Starting phenix.real_space_refine on Sun Aug 24 22:56:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vc7_8658/08_2025/5vc7_8658_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vc7_8658/08_2025/5vc7_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 { model { file = "/net/cci-nas-00/data/ceres_data/5vc7_8658/08_2025/5vc7_8658_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vc7_8658/08_2025/5vc7_8658_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5vc7_8658/08_2025/5vc7_8658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vc7_8658/08_2025/5vc7_8658.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 29, 'ASP:plan': 17, 'ARG:plan': 13, 'ASN:plan1': 5, 'GLN:plan1': 4, 'PHE:plan': 2} 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, D, E, F, G Time building chain proxies: 4.32, per 1000 atoms: 0.19 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 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: 0.97 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: 4.61 Time building geometry restraints manager: 3.18 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: 186 1.92 - 2.66: 1484 2.66 - 3.41: 39449 3.41 - 4.15: 54544 4.15 - 4.90: 91732 Nonbonded interactions: 187395 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 187390 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: 0.08 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 22.420 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.970 ------------------------------------------------------------------------------- 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 : 0.010 0.415 23736 Z= 0.875 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 : 118.04 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (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 ARG 0.008 0.001 ARG G 641 TYR 0.017 0.001 TYR A 189 PHE 0.018 0.001 PHE A 349 TRP 0.007 0.002 TRP A 541 HIS 0.005 0.002 HIS A 648 Details of bonding type rmsd covalent geometry : bond 0.00734 (23724) covalent geometry : angle 1.49592 (32544) hydrogen bonds : bond 0.32786 ( 990) hydrogen bonds : angle 9.82017 ( 2790) Misc. bond : bond 0.29453 ( 12) *********************** 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 to be fit. rotamer outliers: 150 poor density : 866 time to evaluate : 0.918 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: A 240 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 287 ILE cc_start: 0.7490 (mm) cc_final: 0.7100 (mm) REVERT: A 315 LEU cc_start: 0.8135 (mp) cc_final: 0.7853 (mt) REVERT: A 474 ASP cc_start: 0.8005 (p0) cc_final: 0.7576 (p0) REVERT: A 532 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7473 (mm) REVERT: A 568 GLU cc_start: 0.8609 (mp0) cc_final: 0.8254 (mt-10) REVERT: A 570 ASP cc_start: 0.8729 (p0) cc_final: 0.8469 (p0) REVERT: A 687 TYR cc_start: 0.8040 (t80) cc_final: 0.7609 (t80) REVERT: C 240 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 287 ILE cc_start: 0.7505 (mm) cc_final: 0.7039 (mm) REVERT: C 315 LEU cc_start: 0.8214 (mp) cc_final: 0.7927 (mt) REVERT: C 390 MET cc_start: 0.7299 (mtp) cc_final: 0.6764 (mtp) REVERT: C 532 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7674 (mm) REVERT: C 579 THR cc_start: 0.8476 (m) cc_final: 0.8064 (m) REVERT: C 616 ILE cc_start: 0.9212 (mm) cc_final: 0.8933 (mm) REVERT: D 240 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8440 (mt) REVERT: D 287 ILE cc_start: 0.7660 (mm) cc_final: 0.7377 (mm) REVERT: D 315 LEU cc_start: 0.8132 (mp) cc_final: 0.7854 (mt) REVERT: D 570 ASP cc_start: 0.8869 (p0) cc_final: 0.8507 (p0) REVERT: E 240 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8184 (mt) REVERT: E 287 ILE cc_start: 0.7479 (mm) cc_final: 0.7091 (mm) REVERT: E 315 LEU cc_start: 0.8128 (mp) cc_final: 0.7851 (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: 0.7488 (mm) REVERT: E 568 GLU cc_start: 0.8617 (mp0) cc_final: 0.8245 (mt-10) REVERT: E 570 ASP cc_start: 0.8735 (p0) cc_final: 0.8480 (p0) REVERT: F 240 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8335 (mt) REVERT: F 287 ILE cc_start: 0.7509 (mm) cc_final: 0.7037 (mm) REVERT: F 315 LEU cc_start: 0.8205 (mp) cc_final: 0.7927 (mt) REVERT: F 390 MET cc_start: 0.7294 (mtp) cc_final: 0.6660 (mtp) REVERT: F 393 TYR cc_start: 0.6187 (m-80) cc_final: 0.5935 (m-80) REVERT: F 532 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7686 (mm) REVERT: F 570 ASP cc_start: 0.9122 (p0) cc_final: 0.8764 (p0) REVERT: F 579 THR cc_start: 0.8478 (m) cc_final: 0.8071 (m) REVERT: F 616 ILE cc_start: 0.9205 (mm) cc_final: 0.8909 (mm) REVERT: G 240 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8437 (mt) REVERT: G 287 ILE cc_start: 0.7667 (mm) cc_final: 0.7379 (mm) REVERT: G 315 LEU cc_start: 0.8136 (mp) cc_final: 0.7863 (mt) REVERT: G 485 LEU cc_start: 0.7600 (tt) cc_final: 0.7383 (tp) REVERT: G 570 ASP cc_start: 0.8867 (p0) cc_final: 0.8501 (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: 0.1701 time to fit residues: 257.1349 Evaluate side-chains 712 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 608 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 651 ASN A 700 ASN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN C 700 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 HIS D 651 ASN ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN E 700 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN F 700 ASN ** G 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 ASN G 700 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.118308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.095612 restraints weight = 61309.