 495 Processing helix chain 'E' and resid 513 through 525 removed outlier: 3.764A pdb=" N LYS E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 540 removed outlier: 3.624A pdb=" N LEU E 538 " --> pdb=" O GLY E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 560 removed outlier: 3.569A pdb=" N PHE E 553 " --> pdb=" O ILE E 549 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS E 554 " --> pdb=" O ARG E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 573 removed outlier: 3.505A pdb=" N ILE E 572 " --> pdb=" O GLU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 586 removed outlier: 3.661A pdb=" N THR E 585 " --> pdb=" O ASP E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.725A pdb=" N THR E 594 " --> pdb=" O ASN E 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 637 through 650 removed outlier: 4.246A pdb=" N SER E 643 " --> pdb=" O GLU E 639 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E 646 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS E 648 " --> pdb=" O ILE E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 667 removed outlier: 3.750A pdb=" N ALA E 664 " --> pdb=" O LEU E 660 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR E 667 " --> pdb=" O ILE E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 690 removed outlier: 3.603A pdb=" N LEU E 675 " --> pdb=" O VAL E 671 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET E 684 " --> pdb=" O ARG E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 706 removed outlier: 3.716A pdb=" N ALA E 704 " --> pdb=" O ASN E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 724 removed outlier: 3.766A pdb=" N LYS E 718 " --> pdb=" O GLU E 714 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'F' and resid 195 through 212 Proline residue: F 209 - end of helix removed outlier: 3.671A pdb=" N HIS F 212 " --> pdb=" O LEU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 removed outlier: 3.558A pdb=" N LEU F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 249 removed outlier: 3.760A pdb=" N ALA F 241 " --> pdb=" O LYS F 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG F 242 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA F 243 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER F 248 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 261 removed outlier: 4.113A pdb=" N MET F 261 " --> pdb=" O GLY F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 257 through 261' Processing helix chain 'F' and resid 267 through 282 removed outlier: 3.591A pdb=" N ILE F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU F 280 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR F 282 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 321 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 359 through 371 removed outlier: 3.672A pdb=" N LYS F 364 " --> pdb=" O ARG F 360 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR F 371 " --> pdb=" O LEU F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 393 removed outlier: 3.541A pdb=" N ALA F 391 " --> pdb=" O LEU F 387 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP F 392 " --> pdb=" O GLU F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 418 removed outlier: 3.920A pdb=" N ARG F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG F 416 " --> pdb=" O ASN F 412 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR F 417 " --> pdb=" O ALA F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 422 Processing helix chain 'F' and resid 438 through 446 removed outlier: 3.636A pdb=" N PHE F 442 " --> pdb=" O THR F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 469 Processing helix chain 'F' and resid 472 through 489 Proline residue: F 486 - end of helix Processing helix chain 'F' and resid 489 through 495 Processing helix chain 'F' and resid 513 through 525 removed outlier: 3.764A pdb=" N LYS F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 540 removed outlier: 3.625A pdb=" N LEU F 538 " --> pdb=" O GLY F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 560 removed outlier: 3.569A pdb=" N PHE F 553 " --> pdb=" O ILE F 549 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 554 " --> pdb=" O ARG F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 573 removed outlier: 3.504A pdb=" N ILE F 572 " --> pdb=" O GLU F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 586 removed outlier: 3.660A pdb=" N THR F 585 " --> pdb=" O ASP F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.726A pdb=" N THR F 594 " --> pdb=" O ASN F 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP F 597 " --> pdb=" O LEU F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 637 through 650 removed outlier: 4.245A pdb=" N SER F 643 " --> pdb=" O GLU F 639 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS F 646 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS F 648 " --> pdb=" O ILE F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 667 removed outlier: 3.749A pdb=" N ALA F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR F 667 " --> pdb=" O ILE F 663 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 690 removed outlier: 3.603A pdb=" N LEU F 675 " --> pdb=" O VAL F 671 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET F 684 " --> pdb=" O ARG F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 706 removed outlier: 3.716A pdb=" N ALA F 704 " --> pdb=" O ASN F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 724 removed outlier: 3.766A pdb=" N LYS F 718 " --> pdb=" O GLU F 714 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 192 Processing helix chain 'G' and resid 195 through 212 Proline residue: G 209 - end of helix removed outlier: 3.671A pdb=" N HIS G 212 " --> pdb=" O LEU G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 219 removed outlier: 3.558A pdb=" N LEU G 219 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 249 removed outlier: 3.760A pdb=" N ALA G 241 " --> pdb=" O LYS G 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 243 " --> pdb=" O LEU G 239 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 261 removed outlier: 4.113A pdb=" N MET G 261 " --> pdb=" O GLY G 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 257 through 261' Processing helix chain 'G' and resid 267 through 282 removed outlier: 3.592A pdb=" N ILE G 275 " --> pdb=" O LYS G 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE G 276 " --> pdb=" O LEU G 272 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU G 280 " --> pdb=" O PHE G 276 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR G 282 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 321 Processing helix chain 'G' and resid 341 through 345 Processing helix chain 'G' and resid 359 through 371 removed outlier: 3.672A pdb=" N LYS G 364 " --> pdb=" O ARG G 360 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 365 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR G 371 " --> pdb=" O LEU G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 393 removed outlier: 3.541A pdb=" N ALA G 391 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP G 392 " --> pdb=" O GLU G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 418 removed outlier: 3.921A pdb=" N ARG G 407 " --> pdb=" O ALA G 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG G 416 " --> pdb=" O ASN G 412 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 422 Processing helix chain 'G' and resid 438 through 446 removed outlier: 3.636A pdb=" N PHE G 442 " --> pdb=" O THR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 469 Processing helix chain 'G' and resid 472 through 489 Proline residue: G 486 - end of helix Processing helix chain 'G' and resid 489 through 495 Processing helix chain 'G' and resid 513 through 525 removed outlier: 3.764A pdb=" N LYS G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 540 removed outlier: 3.625A pdb=" N LEU G 538 " --> pdb=" O GLY G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 560 removed outlier: 3.569A pdb=" N PHE G 553 " --> pdb=" O ILE G 549 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS G 554 " --> pdb=" O ARG G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 573 removed outlier: 3.504A pdb=" N ILE G 572 " --> pdb=" O GLU G 568 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 586 removed outlier: 3.661A pdb=" N THR G 585 " --> pdb=" O ASP G 581 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.726A pdb=" N THR G 594 " --> pdb=" O ASN G 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP G 597 " --> pdb=" O LEU G 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 623 Processing helix chain 'G' and resid 637 through 650 removed outlier: 4.244A pdb=" N SER G 643 " --> pdb=" O GLU G 639 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS G 646 " --> pdb=" O LEU G 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS G 648 " --> pdb=" O ILE G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 660 through 667 removed outlier: 3.749A pdb=" N ALA G 664 " --> pdb=" O LEU G 660 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR G 667 " --> pdb=" O ILE G 663 " (cutoff:3.500A) Processing helix chain 'G' and resid 671 through 690 removed outlier: 3.602A pdb=" N LEU G 675 " --> pdb=" O VAL G 671 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET G 684 " --> pdb=" O ARG G 680 " (cutoff:3.500A) Processing helix chain 'G' and resid 697 through 706 removed outlier: 3.715A pdb=" N ALA G 704 " --> pdb=" O ASN G 700 " (cutoff:3.500A) Processing helix chain 'G' and resid 713 through 724 removed outlier: 3.766A pdb=" N LYS G 718 " --> pdb=" O GLU G 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 333 removed outlier: 8.636A pdb=" N THR A 333 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 229 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 228 " --> pdb=" O ILE A 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 6.571A pdb=" N ILE A 255 " --> pdb=" O ASP A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 528 through 533 removed outlier: 7.120A pdb=" N ASN A 528 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE A 565 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 530 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP A 567 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 532 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY A 503 " --> pdb=" O LYS A 629 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE A 631 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 505 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 332 through 333 removed outlier: 8.636A pdb=" N THR C 333 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU C 229 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE C 228 " --> pdb=" O ILE C 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.572A pdb=" N ILE C 255 " --> pdb=" O ASP C 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 528 through 533 removed outlier: 7.119A pdb=" N ASN C 528 " --> pdb=" O ILE C 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE C 565 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 530 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP C 567 " --> pdb=" O ILE C 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 532 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY C 503 " --> pdb=" O LYS C 629 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE C 631 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 505 " --> pdb=" O ILE C 631 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 332 through 333 removed outlier: 8.636A pdb=" N THR D 333 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU D 229 " --> pdb=" O THR D 333 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE D 228 " --> pdb=" O ILE D 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 255 through 256 removed outlier: 6.571A pdb=" N ILE D 255 " --> pdb=" O ASP D 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 528 through 533 removed outlier: 7.120A pdb=" N ASN D 528 " --> pdb=" O ILE D 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE D 565 " --> pdb=" O ASN D 528 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE D 530 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP D 567 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE D 532 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY D 503 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE D 631 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU D 505 " --> pdb=" O ILE D 631 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 332 through 333 removed outlier: 8.635A pdb=" N THR E 333 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU E 229 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE E 228 " --> pdb=" O ILE E 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 255 through 256 removed outlier: 6.572A pdb=" N ILE E 255 " --> pdb=" O ASP E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 528 through 533 removed outlier: 7.119A pdb=" N ASN E 528 " --> pdb=" O ILE E 563 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE E 565 " --> pdb=" O ASN E 528 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE E 530 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP E 567 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE E 532 " --> pdb=" O ASP E 567 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY E 503 " --> pdb=" O LYS E 629 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE E 631 " --> pdb=" O GLY E 503 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU E 505 " --> pdb=" O ILE E 631 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 332 through 333 removed outlier: 8.636A pdb=" N THR F 333 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU F 229 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE F 228 " --> pdb=" O ILE F 