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098795 restraints weight = 36148.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101014 restraints weight = 24759.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.102616 restraints weight = 18679.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103779 restraints weight = 15069.569| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23736 Z= 0.243 Angle : 0.946 14.563 32544 Z= 0.484 Chirality : 0.055 0.237 3966 Planarity : 0.010 0.163 4188 Dihedral : 14.267 167.534 4130 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 7.33 % Allowed : 16.19 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.13), residues: 3252 helix: -1.41 (0.11), residues: 1440 sheet: -0.26 (0.24), residues: 378 loop : -0.70 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 626 TYR 0.037 0.005 TYR C 230 PHE 0.040 0.005 PHE G 216 TRP 0.026 0.007 TRP F 466 HIS 0.015 0.004 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00560 (23724) covalent geometry : angle 0.94606 (32544) hydrogen bonds : bond 0.07309 ( 990) hydrogen bonds : angle 7.08479 ( 2790) Misc. bond : bond 0.00383 ( 12) *********************** 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 820 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 666 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.8068 (mp) cc_final: 0.7599 (mt) REVERT: A 216 PHE cc_start: 0.8357 (m-80) cc_final: 0.8050 (m-80) REVERT: A 314 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8980 (tt) REVERT: A 318 MET cc_start: 0.8594 (mmm) cc_final: 0.8385 (mmm) REVERT: A 352 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: A 398 VAL cc_start: 0.9333 (p) cc_final: 0.8972 (p) REVERT: A 401 ASP cc_start: 0.9288 (m-30) cc_final: 0.9057 (m-30) REVERT: A 488 LEU cc_start: 0.8872 (tt) cc_final: 0.8336 (mm) REVERT: C 352 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: C 576 ARG cc_start: 0.7014 (ptp-110) cc_final: 0.6706 (mtt180) REVERT: C 648 HIS cc_start: 0.7221 (t70) cc_final: 0.7002 (t-90) REVERT: C 676 GLU cc_start: 0.8357 (tp30) cc_final: 0.8154 (tp30) REVERT: C 720 TYR cc_start: 0.8892 (m-10) cc_final: 0.8490 (m-10) REVERT: D 314 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9213 (tp) REVERT: D 352 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: D 398 VAL cc_start: 0.9227 (p) cc_final: 0.8950 (p) REVERT: D 467 ASP cc_start: 0.8469 (m-30) cc_final: 0.8221 (p0) REVERT: D 488 LEU cc_start: 0.8852 (tt) cc_final: 0.8404 (mm) REVERT: D 546 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: E 187 ILE cc_start: 0.8069 (mp) cc_final: 0.7610 (mt) REVERT: E 216 PHE cc_start: 0.8355 (m-80) cc_final: 0.8046 (m-80) REVERT: E 314 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8982 (tt) REVERT: E 318 MET cc_start: 0.8494 (mmm) cc_final: 0.8289 (mmm) REVERT: E 352 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: E 353 ILE cc_start: 0.8525 (pt) cc_final: 0.7589 (pt) REVERT: E 398 VAL cc_start: 0.9338 (p) cc_final: 0.8979 (p) REVERT: E 401 ASP cc_start: 0.9289 (m-30) cc_final: 0.9056 (m-30) REVERT: E 474 ASP cc_start: 0.9194 (p0) cc_final: 0.8836 (p0) REVERT: E 485 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8044 (tp) REVERT: E 488 LEU cc_start: 0.8875 (tt) cc_final: 0.8349 (mm) REVERT: F 352 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: F 613 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7475 (mtp85) REVERT: F 720 TYR cc_start: 0.8846 (m-10) cc_final: 0.8451 (m-10) REVERT: G 314 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9206 (tp) REVERT: G 352 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: G 398 VAL cc_start: 0.9227 (p) cc_final: 0.8950 (p) REVERT: G 467 ASP cc_start: 0.8349 (m-30) cc_final: 0.8123 (p0) REVERT: G 474 ASP cc_start: 0.9059 (p0) cc_final: 0.8776 (p0) REVERT: G 488 LEU cc_start: 0.8831 (tt) cc_final: 0.8351 (mm) REVERT: G 546 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7631 (pm20) outliers start: 154 outliers final: 78 residues processed: 761 average time/residue: 0.1467 time to fit residues: 184.8832 Evaluate side-chains 656 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 565 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 352 GLU 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 228 ILE Chi-restraints excluded: chain C residue 260 ILE 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 352 GLU Chi-restraints excluded: chain C residue 371 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 541 TRP Chi-restraints excluded: chain C residue 578 THR 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 352 GLU Chi-restraints excluded: chain D residue 371 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 546 GLU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 593 LEU 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 352 GLU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 485 LEU 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 228 ILE Chi-restraints excluded: chain F residue 260 ILE 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 352 GLU Chi-restraints excluded: chain F residue 371 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 541 TRP Chi-restraints excluded: chain F residue 578 THR 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 352 GLU Chi-restraints excluded: chain G residue 371 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 546 GLU Chi-restraints excluded: chain G residue 578 THR Chi-restraints excluded: chain G residue 593 LEU 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 77 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 111 optimal weight: 0.0270 chunk 53 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 235 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 114 optimal weight: 0.0570 chunk 225 optimal weight: 9.9990 chunk 311 optimal weight: 4.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 651 ASN A 700 ASN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 HIS C 651 ASN ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 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 651 ASN E 700 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN F 700 ASN G 603 ASN G 651 ASN G 698 GLN G 700 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.118881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097050 restraints weight = 60678.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100256 restraints weight = 35208.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102540 restraints weight = 23797.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104136 restraints weight = 17726.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.105350 restraints weight = 14208.131| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23736 Z= 0.171 Angle : 0.798 11.196 32544 Z= 0.399 Chirality : 0.049 0.214 3966 Planarity : 0.011 0.357 4188 Dihedral : 12.332 131.178 3956 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 6.62 % Allowed : 19.00 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.14), residues: 3252 helix: -1.03 (0.12), residues: 1440 sheet: -0.40 (0.24), residues: 378 loop : -0.52 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG E 626 TYR 0.026 0.003 TYR C 230 PHE 0.020 0.002 PHE C 553 TRP 0.010 0.002 TRP G 466 HIS 0.007 0.002 HIS G 648 Details of bonding type rmsd covalent geometry : bond 0.00383 (23724) covalent geometry : angle 0.79801 (32544) hydrogen bonds : bond 0.05366 ( 990) hydrogen bonds : angle 6.53092 ( 2790) Misc. bond : bond 0.00625 ( 12) *********************** 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 763 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 624 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 VAL cc_start: 0.9257 (p) cc_final: 0.8758 (p) REVERT: A 401 ASP cc_start: 0.9265 (m-30) cc_final: 0.8988 (m-30) REVERT: A 439 GLU cc_start: 0.8367 (mp0) cc_final: 0.8034 (mp0) REVERT: A 488 LEU cc_start: 0.8901 (tt) cc_final: 0.8375 (mm) REVERT: A 541 TRP cc_start: 0.7661 (OUTLIER) cc_final: 0.7166 (m100) REVERT: A 546 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: A 591 GLN cc_start: 0.8191 (tp40) cc_final: 0.7831 (tp-100) REVERT: A 641 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7461 (mtt180) REVERT: A 646 LYS cc_start: 0.8464 (mtmm) cc_final: 0.7889 (ptpt) REVERT: A 662 ASP cc_start: 0.9024 (t0) cc_final: 0.8812 (t0) REVERT: A 687 TYR cc_start: 0.8573 (t80) cc_final: 0.8164 (t80) REVERT: C 216 PHE cc_start: 0.8591 (m-80) cc_final: 0.8083 (m-80) REVERT: C 368 MET cc_start: 0.9262 (ptm) cc_final: 0.8774 (ptm) REVERT: C 439 GLU cc_start: 0.8359 (mp0) cc_final: 0.7974 (mp0) REVERT: C 474 ASP cc_start: 0.9173 (p0) cc_final: 0.8834 (p0) REVERT: C 558 GLN cc_start: 0.9134 (mt0) cc_final: 0.8563 (mt0) REVERT: C 576 ARG cc_start: 0.7268 (ptp-110) cc_final: 0.6745 (mtt180) REVERT: C 591 GLN cc_start: 0.8495 (tp40) cc_final: 0.8242 (tm-30) REVERT: C 617 MET cc_start: 0.8582 (ptp) cc_final: 0.8296 (ptp) REVERT: C 618 ASP cc_start: 0.8901 (t0) cc_final: 0.8696 (t0) REVERT: C 646 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8077 (ptpt) REVERT: C 720 TYR cc_start: 0.8919 (m-10) cc_final: 0.8661 (m-10) REVERT: D 205 MET cc_start: 0.9080 (tmm) cc_final: 0.8376 (mtp) REVERT: D 352 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: D 368 MET cc_start: 0.9250 (ptm) cc_final: 0.8814 (ptm) REVERT: D 389 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: D 398 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.9148 (p) REVERT: D 411 MET cc_start: 0.9119 (tpp) cc_final: 0.8918 (tpp) REVERT: D 467 ASP cc_start: 0.8575 (m-30) cc_final: 0.8355 (p0) REVERT: D 488 LEU cc_start: 0.8933 (tt) cc_final: 0.8408 (mm) REVERT: D 498 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8888 (pt) REVERT: D 541 TRP cc_start: 0.7590 (OUTLIER) cc_final: 0.6936 (m100) REVERT: D 546 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: D 591 GLN cc_start: 0.8729 (tp40) cc_final: 0.8189 (tm-30) REVERT: D 646 LYS cc_start: 0.8472 (mtmm) cc_final: 0.7901 (ptpt) REVERT: E 398 VAL cc_start: 0.9264 (p) cc_final: 0.8766 (p) REVERT: E 401 ASP cc_start: 0.9262 (m-30) cc_final: 0.8985 (m-30) REVERT: E 439 GLU cc_start: 0.8365 (mp0) cc_final: 0.8032 (mp0) REVERT: E 488 LEU cc_start: 0.8901 (tt) cc_final: 0.8364 (mm) REVERT: E 541 TRP cc_start: 0.7651 (OUTLIER) cc_final: 0.7154 (m100) REVERT: E 546 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: E 591 GLN cc_start: 0.8163 (tp40) cc_final: 0.7834 (tp-100) REVERT: E 641 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7296 (mtt-85) REVERT: E 652 MET cc_start: 0.8234 (tpp) cc_final: 0.8012 (mmm) REVERT: F 368 MET cc_start: 0.9256 (ptm) cc_final: 0.8765 (ptm) REVERT: F 389 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8894 (pm20) REVERT: F 393 TYR cc_start: 0.7478 (m-80) cc_final: 0.7188 (m-80) REVERT: F 439 GLU cc_start: 0.8335 (mp0) cc_final: 0.8055 (mp0) REVERT: F 474 ASP cc_start: 0.9181 (p0) cc_final: 0.8848 (p0) REVERT: F 558 GLN cc_start: 0.9129 (mt0) cc_final: 0.8547 (mt0) REVERT: F 576 ARG cc_start: 0.7273 (ptp-110) cc_final: 0.6959 (mtt180) REVERT: F 591 GLN cc_start: 0.8696 (tp40) cc_final: 0.8223 (tm-30) REVERT: F 646 LYS cc_start: 0.8545 (mtmm) cc_final: 0.7963 (ptpt) REVERT: F 720 TYR cc_start: 0.8928 (m-10) cc_final: 0.8658 (m-10) REVERT: G 205 MET cc_start: 0.9075 (tmm) cc_final: 0.8470 (mtp) REVERT: G 352 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: G 368 MET cc_start: 0.9249 (ptm) cc_final: 0.8813 (ptm) REVERT: G 389 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8899 (pm20) REVERT: G 398 VAL cc_start: 0.9413 (OUTLIER) cc_final: 0.9131 (p) REVERT: G 467 ASP cc_start: 0.8559 (m-30) cc_final: 0.8341 (p0) REVERT: G 485 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8519 (tp) REVERT: G 488 LEU cc_start: 0.8912 (tt) cc_final: 0.8371 (mm) REVERT: G 498 ILE cc_start: 0.9221 (pt) cc_final: 0.8957 (pt) REVERT: G 541 TRP cc_start: 0.7591 (OUTLIER) cc_final: 0.6931 (m100) REVERT: G 546 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: G 591 GLN cc_start: 0.8735 (tp40) cc_final: 0.8097 (tm-30) outliers start: 139 outliers final: 70 residues processed: 710 average time/residue: 0.1330 time to fit residues: 160.6114 Evaluate side-chains 617 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 528 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 328 ILE Chi-restraints excluded: chain A residue 389 GLU 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 599 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 641 ARG 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 314 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE 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 541 TRP Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 593 LEU 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 328 ILE Chi-restraints excluded: chain E residue 389 GLU 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 599 ILE Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 641 ARG 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 314 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 389 GLU 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 589 VAL 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 260 ILE Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 485 LEU 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 569 ILE Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 637 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 154 optimal weight: 0.0020 chunk 167 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 55 optimal weight: 0.0000 chunk 137 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 698 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.120230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098130 restraints weight = 60852.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.101346 restraints weight = 35551.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.103648 restraints weight = 24148.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105296 restraints weight = 18028.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.106495 restraints weight = 14409.802| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23736 Z= 0.153 Angle : 0.729 9.639 32544 Z= 0.368 Chirality : 0.047 0.295 3966 Planarity : 0.007 0.173 4188 Dihedral : 11.926 160.688 3932 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 6.52 % Allowed : 21.19 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3252 helix: -0.65 (0.13), residues: 1398 sheet: -0.68 (0.22), residues: 372 loop : -0.56 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 626 TYR 0.020 0.002 TYR D 687 PHE 0.032 0.002 PHE C 386 TRP 0.011 0.001 TRP F 466 HIS 0.007 0.001 HIS G 648 Details of bonding type rmsd covalent geometry : bond 0.00344 (23724) covalent geometry : angle 0.72864 (32544) hydrogen bonds : bond 0.04705 ( 990) hydrogen bonds : angle 6.10708 ( 2790) Misc. bond : bond 0.00416 ( 12) *********************** 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 748 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 611 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8734 (tmm160) cc_final: 0.8357 (ppt170) REVERT: A 314 LEU cc_start: 0.9365 (tp) cc_final: 0.9089 (tp) REVERT: A 398 VAL cc_start: 0.9327 (p) cc_final: 0.8646 (p) REVERT: A 401 ASP cc_start: 0.9161 (m-30) cc_final: 0.8857 (m-30) REVERT: A 439 GLU cc_start: 0.8322 (mp0) cc_final: 0.8016 (mp0) REVERT: A 466 TRP cc_start: 0.8264 (m-90) cc_final: 0.7531 (m-90) REVERT: A 488 LEU cc_start: 0.8920 (tt) cc_final: 0.8365 (mm) REVERT: A 541 TRP cc_start: 0.7494 (OUTLIER) cc_final: 0.7087 (m100) REVERT: A 546 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: A 572 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 662 ASP cc_start: 0.9169 (t0) cc_final: 0.8919 (t0) REVERT: C 368 MET cc_start: 0.9295 (ptm) cc_final: 0.8815 (ptm) REVERT: C 439 GLU cc_start: 0.8334 (mp0) cc_final: 0.8018 (mp0) REVERT: C 478 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8582 (tm-30) REVERT: C 541 TRP cc_start: 0.6778 (OUTLIER) cc_final: 0.6468 (m100) REVERT: C 558 GLN cc_start: 0.9076 (mt0) cc_final: 0.8460 (mt0) REVERT: D 203 ARG cc_start: 0.8620 (tmm160) cc_final: 0.8356 (ptt90) REVERT: D 205 MET cc_start: 0.9143 (tmm) cc_final: 0.8585 (mtp) REVERT: D 208 LEU cc_start: 0.9249 (mt) cc_final: 0.8823 (tp) REVERT: D 328 ILE cc_start: 0.9405 (mp) cc_final: 0.8834 (mm) REVERT: D 368 MET cc_start: 0.9290 (ptm) cc_final: 0.8793 (ptm) REVERT: D 389 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8820 (pm20) REVERT: D 398 VAL cc_start: 0.9377 (p) cc_final: 0.9139 (p) REVERT: D 478 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8436 (tm-30) REVERT: D 488 LEU cc_start: 0.8966 (tt) cc_final: 0.8452 (mm) REVERT: D 498 