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 255 through 256 removed outlier: 6.571A pdb=" N ILE F 255 " --> pdb=" O ASP F 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 528 through 533 removed outlier: 7.120A pdb=" N ASN F 528 " --> pdb=" O ILE F 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE F 565 " --> pdb=" O ASN F 528 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE F 530 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP F 567 " --> pdb=" O ILE F 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE F 532 " --> pdb=" O ASP F 567 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY F 503 " --> pdb=" O LYS F 629 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE F 631 " --> pdb=" O GLY F 503 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU F 505 " --> pdb=" O ILE F 631 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 332 through 333 removed outlier: 8.636A pdb=" N THR G 333 " --> pdb=" O VAL G 227 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU G 229 " --> pdb=" O THR G 333 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE G 228 " --> pdb=" O ILE G 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 255 through 256 removed outlier: 6.571A pdb=" N ILE G 255 " --> pdb=" O ASP G 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 528 through 533 removed outlier: 7.119A pdb=" N ASN G 528 " --> pdb=" O ILE G 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE G 565 " --> pdb=" O ASN G 528 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE G 530 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP G 567 " --> pdb=" O ILE G 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE G 532 " --> pdb=" O ASP G 567 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY G 503 " --> pdb=" O LYS G 629 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE G 631 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU G 505 " --> pdb=" O ILE G 631 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2790 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: 7.12 Time building geometry restraints manager: 8.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3925 1.32 - 1.44: 5552 1.44 - 1.56: 14073 1.56 - 1.68: 60 1.68 - 1.80: 114 Bond restraints: 23724 Sorted by residual: bond pdb=" C4 ATP C 801 " pdb=" C5 ATP C 801 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.33e+01 bond pdb=" C4 ATP E 801 " pdb=" C5 ATP E 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.18e+01 bond pdb=" C4 ATP G 801 " pdb=" C5 ATP G 801 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.13e+01 ... (remaining 23719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 31907 4.54 - 9.08: 523 9.08 - 13.62: 80 13.62 - 18.16: 10 18.16 - 22.70: 24 Bond angle restraints: 32544 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 117.17 22.70 1.00e+00 1.00e+00 5.15e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 117.19 22.68 1.00e+00 1.00e+00 5.14e+02 angle pdb=" PB ATP D 801 " pdb=" O3B ATP D 801 " pdb=" PG ATP D 801 " ideal model delta sigma weight residual 139.87 117.21 22.66 1.00e+00 1.00e+00 5.13e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 117.22 22.65 1.00e+00 1.00e+00 5.13e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 117.23 22.64 1.00e+00 1.00e+00 5.12e+02 ... (remaining 32539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 13626 16.47 - 32.94: 630 32.94 - 49.40: 162 49.40 - 65.87: 90 65.87 - 82.34: 48 Dihedral angle restraints: 14556 sinusoidal: 5166 harmonic: 9390 Sorted by residual: dihedral pdb=" CA ILE G 292 " pdb=" C ILE G 292 " pdb=" N ASP G 293 " pdb=" CA ASP G 293 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ILE D 292 " pdb=" C ILE D 292 " pdb=" N ASP D 293 " pdb=" CA ASP D 293 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ILE F 292 " pdb=" C ILE F 292 " pdb=" N ASP F 293 " pdb=" CA ASP F 293 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 14553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3229 0.078 - 0.155: 526 0.155 - 0.233: 142 0.233 - 0.310: 57 0.310 - 0.388: 12 Chirality restraints: 3966 Sorted by residual: chirality pdb=" CA LEU C 210 " pdb=" N LEU C 210 " pdb=" C LEU C 210 " pdb=" CB LEU C 210 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA LEU D 210 " pdb=" N LEU D 210 " pdb=" C LEU D 210 " pdb=" CB LEU D 210 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA LEU F 210 " pdb=" N LEU F 210 " pdb=" C LEU F 210 " pdb=" CB LEU F 210 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 3963 not shown) Planarity restraints: 4188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 339 " 0.013 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ILE D 339 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE D 339 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP D 340 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 229 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C LEU C 229 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU C 229 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR C 230 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 206 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C ILE G 206 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE G 206 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU G 207 " 0.014 2.00e-02 2.50e+03 ... (remaining 4185 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.92: 192 1.92 - 2.66: 1496 2.66 - 3.41: 39449 3.41 - 4.15: 54544 4.15 - 4.90: 91732 Nonbonded interactions: 187413 Sorted by model distance: nonbonded pdb=" NH2 ARG F 344 " pdb=" OE2 GLU F 352 " model vdw 1.173 3.120 nonbonded pdb=" NH2 ARG C 344 " pdb=" OE2 GLU C 352 " model vdw 1.173 3.120 nonbonded pdb=" NH2 ARG D 344 " pdb=" OE2 GLU D 352 " model vdw 1.174 3.120 nonbonded pdb=" NH2 ARG A 344 " pdb=" OE2 GLU A 352 " model vdw 1.174 3.120 nonbonded pdb=" NH2 ARG E 344 " pdb=" OE2 GLU E 352 " model vdw 1.174 3.120 ... (remaining 187408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 51.260 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 0.080 23724 Z= 0.503 Angle : 1.496 22.696 32544 Z= 1.133 Chirality : 0.070 0.388 3966 Planarity : 0.005 0.049 4188 Dihedral : 12.725 82.340 8496 Min Nonbonded Distance : 1.173 Molprobity Statistics. All-atom Clashscore : 117.