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8971 (pt) REVERT: D 541 TRP cc_start: 0.7356 (OUTLIER) cc_final: 0.7116 (m100) REVERT: D 546 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: D 591 GLN cc_start: 0.8624 (tp40) cc_final: 0.8237 (tm-30) REVERT: D 649 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8576 (t) REVERT: D 652 MET cc_start: 0.8801 (mmp) cc_final: 0.8110 (mmm) REVERT: D 676 GLU cc_start: 0.8710 (tp30) cc_final: 0.8237 (tp30) REVERT: D 687 TYR cc_start: 0.8260 (t80) cc_final: 0.7796 (t80) REVERT: E 203 ARG cc_start: 0.8728 (tmm160) cc_final: 0.8349 (ppt170) REVERT: E 314 LEU cc_start: 0.9368 (tp) cc_final: 0.9094 (tp) REVERT: E 398 VAL cc_start: 0.9323 (p) cc_final: 0.8635 (p) REVERT: E 401 ASP cc_start: 0.9155 (m-30) cc_final: 0.8850 (m-30) REVERT: E 439 GLU cc_start: 0.8305 (mp0) cc_final: 0.8003 (mp0) REVERT: E 466 TRP cc_start: 0.8248 (m-90) cc_final: 0.7549 (m-90) REVERT: E 474 ASP cc_start: 0.9215 (p0) cc_final: 0.8900 (p0) REVERT: E 488 LEU cc_start: 0.8929 (tt) cc_final: 0.8372 (mm) REVERT: E 532 ILE cc_start: 0.9102 (mm) cc_final: 0.8684 (tp) REVERT: E 541 TRP cc_start: 0.7496 (OUTLIER) cc_final: 0.7074 (m100) REVERT: E 546 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: E 572 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8308 (tt) REVERT: E 641 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7408 (mtt180) REVERT: F 368 MET cc_start: 0.9287 (ptm) cc_final: 0.8807 (ptm) REVERT: F 393 TYR cc_start: 0.7822 (m-80) cc_final: 0.7181 (m-80) REVERT: F 439 GLU cc_start: 0.8292 (mp0) cc_final: 0.8046 (mp0) REVERT: F 478 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8584 (tm-30) REVERT: F 541 TRP cc_start: 0.6728 (OUTLIER) cc_final: 0.6435 (m100) REVERT: F 558 GLN cc_start: 0.9109 (mt0) cc_final: 0.8514 (mt0) REVERT: F 576 ARG cc_start: 0.7181 (ptp-110) cc_final: 0.6746 (mtt180) REVERT: F 612 ASN cc_start: 0.8287 (m110) cc_final: 0.7975 (m110) REVERT: F 649 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8071 (t) REVERT: F 676 GLU cc_start: 0.8464 (tp30) cc_final: 0.8259 (tp30) REVERT: G 203 ARG cc_start: 0.8680 (tmm160) cc_final: 0.8416 (ptt90) REVERT: G 205 MET cc_start: 0.9159 (tmm) cc_final: 0.8596 (mtp) REVERT: G 208 LEU cc_start: 0.9258 (mt) cc_final: 0.8830 (tp) REVERT: G 328 ILE cc_start: 0.9406 (mp) cc_final: 0.8834 (mm) REVERT: G 368 MET cc_start: 0.9289 (ptm) cc_final: 0.8792 (ptm) REVERT: G 389 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8786 (pm20) REVERT: G 398 VAL cc_start: 0.9374 (p) cc_final: 0.9128 (p) REVERT: G 467 ASP cc_start: 0.8645 (m-30) cc_final: 0.8405 (p0) REVERT: G 478 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8518 (tm-30) REVERT: G 488 LEU cc_start: 0.8972 (tt) cc_final: 0.8413 (mm) REVERT: G 537 VAL cc_start: 0.9471 (p) cc_final: 0.9200 (p) REVERT: G 541 TRP cc_start: 0.7396 (OUTLIER) cc_final: 0.7151 (m100) REVERT: G 546 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: G 591 GLN cc_start: 0.8642 (tp40) cc_final: 0.8239 (tm-30) REVERT: G 649 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8450 (t) REVERT: G 652 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7859 (mmm) REVERT: G 687 TYR cc_start: 0.8252 (t80) cc_final: 0.7829 (t80) outliers start: 137 outliers final: 75 residues processed: 685 average time/residue: 0.1216 time to fit residues: 141.3355 Evaluate side-chains 626 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 531 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 367 LEU 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 541 TRP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 641 ARG 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 389 GLU 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 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 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 333 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 649 THR 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 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 572 ILE Chi-restraints excluded: chain E residue 599 ILE Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 641 ARG 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 333 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 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 649 THR Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 260 ILE 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 389 GLU 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 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 593 LEU Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 649 THR Chi-restraints excluded: chain G residue 652 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 84 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 218 optimal weight: 0.0570 chunk 312 optimal weight: 6.9990 chunk 188 optimal weight: 0.5980 chunk 229 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 195 optimal weight: 0.7980 chunk 300 optimal weight: 0.9990 chunk 271 optimal weight: 0.0060 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS D 591 GLN E 528 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS G 698 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.118899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097841 restraints weight = 60648.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101032 restraints weight = 35164.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.103282 restraints weight = 23626.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104895 restraints weight = 17485.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106062 restraints weight = 13881.387| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23736 Z= 0.138 Angle : 0.698 9.451 32544 Z= 0.351 Chirality : 0.046 0.195 3966 Planarity : 0.006 0.077 4188 Dihedral : 11.798 175.907 3922 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 7.10 % Allowed : 24.05 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.14), residues: 3252 helix: -0.47 (0.13), residues: 1458 sheet: -0.63 (0.22), residues: 372 loop : -0.56 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 680 TYR 0.016 0.002 TYR F 265 PHE 0.024 0.002 PHE C 386 TRP 0.014 0.001 TRP C 466 HIS 0.003 0.001 HIS F 648 Details of bonding type rmsd covalent geometry : bond 0.00308 (23724) covalent geometry : angle 0.69821 (32544) hydrogen bonds : bond 0.04377 ( 990) hydrogen bonds : angle 5.84829 ( 2790) Misc. bond : bond 0.00538 ( 12) *********************** 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 728 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 579 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8666 (tmm160) cc_final: 0.8323 (ppt170) REVERT: A 314 LEU cc_start: 0.9397 (tp) cc_final: 0.8985 (tp) REVERT: A 352 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: A 389 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8963 (pm20) REVERT: A 398 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 401 ASP cc_start: 0.9115 (m-30) cc_final: 0.8784 (m-30) REVERT: A 439 GLU cc_start: 0.8324 (mp0) cc_final: 0.8040 (mp0) REVERT: A 466 TRP cc_start: 0.8247 (m-10) cc_final: 0.7536 (m-90) REVERT: A 488 LEU cc_start: 0.8924 (tt) cc_final: 0.8361 (mm) REVERT: A 541 TRP cc_start: 0.7553 (OUTLIER) cc_final: 0.7259 (m100) REVERT: A 546 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: A 641 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7072 (mtt180) REVERT: A 662 ASP cc_start: 0.9154 (t0) cc_final: 0.8883 (t0) REVERT: C 326 HIS cc_start: 0.7023 (m-70) cc_final: 0.6543 (t-90) REVERT: C 368 MET cc_start: 0.9283 (ptm) cc_final: 0.8783 (ptm) REVERT: C 439 GLU cc_start: 0.8280 (mp0) cc_final: 0.8022 (mp0) REVERT: C 478 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 541 TRP cc_start: 0.6755 (OUTLIER) cc_final: 0.6383 (m100) REVERT: C 558 GLN cc_start: 0.9118 (mt0) cc_final: 0.8533 (mt0) REVERT: D 203 ARG cc_start: 0.8755 (tmm160) cc_final: 0.8423 (ptt90) REVERT: D 208 LEU cc_start: 0.9228 (mt) cc_final: 0.8800 (tp) REVERT: D 305 GLU cc_start: 0.4825 (OUTLIER) cc_final: 0.4511 (tp30) REVERT: D 328 ILE cc_start: 0.9212 (mp) cc_final: 0.8663 (mm) REVERT: D 368 MET cc_start: 0.9304 (ptm) cc_final: 0.8855 (ptm) REVERT: D 439 GLU cc_start: 0.8525 (mp0) cc_final: 0.8299 (mp0) REVERT: D 488 LEU cc_start: 0.8997 (tt) cc_final: 0.8454 (mm) REVERT: D 541 TRP cc_start: 0.7174 (OUTLIER) cc_final: 0.6855 (m100) REVERT: D 546 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: D 591 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8467 (tm-30) REVERT: D 613 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7454 (mtp85) REVERT: D 645 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9102 (mm) REVERT: D 687 TYR cc_start: 0.8273 (t80) cc_final: 0.7734 (t80) REVERT: E 203 ARG cc_start: 0.8668 (tmm160) cc_final: 0.8311 (ppt170) REVERT: E 314 LEU cc_start: 0.9375 (tp) cc_final: 0.9075 (tp) REVERT: E 352 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: E 389 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8965 (pm20) REVERT: E 398 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.8451 (p) REVERT: E 401 ASP cc_start: 0.9112 (m-30) cc_final: 0.8781 (m-30) REVERT: E 439 GLU cc_start: 0.8306 (mp0) cc_final: 0.8026 (mp0) REVERT: E 466 TRP cc_start: 0.8350 (m-10) cc_final: 0.7640 (m-90) REVERT: E 488 LEU cc_start: 0.8938 (tt) cc_final: 0.8371 (mm) REVERT: E 541 TRP cc_start: 0.7560 (OUTLIER) cc_final: 0.7252 (m100) REVERT: E 546 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: E 641 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7012 (mtt180) REVERT: F 368 MET cc_start: 0.9281 (ptm) cc_final: 0.8774 (ptm) REVERT: F 389 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8677 (pm20) REVERT: F 390 MET cc_start: 0.8126 (mmm) cc_final: 0.7651 (mmm) REVERT: F 393 TYR cc_start: 0.7711 (m-80) cc_final: 0.6902 (m-80) REVERT: F 439 GLU cc_start: 0.8239 (mp0) cc_final: 0.8013 (mp0) REVERT: F 466 TRP cc_start: 0.8130 (m-10) cc_final: 0.7384 (m-90) REVERT: F 478 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8530 (tm-30) REVERT: F 541 TRP cc_start: 0.6712 (OUTLIER) cc_final: 0.6344 (m100) REVERT: F 558 GLN cc_start: 0.9120 (mt0) cc_final: 0.8503 (mt0) REVERT: F 576 ARG cc_start: 0.7049 (ptp-110) cc_final: 0.6741 (mtt180) REVERT: G 203 ARG cc_start: 0.8751 (tmm160) cc_final: 0.8430 (ptt90) REVERT: G 208 LEU cc_start: 0.9241 (mt) cc_final: 0.8809 (tp) REVERT: G 305 GLU cc_start: 0.4820 (OUTLIER) cc_final: 0.4517 (tp30) REVERT: G 328 ILE cc_start: 0.9210 (mp) cc_final: 0.8655 (mm) REVERT: G 368 MET cc_start: 0.9290 (ptm) cc_final: 0.8814 (ptm) REVERT: G 439 GLU cc_start: 0.8516 (mp0) cc_final: 0.8284 (mp0) REVERT: G 467 ASP cc_start: 0.8722 (m-30) cc_final: 0.8354 (p0) REVERT: G 541 TRP cc_start: 0.7118 (OUTLIER) cc_final: 0.6883 (m100) REVERT: G 546 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6775 (pm20) REVERT: G 591 GLN cc_start: 0.8692 (tp40) cc_final: 0.8285 (tm-30) REVERT: G 652 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7704 (tmm) REVERT: G 687 TYR cc_start: 0.8270 (t80) cc_final: 0.7733 (t80) outliers start: 149 outliers final: 71 residues processed: 671 average time/residue: 0.1321 time to fit residues: 150.4427 Evaluate