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 1.48 % Favored : 98.15 % Rotamer: Outliers : 7.14 % Allowed : 6.29 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3252 helix: -1.83 (0.13), residues: 1374 sheet: -0.36 (0.24), residues: 396 loop : -0.87 (0.14), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 541 HIS 0.005 0.002 HIS A 648 PHE 0.018 0.001 PHE A 349 TYR 0.017 0.001 TYR A 189 ARG 0.008 0.001 ARG G 641 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 866 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8189 (mt) REVERT: A 287 ILE cc_start: 0.7490 (mm) cc_final: 0.7101 (mm) REVERT: A 315 LEU cc_start: 0.8135 (mp) cc_final: 0.7855 (mt) REVERT: A 474 ASP cc_start: 0.8005 (p0) cc_final: 0.7575 (p0) REVERT: A 532 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7477 (mm) REVERT: A 568 GLU cc_start: 0.8609 (mp0) cc_final: 0.8255 (mt-10) REVERT: A 570 ASP cc_start: 0.8729 (p0) cc_final: 0.8463 (p0) REVERT: A 687 TYR cc_start: 0.8040 (t80) cc_final: 0.7604 (t80) REVERT: C 240 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8314 (mt) REVERT: C 287 ILE cc_start: 0.7505 (mm) cc_final: 0.7040 (mm) REVERT: C 315 LEU cc_start: 0.8214 (mp) cc_final: 0.7929 (mt) REVERT: C 390 MET cc_start: 0.7299 (mtp) cc_final: 0.6769 (mtp) REVERT: C 532 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7679 (mm) REVERT: C 579 THR cc_start: 0.8476 (m) cc_final: 0.8059 (m) REVERT: C 616 ILE cc_start: 0.9212 (mm) cc_final: 0.8819 (mm) REVERT: D 240 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8442 (mt) REVERT: D 287 ILE cc_start: 0.7660 (mm) cc_final: 0.7378 (mm) REVERT: D 315 LEU cc_start: 0.8132 (mp) cc_final: 0.7853 (mt) REVERT: D 570 ASP cc_start: 0.8869 (p0) cc_final: 0.8520 (p0) REVERT: E 240 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8186 (mt) REVERT: E 287 ILE cc_start: 0.7479 (mm) cc_final: 0.7092 (mm) REVERT: E 315 LEU cc_start: 0.8128 (mp) cc_final: 0.7853 (mt) REVERT: E 474 ASP cc_start: 0.8015 (p0) cc_final: 0.7582 (p0) REVERT: E 532 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7491 (mm) REVERT: E 568 GLU cc_start: 0.8617 (mp0) cc_final: 0.8248 (mt-10) REVERT: E 570 ASP cc_start: 0.8735 (p0) cc_final: 0.8474 (p0) REVERT: F 240 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8329 (mt) REVERT: F 287 ILE cc_start: 0.7509 (mm) cc_final: 0.7038 (mm) REVERT: F 315 LEU cc_start: 0.8205 (mp) cc_final: 0.7928 (mt) REVERT: F 390 MET cc_start: 0.7294 (mtp) cc_final: 0.6670 (mtp) REVERT: F 393 TYR cc_start: 0.6187 (m-80) cc_final: 0.5932 (m-80) REVERT: F 532 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7690 (mm) REVERT: F 570 ASP cc_start: 0.9122 (p0) cc_final: 0.8775 (p0) REVERT: F 579 THR cc_start: 0.8478 (m) cc_final: 0.8075 (m) REVERT: F 616 ILE cc_start: 0.9205 (mm) cc_final: 0.8814 (mm) REVERT: G 240 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8439 (mt) REVERT: G 287 ILE cc_start: 0.7667 (mm) cc_final: 0.7381 (mm) REVERT: G 315 LEU cc_start: 0.8136 (mp) cc_final: 0.7861 (mt) REVERT: G 485 LEU cc_start: 0.7600 (tt) cc_final: 0.7380 (tp) REVERT: G 570 ASP cc_start: 0.8867 (p0) cc_final: 0.8513 (p0) REVERT: G 648 HIS cc_start: 0.6264 (t-90) cc_final: 0.6061 (t70) outliers start: 150 outliers final: 94 residues processed: 972 average time/residue: 0.3457 time to fit residues: 517.9011 Evaluate side-chains 717 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 613 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 586 GLU Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 586 GLU Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 536 GLU Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 546 GLU Chi-restraints excluded: chain G residue 572 ILE Chi-restraints excluded: chain G residue 586 GLU Chi-restraints excluded: chain G residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.2980 chunk 245 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 294 optimal weight: 20.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 HIS ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 ASN ** G 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 700 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 23724 Z= 0.368 Angle : 0.932 9.608 32544 Z= 0.481 Chirality : 0.055 0.283 3966 Planarity : 0.009 0.167 4188 Dihedral : 13.680 68.901 4130 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 6.48 % Allowed : 16.90 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 3252 helix: -1.37 (0.11), residues: 1440 sheet: -0.19 (0.25), residues: 378 loop : -0.67 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP A 466 HIS 0.012 0.004 HIS D 326 PHE 0.038 0.004 PHE A 553 TYR 0.032 0.004 TYR F 230 ARG 0.009 0.001 ARG C 641 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 676 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.8115 (mp) cc_final: 0.7840 (mt) REVERT: A 216 PHE cc_start: 0.7404 (m-80) cc_final: 0.7178 (m-80) REVERT: A 314 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8062 (tt) REVERT: A 398 VAL cc_start: 0.7747 (p) cc_final: 0.7508 (p) REVERT: A 488 LEU cc_start: 0.8199 (tt) cc_final: 0.7994 (mm) REVERT: A 546 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6583 (pm20) REVERT: A 596 LEU cc_start: 0.8994 (mm) cc_final: 0.8640 (tp) REVERT: C 314 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8382 (tt) REVERT: C 676 GLU cc_start: 0.8207 (tp30) cc_final: 0.7918 (tp30) REVERT: D 314 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8307 (tp) REVERT: D 398 VAL cc_start: 0.7532 (p) cc_final: 0.6912 (p) REVERT: E 187 ILE cc_start: 0.8107 (mp) cc_final: 0.7837 (mt) REVERT: E 216 PHE cc_start: 0.7410 (m-80) cc_final: 0.7181 (m-80) REVERT: E 314 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8061 (tt) REVERT: E 353 ILE cc_start: 0.8465 (pt) cc_final: 0.7778 (pt) REVERT: E 398 VAL cc_start: 0.7738 (p) cc_final: 0.7508 (p) REVERT: E 474 ASP cc_start: 0.7853 (p0) cc_final: 0.7482 (p0) REVERT: E 488 LEU cc_start: 0.8341 (tt) cc_final: 0.8094 (mm) REVERT: E 546 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6591 (pm20) REVERT: E 596 LEU cc_start: 0.8988 (mm) cc_final: 0.8634 (tp) REVERT: F 314 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8379 (tt) REVERT: F 613 ARG cc_start: 0.8339 (mtt180) cc_final: 0.8088 (mtp85) REVERT: F 676 GLU cc_start: 0.8272 (tp30) cc_final: 0.8027 (tp30) REVERT: G 314 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8307 (tp) REVERT: G 398 VAL cc_start: 0.7539 (p) cc_final: 0.6931 (p) REVERT: G 474 ASP cc_start: 0.7503 (p0) cc_final: 0.7173 (p0) outliers start: 136 outliers final: 70 residues processed: 761 average time/residue: 0.3026 time to fit residues: 373.2335 Evaluate side-chains 642 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 564 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 645 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 200 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 ASN ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 GLN D 700 ASN ** E 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 ASN F 700 ASN G 603 ASN ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 698 GLN G 700 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23724 Z= 0.301 Angle : 0.808 12.123 32544 Z= 0.404 Chirality : 0.048 0.213 3966 Planarity : 0.007 0.124 4188 Dihedral : 11.892 65.770 3942 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.43 % Allowed : 20.10 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3252 helix: -1.05 (0.12), residues: 1452 sheet: -0.32 (0.25), residues: 378 loop : -0.48 