side-chains 638 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 544 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 333 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 GLU 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 492 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 A residue 641 ARG Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 GLU 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 541 TRP Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain D residue 199 LEU 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 389 GLU 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 541 TRP Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 705 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 333 THR Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 389 GLU 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 465 HIS Chi-restraints excluded: chain E residue 492 VAL 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 637 ASP Chi-restraints excluded: chain E residue 641 ARG Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 386 PHE Chi-restraints excluded: chain F residue 389 GLU Chi-restraints excluded: chain F residue 437 VAL 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 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 G residue 199 LEU 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 389 GLU 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 541 TRP Chi-restraints excluded: chain G residue 546 GLU Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 652 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 148 optimal weight: 0.7980 chunk 182 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 253 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 164 optimal weight: 0.0970 chunk 299 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 287 optimal weight: 0.0000 chunk 302 optimal weight: 0.7980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS D 648 HIS ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS G 698 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.118826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097747 restraints weight = 61147.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.100924 restraints weight = 35467.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.103186 restraints weight = 23816.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.104799 restraints weight = 17573.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105987 restraints weight = 13918.446| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23736 Z= 0.137 Angle : 0.711 9.554 32544 Z= 0.350 Chirality : 0.046 0.201 3966 Planarity : 0.005 0.070 4188 Dihedral : 11.728 176.093 3910 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.67 % Allowed : 26.10 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.14), residues: 3252 helix: -0.30 (0.13), residues: 1482 sheet: -0.88 (0.23), residues: 390 loop : -0.33 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 641 TYR 0.018 0.002 TYR G 687 PHE 0.024 0.002 PHE C 386 TRP 0.015 0.001 TRP D 466 HIS 0.006 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00313 (23724) covalent geometry : angle 0.71051 (32544) hydrogen bonds : bond 0.04159 ( 990) hydrogen bonds : angle 5.68325 ( 2790) Misc. bond : bond 0.00432 ( 12) *********************** 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 711 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 571 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8617 (tmm160) cc_final: 0.8267 (ppt170) REVERT: A 314 LEU cc_start: 0.9346 (tp) cc_final: 0.8975 (tp) REVERT: A 398 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.8477 (p) REVERT: A 401 ASP cc_start: 0.8846 (m-30) cc_final: 0.8548 (m-30) REVERT: A 439 GLU cc_start: 0.8360 (mp0) cc_final: 0.8102 (mp0) REVERT: A 466 TRP cc_start: 0.8336 (m-10) cc_final: 0.7608 (m-90) REVERT: A 541 TRP cc_start: 0.7393 (OUTLIER) cc_final: 0.7022 (m100) REVERT: A 641 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6910 (mtt180) REVERT: A 662 ASP cc_start: 0.9173 (t0) cc_final: 0.8895 (t0) REVERT: C 326 HIS cc_start: 0.7219 (m-70) cc_final: 0.6675 (t-90) REVERT: C 352 GLU cc_start: 0.8791 (pt0) cc_final: 0.8278 (pm20) REVERT: C 368 MET cc_start: 0.9308 (ptm) cc_final: 0.8874 (ptm) REVERT: C 439 GLU cc_start: 0.8255 (mp0) cc_final: 0.7992 (mp0) REVERT: C 541 TRP cc_start: 0.6703 (OUTLIER) cc_final: 0.6293 (m100) REVERT: C 558 GLN cc_start: 0.9123 (mt0) cc_final: 0.8543 (mt0) REVERT: D 203 ARG cc_start: 0.8721 (tmm160) cc_final: 0.8404 (ptt90) REVERT: D 208 LEU cc_start: 0.9283 (mt) cc_final: 0.8781 (tp) REVERT: D 305 GLU cc_start: 0.4970 (OUTLIER) cc_final: 0.4759 (tp30) REVERT: D 328 ILE cc_start: 0.9155 (mp) cc_final: 0.8618 (mm) REVERT: D 368 MET cc_start: 0.9237 (ptm) cc_final: 0.8745 (ptm) REVERT: D 478 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8374 (tm-30) REVERT: D 488 LEU cc_start: 0.9011 (tt) cc_final: 0.8464 (mm) REVERT: D 541 TRP cc_start: 0.7236 (OUTLIER) cc_final: 0.6968 (m100) REVERT: D 546 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: D 591 GLN cc_start: 0.8769 (tp-100) cc_final: 0.8472 (tm-30) REVERT: D 613 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7085 (mtp85) REVERT: D 648 HIS cc_start: 0.7920 (m-70) cc_final: 0.7273 (m170) REVERT: D 676 GLU cc_start: 0.8852 (tp30) cc_final: 0.8523 (tp30) REVERT: D 687 TYR cc_start: 0.8396 (t80) cc_final: 0.7809 (t80) REVERT: E 203 ARG cc_start: 0.8644 (tmm160) cc_final: 0.8306 (ppt170) REVERT: E 239 LEU cc_start: 0.9632 (tt) cc_final: 0.9414 (mt) REVERT: E 314 LEU cc_start: 