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 466 HIS 0.009 0.002 HIS G 648 PHE 0.019 0.002 PHE C 553 TYR 0.024 0.003 TYR E 230 ARG 0.007 0.001 ARG F 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 603 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 VAL cc_start: 0.7260 (p) cc_final: 0.6869 (p) REVERT: A 488 LEU cc_start: 0.8252 (tt) cc_final: 0.8036 (mm) REVERT: A 546 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: A 568 GLU cc_start: 0.8704 (mp0) cc_final: 0.8280 (mt-10) REVERT: A 670 TYR cc_start: 0.6088 (m-80) cc_final: 0.5752 (m-80) REVERT: C 352 GLU cc_start: 0.6776 (tm-30) cc_final: 0.5846 (tm-30) REVERT: C 474 ASP cc_start: 0.8038 (p0) cc_final: 0.7535 (p0) REVERT: C 593 LEU cc_start: 0.8529 (mm) cc_final: 0.8205 (mm) REVERT: C 613 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7919 (mtp85) REVERT: D 368 MET cc_start: 0.8888 (ptm) cc_final: 0.8608 (ptm) REVERT: D 398 VAL cc_start: 0.7248 (p) cc_final: 0.6929 (p) REVERT: D 541 TRP cc_start: 0.7226 (OUTLIER) cc_final: 0.6669 (m100) REVERT: D 591 GLN cc_start: 0.7568 (tp40) cc_final: 0.7365 (tm-30) REVERT: E 398 VAL cc_start: 0.7256 (p) cc_final: 0.6836 (p) REVERT: E 488 LEU cc_start: 0.8261 (tt) cc_final: 0.8033 (mm) REVERT: E 532 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8892 (tp) REVERT: E 546 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: E 568 GLU cc_start: 0.8582 (mp0) cc_final: 0.8181 (mt-10) REVERT: E 670 TYR cc_start: 0.6079 (m-80) cc_final: 0.5695 (m-80) REVERT: F 593 LEU cc_start: 0.8509 (mm) cc_final: 0.8167 (mm) REVERT: G 368 MET cc_start: 0.8862 (ptm) cc_final: 0.8593 (ptm) REVERT: G 398 VAL cc_start: 0.7256 (p) cc_final: 0.6946 (p) REVERT: G 541 TRP cc_start: 0.6924 (OUTLIER) cc_final: 0.6378 (m100) REVERT: G 698 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7911 (mm-40) outliers start: 135 outliers final: 82 residues processed: 689 average time/residue: 0.2841 time to fit residues: 322.6140 Evaluate side-chains 599 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 511 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 652 MET Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 588 ILE Chi-restraints excluded: chain E residue 599 ILE Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 575 ARG Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 641 ARG Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 645 LEU Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 698 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 197 optimal weight: 0.4980 chunk 295 optimal weight: 0.0030 chunk 313 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN A 648 HIS C 700 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23724 Z= 0.245 Angle : 0.760 10.876 32544 Z= 0.384 Chirality : 0.047 0.197 3966 Planarity : 0.006 0.103 4188 Dihedral : 11.370 63.561 3924 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 6.33 % Allowed : 21.90 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3252 helix: -0.85 (0.12), residues: 1446 sheet: -0.51 (0.24), residues: 372 loop : -0.46 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 466 HIS 0.008 0.002 HIS G 648 PHE 0.024 0.002 PHE D 386 TYR 0.019 0.002 TYR D 687 ARG 0.007 0.001 ARG F 641 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 599 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 VAL cc_start: 0.7033 (OUTLIER) cc_final: 0.6746 (p) REVERT: A 466 TRP cc_start: 0.8170 (m-90) cc_final: 0.7756 (m-90) REVERT: A 488 LEU cc_start: 0.8389 (tt) cc_final: 0.8117 (mm) REVERT: A 546 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: A 568 GLU cc_start: 0.8430 (mp0) cc_final: 0.8171 (mt-10) REVERT: C 216 PHE cc_start: 0.7851 (m-80) cc_final: 0.7568 (m-80) REVERT: C 558 GLN cc_start: 0.8587 (mt0) cc_final: 0.8028 (mt0) REVERT: C 593 LEU cc_start: 0.8539 (mm) cc_final: 0.7999 (mm) REVERT: C 613 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7350 (ttm110) REVERT: C 617 MET cc_start: 0.7945 (ptp) cc_final: 0.6985 (ptp) REVERT: D 368 MET cc_start: 0.9151 (ptm) cc_final: 0.8823 (ptm) REVERT: D 398 VAL cc_start: 0.6904 (OUTLIER) cc_final: 0.6639 (p) REVERT: D 478 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7711 (tm-30) REVERT: D 687 TYR cc_start: 0.7564 (t80) cc_final: 0.7298 (t80) REVERT: E 398 VAL cc_start: 0.7030 (OUTLIER) cc_final: 0.6733 (p) REVERT: E 466 TRP cc_start: 0.8193 (m-90) cc_final: 0.7775 (m-90) REVERT: E 474 ASP cc_start: 0.7505 (p0) cc_final: 0.7223 (p0) REVERT: E 488 LEU cc_start: 0.8388 (tt) cc_final: 0.8125 (mm) REVERT: E 541 TRP cc_start: 0.6900 (OUTLIER) cc_final: 0.6691 (m100) REVERT: E 546 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: E 568 GLU cc_start: 0.8484 (mp0) cc_final: 0.8183 (mt-10) REVERT: F 216 PHE cc_start: 0.7841 (m-80) cc_final: 0.7572 (m-80) REVERT: F 558 GLN cc_start: 0.8807 (mt0) cc_final: 0.8261 (mt0) REVERT: F 593 LEU cc_start: 0.8494 (mm) cc_final: 0.7956 (mm) REVERT: G 368 MET cc_start: 0.9126 (ptm) cc_final: 0.8800 (ptm) REVERT: G 398 VAL cc_start: 0.6969 (OUTLIER) cc_final: 0.6672 (p) REVERT: G 541 TRP cc_start: 0.7176 (OUTLIER) cc_final: 0.6976 (m100) REVERT: G 687 TYR cc_start: 0.7565 (t80) cc_final: 0.7296 (t80) outliers start: 133 outliers final: 86 residues processed: 665 average time/residue: 0.2712 time to fit residues: 300.6039 Evaluate side-chains 605 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 511 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 599 ILE Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 652 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 575 ARG Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 641 ARG Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 667 THR Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 386 PHE Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 705 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 281 optimal weight: 0.0970 chunk 79 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS C 700 ASN E 591 GLN E 648 HIS F 465 HIS G 698 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23724 Z= 0.260 Angle : 0.730 11.347 32544 Z= 0.368 Chirality : 0.045 0.216 3966 Planarity : 0.006 0.089 4188 Dihedral : 11.266 69.423 3920 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 7.10 % Allowed : 24.00 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.94 (0.14), residues: 3252 helix: -0.57 (0.13), residues: 1458 sheet: -0.65 (0.24), residues: 372 loop : -0.46 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 466 HIS 0.009 0.001 HIS G 648 PHE 0.017 0.002 PHE D 386 TYR 0.018 0.002 TYR F 265 ARG 0.008 0.001 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 547 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 VAL cc_start: 0.7056 (OUTLIER) cc_final: 0.6726 (p) REVERT: A 466 TRP cc_start: 0.8144 (m-90) cc_final: 0.7722 (m-90) REVERT: A 546 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6324 (pm20) REVERT: C 390 MET cc_start: 0.5700 (mmm) cc_final: 0.4790 (mmm) REVERT: C 492 VAL cc_start: 0.7444 (OUTLIER) cc_final: 0.7232 (p) REVERT: C 558 GLN cc_start: 0.8677 (mt0) cc_final: 0.8032 (mt0) REVERT: C 593 LEU cc_start: 0.8622 (mm) cc_final: 0.8207 (mm) REVERT: C 613 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7308 (ttm110) REVERT: D 208 LEU cc_start: 0.8876 (mt) cc_final: 0.8435 (tp) REVERT: D 305 GLU cc_start: 0.4438 (OUTLIER) cc_final: 0.3855 (tp30) REVERT: D 364 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8650 (ptmt) REVERT: D 368 MET cc_start: 0.9071 (ptm) cc_final: 0.8748 (ptm) REVERT: E 398 VAL cc_start: 0.7070 (OUTLIER) cc_final: 0.6760 (p) REVERT: E 466 TRP cc_start: 0.8152 (m-90) cc_final: 0.7725 (m-90) REVERT: E 532 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8877 (tp) REVERT: E 541 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.6503 (m100) REVERT: E 546 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6568 (pm20) REVERT: F 492 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7214 (p) REVERT: F 558 GLN cc_start: 0.8697 (mt0) cc_final: 0.8036 (mt0) REVERT: F 567 ASP cc_start: 0.7593 (p0) cc_final: 0.7373 (p0) REVERT: F 593 LEU cc_start: 0.8602 (mm) cc_final: 0.8158 (mm) REVERT: G 208 LEU cc_start: 0.8875 (mt) cc_final: 0.8438 (tp) REVERT: G 305 GLU cc_start: 0.4446 (OUTLIER) cc_final: 0.3883 (tp30) REVERT: G 364 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8644 (ptmt) REVERT: G 368 MET cc_start: 0.9083 (ptm) cc_final: 0.8753 (ptm) REVERT: G 541 TRP cc_start: 0.6897 (OUTLIER) cc_final: 0.6377 (m100) outliers start: 149 outliers final: 95 residues processed: 633 average time/residue: 0.2726 time to fit residues: 289.1100 Evaluate side-chains 617 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 509 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 364 LYS Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 652 MET Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 389 GLU Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 465 HIS Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 641 ARG Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 667 THR Chi-restraints excluded: chain F residue 723 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 364 LYS Chi-restraints excluded: chain G residue 386 PHE Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 546 GLU Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 662 ASP Chi-restraints excluded: chain G residue 705 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 61 optimal weight: 0.0970 chunk 183 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 313 optimal weight: 0.0670 chunk 260 optimal weight: 0.0570 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 103 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 overall best weight: 0.1892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS C 700 ASN E 648 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23724 Z= 0.206 Angle : 0.732 10.184 32544 Z= 0.363 Chirality : 0.046 0.202 3966 Planarity : 0.005 0.080 4188 Dihedral : 10.985 68.917 3916 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 6.57 % Allowed : 24.71 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3252 helix: -0.51 (0.13), residues: 1476 sheet: -0.64 (0.24), residues: 378 loop : -0.45 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 466 HIS 0.029 0.001 HIS F 465 PHE 0.022 0.002 PHE F 386 TYR 0.036 0.002 TYR C 393 ARG 0.006 0.000 ARG F 641 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 582 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.8192 (tp) cc_final: 0.7867 (tp) REVERT: A 390 MET cc_start: 0.6004 (mmm) cc_final: 0.5467 (mmm) REVERT: A 466 TRP cc_start: 0.8230 (m-10) cc_final: 0.7716 (m-90) REVERT: C 558 GLN cc_start: 0.8686 (mt0) cc_final: 0.8043 (mt0) REVERT: C 591 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7654 (tm-30) REVERT: C 593 LEU cc_start: 0.8568 (mm) cc_final: 0.8191 (mm) REVERT: C 613 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7408 (ttm110) REVERT: D 205 MET cc_start: 0.7932 (ppp) cc_final: 0.7062 (ptm) REVERT: D 208 LEU cc_start: 0.8832 (mt) cc_final: 0.8347 (tp) REVERT: D 305 GLU cc_start: 0.4087 (OUTLIER) cc_final: 0.3695 (tp30) REVERT: D 368 MET cc_start: 0.9019 (ptm) cc_final: 0.8698 (ptm) REVERT: D 478 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7350 (tm-30) REVERT: E 314 LEU cc_start: 0.8178 (tp) cc_final: 0.7861 (tp) REVERT: E 390 MET cc_start: 0.5991 (mmm) cc_final: 0.5457 (mmm) REVERT: E 466 TRP cc_start: 0.8229 (m-10) cc_final: 0.7710 (m-90) REVERT: E 474 ASP cc_start: 0.7582 (p0) cc_final: 0.7360 (p0) REVERT: E 532 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8913 (tp) REVERT: E 546 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: F 478 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8011 (tm-30) REVERT: F 558 GLN cc_start: 0.8705 (mt0) cc_final: 0.8060 (mt0) REVERT: F 567 ASP cc_start: 0.7668 (p0) cc_final: 0.7426 (p0) REVERT: F 575 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6785 (tpp80) REVERT: F 591 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7486 (tm-30) REVERT: F 593 LEU cc_start: 0.8545 (mm) cc_final: 0.8191 (mm) REVERT: G 205 MET cc_start: 0.7935 (ppp) cc_final: 0.7083 (ptm) REVERT: G 208 LEU cc_start: 0.8837 (mt) cc_final: 0.8356 (tp) REVERT: G 305 GLU cc_start: 0.4215 (OUTLIER) cc_final: 0.3840 (tp30) REVERT: G 328 ILE cc_start: 0.8520 (mp) cc_final: 0.8320 (mm) REVERT: G 368 MET cc_start: 0.9019 (ptm) cc_final: 0.8726 (ptm) REVERT: G 478 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7540 (tm-30) outliers start: 138 outliers final: 80 residues processed: 662 average time/residue: 0.2737 time to fit residues: 303.8841 Evaluate side-chains 612 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 527 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 465 HIS Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 618 ASP Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 254 SER Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 575 ARG Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 386 PHE Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 662 ASP Chi-restraints excluded: chain G residue 705 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 228 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 263 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 312 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 190 optimal weight: 0.0040 chunk 144 optimal weight: 6.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN A 648 HIS E 528 ASN E 648 HIS ** E 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23724 Z= 0.226 Angle : 0.745 10.203 32544 Z= 0.369 Chirality : 0.046 0.190 3966 Planarity : 0.005 0.070 4188 Dihedral : 10.793 70.516 3905 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.24 % Allowed : 27.24 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3252 helix: -0.41 (0.13), residues: 1488 sheet: -0.76 (0.24), residues: 390 loop : -0.38 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 466 HIS 0.003 0.001 HIS F 465 PHE 0.042 0.002 PHE C 386 TYR 0.027 0.002 TYR C 393 ARG 0.009 0.001 ARG D 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 549 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7919 (tp) REVERT: A 466 TRP cc_start: 0.8261 (m-10) cc_final: 0.7620 (m-90) REVERT: C 558 GLN cc_start: 0.8707 (mt0) cc_final: 0.8114 (mt0) REVERT: C 593 LEU cc_start: 0.8633 (mm) cc_final: 0.8319 (mm) REVERT: D 205 MET cc_start: 0.7957 (ppp) cc_final: 0.7364 (ptm) REVERT: D 208 LEU cc_start: 0.8861 (mt) cc_final: 0.8396 (tp) REVERT: D 305 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.4512 (tp30) REVERT: D 368 MET cc_start: 0.8971 (ptm) cc_final: 0.8673 (ptm) REVERT: D 478 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7447 (tm-30) REVERT: D 597 ASP cc_start: 0.7319 (m-30) cc_final: 0.7099 (m-30) REVERT: E 314 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7862 (tp) REVERT: E 466 TRP cc_start: 0.8254 (m-10) cc_final: 0.7662 (m-90) REVERT: E 478 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7926 (tm-30) REVERT: E 546 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6166 (pm20) REVERT: F 498 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7474 (mt) REVERT: F 558 GLN cc_start: 0.8702 (mt0) cc_final: 0.8140 (mt0) REVERT: F 567 ASP cc_start: 0.7659 (p0) cc_final: 0.7421 (p0) REVERT: F 575 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6770 (tpp80) REVERT: F 591 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7611 (tm-30) REVERT: F 593 LEU cc_start: 0.8575 (mm) cc_final: 0.8264 (mm) REVERT: G 205 MET cc_start: 0.7976 (ppp) cc_final: 0.7383 (ptm) REVERT: G 208 LEU cc_start: 0.8836 (mt) cc_final: 0.8445 (tp) REVERT: G 305 GLU cc_start: 0.4765 (OUTLIER) cc_final: 0.4516 (tp30) REVERT: G 364 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8662 (ptmt) REVERT: G 368 MET cc_start: 0.8996 (ptm) cc_final: 0.8753 (ptm) REVERT: G 390 MET cc_start: 0.6065 (mmm) cc_final: 0.5865 (mmm) REVERT: G 478 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7451 (tm-30) REVERT: G 613 ARG cc_start: 0.8513 (mtt180) cc_final: 0.7736 (mtp85) outliers start: 131 outliers final: 92 residues processed: 632 average time/residue: 0.2687 time to fit residues: 288.0381 Evaluate side-chains 625 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 525 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 465 HIS Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 528 ASN Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 618 ASP Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 254 SER Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 498 ILE Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 575 ARG Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 364 LYS Chi-restraints excluded: chain G residue 386 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 662 ASP Chi-restraints excluded: chain G residue 705 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.0020 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 94 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 overall best weight: 1.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS E 648 HIS G 465 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 23724 Z= 0.267 Angle : 0.756 10.199 32544 Z= 0.380 Chirality : 0.046 0.186 3966 Planarity : 0.005 0.064 4188 Dihedral : 10.779 72.514 3901 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.71 % Allowed : 28.00 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3252 helix: -0.36 (0.13), residues: 1500 sheet: -0.75 (0.24), residues: 390 loop : -0.40 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 466 HIS 0.003 0.001 HIS E 370 PHE 0.024 0.002 PHE F 386 TYR 0.029 0.002 TYR C 393 ARG 0.017 0.001 ARG G 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 537 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7767 (tp) REVERT: A 466 TRP cc_start: 0.8274 (m-10) cc_final: 0.7605 (m-90) REVERT: A 474 ASP cc_start: 0.7633 (p0) cc_final: 0.7379 (p0) REVERT: A 617 MET cc_start: 0.7912 (ptp) cc_final: 0.7661 (ptp) REVERT: C 558 GLN cc_start: 0.8735 (mt0) cc_final: 0.8161 (mt0) REVERT: C 593 LEU cc_start: 0.8619 (mm) cc_final: 0.8401 (mm) REVERT: D 205 MET cc_start: 0.7956 (ppp) cc_final: 0.7327 (ptm) REVERT: D 208 LEU cc_start: 0.8870 (mt) cc_final: 0.8459 (tp) REVERT: D 305 GLU cc_start: 0.4959 (OUTLIER) cc_final: 0.4740 (tp30) REVERT: D 364 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8526 (ptmt) REVERT: D 368 MET cc_start: 0.8923 (ptm) cc_final: 0.8690 (ptm) REVERT: D 478 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7401 (tm-30) REVERT: E 314 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7881 (tp) REVERT: E 354 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7205 (mm-30) REVERT: E 466 TRP cc_start: 0.8289 (m-10) cc_final: 0.7646 (m-90) REVERT: E 474 ASP cc_start: 0.7628 (p0) cc_final: 0.7372 (p0) REVERT: E 478 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7996 (tm-30) REVERT: E 652 MET cc_start: 0.8072 (mmm) cc_final: 0.7858 (mmp) REVERT: F 478 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8036 (tm-30) REVERT: F 558 GLN cc_start: 0.8759 (mt0) cc_final: 0.8151 (mt0) REVERT: F 567 ASP cc_start: 0.7608 (p0) cc_final: 0.7383 (p0) REVERT: F 593 LEU cc_start: 0.8607 (mm) cc_final: 0.8296 (mm) REVERT: F 698 GLN cc_start: 0.8233 (mm110) cc_final: 0.6877 (mm-40) REVERT: G 205 MET cc_start: 0.8003 (ppp) cc_final: 0.7375 (ptm) REVERT: G 208 LEU cc_start: 0.8870 (mt) cc_final: 0.8483 (tp) REVERT: G 305 GLU cc_start: 0.4970 (OUTLIER) cc_final: 0.4749 (tp30) REVERT: G 368 MET cc_start: 0.8965 (ptm) cc_final: 0.8698 (ptm) REVERT: G 478 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7407 (tm-30) REVERT: G 613 ARG cc_start: 0.8537 (mtt180) cc_final: 0.7761 (mtp85) outliers start: 120 outliers final: 93 residues processed: 607 average time/residue: 0.2712 time to fit residues: 277.8116 Evaluate side-chains 611 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 513 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 364 LYS Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 386 PHE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 465 HIS Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 618 ASP Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 254 SER Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 498 ILE Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 667 THR Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 637 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.1980 chunk 299 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 262 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 289 optimal weight: 0.0170 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23724 Z= 0.209 Angle : 0.772 10.512 32544 Z= 0.379 Chirality : 0.046 0.195 3966 Planarity : 0.005 0.056 4188 Dihedral : 10.708 76.588 3901 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.72 % Rotamer: Outliers : 4.76 % Allowed : 29.90 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3252 helix: -0.37 (0.13), residues: 1500 sheet: -0.67 (0.24), residues: 390 loop : -0.37 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 466 HIS 0.003 0.001 HIS D 370 PHE 0.026 0.002 PHE F 386 TYR 0.030 0.002 TYR D 393 ARG 0.005 0.001 ARG F 641 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 551 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 354 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 466 TRP cc_start: 0.8211 (m-10) cc_final: 0.7540 (m-90) REVERT: A 478 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7834 (tm-30) REVERT: C 205 MET cc_start: 0.8318 (ppp) cc_final: 0.7876 (ppp) REVERT: C 318 MET cc_start: 0.7371 (mmm) cc_final: 0.7156 (mmm) REVERT: C 558 GLN cc_start: 0.8653 (mt0) cc_final: 0.8112 (mt0) REVERT: D 205 MET cc_start: 0.7882 (ppp) cc_final: 0.7213 (ptm) REVERT: D 208 LEU cc_start: 0.8853 (mt) cc_final: 0.8499 (tp) REVERT: D 368 MET cc_start: 0.8835 (ptm) cc_final: 0.8566 (ptm) REVERT: D 478 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7505 (tm-30) REVERT: E 314 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8006 (tp) REVERT: E 466 TRP cc_start: 0.8226 (m-10) cc_final: 0.7597 (m-90) REVERT: E 478 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7851 (tm-30) REVERT: E 652 MET cc_start: 0.8013 (mmm) cc_final: 0.7786 (mmp) REVERT: F 205 MET cc_start: 0.8358 (ppp) cc_final: 0.7897 (ppp) REVERT: F 318 MET cc_start: 0.7401 (mmm) cc_final: 0.7194 (mmm) REVERT: F 478 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7979 (tm-30) REVERT: F 558 GLN cc_start: 0.8735 (mt0) cc_final: 0.8101 (mt0) REVERT: F 567 ASP cc_start: 0.7573 (p0) cc_final: 0.7337 (p0) REVERT: F 593 LEU cc_start: 0.8535 (mm) cc_final: 0.8321 (mm) REVERT: G 205 MET cc_start: 0.7934 (ppp) cc_final: 0.7273 (ptm) REVERT: G 208 LEU cc_start: 0.8870 (mt) cc_final: 0.8498 (tp) REVERT: G 364 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8511 (ptmt) REVERT: G 478 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7349 (tm-30) REVERT: G 613 ARG cc_start: 0.8504 (mtt180) cc_final: 0.7766 (mtp85) REVERT: G 677 ASN cc_start: 0.6970 (m-40) cc_final: 0.6736 (t0) outliers start: 100 outliers final: 70 residues processed: 614 average time/residue: 0.2766 time to fit residues: 286.9747 Evaluate side-chains 587 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 514 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 465 HIS Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 254 SER Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 364 LYS Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 589 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.9980 chunk 307 optimal weight: 0.0570 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 322 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23724 Z= 0.248 Angle : 0.773 11.241 32544 Z= 0.384 Chirality : 0.046 0.191 3966 Planarity : 0.005 0.054 4188 Dihedral : 10.498 71.859 3890 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.38 % Allowed : 29.95 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3252 helix: -0.30 (0.13), residues: 1500 sheet: -0.72 (0.24), residues: 390 loop : -0.32 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 466 HIS 0.004 0.001 HIS G 370 PHE 0.040 0.002 PHE C 386 TYR 0.028 0.002 TYR C 393 ARG 0.008 0.001 ARG F 641 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 518 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8038 (tp) REVERT: A 354 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7287 (mm-30) REVERT: A 466 TRP cc_start: 0.8246 (m-10) cc_final: 0.7565 (m-90) REVERT: A 715 GLU cc_start: 0.6905 (mp0) cc_final: 0.6568 (mp0) REVERT: C 558 GLN cc_start: 0.8726 (mt0) cc_final: 0.8142 (mt0) REVERT: C 715 GLU cc_start: 0.6781 (mp0) cc_final: 0.6571 (mp0) REVERT: D 205 MET cc_start: 0.7863 (ppp) cc_final: 0.7059 (ptm) REVERT: D 208 LEU cc_start: 0.8889 (mt) cc_final: 0.8527 (tp) REVERT: D 364 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8565 (ptmt) REVERT: D 478 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7564 (tm-30) REVERT: E 314 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8006 (tp) REVERT: E 466 TRP cc_start: 0.8259 (m-10) cc_final: 0.7611 (m-90) REVERT: E 474 ASP cc_start: 0.7623 (p0) cc_final: 0.7354 (p0) REVERT: E 478 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7815 (tm-30) REVERT: E 715 GLU cc_start: 0.6910 (mp0) cc_final: 0.6559 (mp0) REVERT: F 478 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8029 (tm-30) REVERT: F 558 GLN cc_start: 0.8723 (mt0) cc_final: 0.8157 (mt0) REVERT: F 567 ASP cc_start: 0.7564 (p0) cc_final: 0.7358 (p0) REVERT: F 593 LEU cc_start: 0.8438 (mm) cc_final: 0.8205 (mm) REVERT: F 715 GLU cc_start: 0.6741 (mp0) cc_final: 0.6507 (mp0) REVERT: G 205 MET cc_start: 0.7874 (ppp) cc_final: 0.7041 (ptm) REVERT: G 208 LEU cc_start: 0.8935 (mt) cc_final: 0.8524 (tp) REVERT: G 478 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7545 (tm-30) REVERT: G 552 ILE cc_start: 0.9091 (mt) cc_final: 0.8846 (tp) REVERT: G 613 ARG cc_start: 0.8523 (mtt180) cc_final: 0.7771 (mtp85) outliers start: 92 outliers final: 70 residues processed: 576 average time/residue: 0.2595 time to fit residues: 254.6455 Evaluate side-chains 570 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 497 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 364 LYS Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 465 HIS Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain G residue 663 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 2.9990 chunk 273 optimal weight: 0.5980 chunk 78 optimal weight: 20.0000 chunk 237 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 264 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 30.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095080 restraints weight = 61207.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098203 restraints weight = 35627.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100426 restraints weight = 24205.811| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23724 Z= 0.248 Angle : 0.776 11.491 32544 Z= 0.385 Chirality : 0.046 0.185 3966 Planarity : 0.005 0.056 4188 Dihedral : 10.519 73.357 3888 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.14 % Allowed : 30.48 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3252 helix: -0.28 (0.13), residues: 1488 sheet: -0.79 (0.24), residues: 390 loop : -0.29 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 541 HIS 0.003 0.001 HIS D 370 PHE 0.030 0.002 PHE G 386 TYR 0.028 0.002 TYR D 393 ARG 0.007 0.001 ARG C 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5778.07 seconds wall clock time: 102 minutes 43.39 seconds (6163.39 seconds total)