0.9338 (tp) cc_final: 0.9059 (tp) REVERT: E 398 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.8506 (p) REVERT: E 401 ASP cc_start: 0.8889 (m-30) cc_final: 0.8602 (m-30) REVERT: E 439 GLU cc_start: 0.8340 (mp0) cc_final: 0.8086 (mp0) REVERT: E 466 TRP cc_start: 0.8317 (m-10) cc_final: 0.7557 (m-90) REVERT: E 474 ASP cc_start: 0.9142 (p0) cc_final: 0.8852 (p0) REVERT: E 541 TRP cc_start: 0.7393 (OUTLIER) cc_final: 0.7057 (m100) REVERT: E 546 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: E 572 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8127 (tt) REVERT: E 617 MET cc_start: 0.8224 (ptm) cc_final: 0.7807 (ptp) REVERT: E 641 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6799 (mtt180) REVERT: F 205 MET cc_start: 0.9275 (ppp) cc_final: 0.8744 (ppp) REVERT: F 352 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: F 368 MET cc_start: 0.9304 (ptm) cc_final: 0.8866 (ptm) REVERT: F 389 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8849 (pm20) REVERT: F 541 TRP cc_start: 0.6658 (OUTLIER) cc_final: 0.6242 (m100) REVERT: F 558 GLN cc_start: 0.9135 (mt0) cc_final: 0.8529 (mt0) REVERT: G 203 ARG cc_start: 0.8718 (tmm160) cc_final: 0.8412 (ptt90) REVERT: G 208 LEU cc_start: 0.9292 (mt) cc_final: 0.8791 (tp) REVERT: G 305 GLU cc_start: 0.4955 (OUTLIER) cc_final: 0.4753 (tp30) REVERT: G 328 ILE cc_start: 0.9160 (mp) cc_final: 0.8619 (mm) REVERT: G 368 MET cc_start: 0.9272 (ptm) cc_final: 0.8795 (ptm) REVERT: G 467 ASP cc_start: 0.8559 (m-30) cc_final: 0.8348 (p0) REVERT: G 478 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8413 (tm-30) REVERT: G 541 TRP cc_start: 0.7067 (OUTLIER) cc_final: 0.6843 (m100) REVERT: G 546 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: G 591 GLN cc_start: 0.8647 (tp40) cc_final: 0.8349 (tm-30) REVERT: G 687 TYR cc_start: 0.8383 (t80) cc_final: 0.7798 (t80) outliers start: 140 outliers final: 82 residues processed: 656 average time/residue: 0.1333 time to fit residues: 148.7875 Evaluate side-chains 633 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 533 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 465 HIS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 THR 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 389 GLU 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 498 ILE Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 612 ASN 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 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 389 GLU 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 541 TRP Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 586 GLU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 705 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 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 465 HIS Chi-restraints excluded: chain E residue 492 VAL 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 572 ILE Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 641 ARG 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 333 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 386 PHE 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 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 G residue 199 LEU 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 389 GLU 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 541 TRP Chi-restraints excluded: chain G residue 546 GLU Chi-restraints excluded: chain G residue 586 GLU Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 663 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 322 optimal weight: 0.0980 chunk 184 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 125 optimal weight: 0.0980 chunk 181 optimal weight: 0.0570 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS E 648 HIS ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.3861 r_free = 0.3861 target = 0.119773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098894 restraints weight = 60720.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.102091 restraints weight = 35023.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104368 restraints weight = 23387.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.106012 restraints weight = 17166.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107209 restraints weight = 13522.424| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23736 Z= 0.135 Angle : 0.725 12.204 32544 Z= 0.353 Chirality : 0.045 0.206 3966 Planarity : 0.006 0.070 4188 Dihedral : 11.536 171.640 3907 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.57 % Allowed : 27.86 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.14), residues: 3252 helix: -0.30 (0.13), residues: 1446 sheet: -0.74 (0.23), residues: 384 loop : -0.46 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 626 TYR 0.021 0.002 TYR F 265 PHE 0.019 0.002 PHE C 386 TRP 0.017 0.001 TRP D 466 HIS 0.004 0.001 HIS D 648 Details of bonding type rmsd covalent geometry : bond 0.00305 (23724) covalent geometry : angle 0.72526 (32544) hydrogen bonds : bond 0.04097 ( 990) hydrogen bonds : angle 5.57407 ( 2790) Misc. bond : bond 0.00275 ( 12) *********************** 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 682 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 565 time to evaluate : 0.921 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: A 187 ILE cc_start: 0.8135 (mp) cc_final: 0.7860 (mp) REVERT: A 203 ARG cc_start: 0.8636 (tmm160) cc_final: 0.8278 (ppt170) REVERT: A 314 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8945 (tp) REVERT: A 439 GLU cc_start: 0.8372 (mp0) cc_final: 0.8110 (mp0) REVERT: A 466 TRP cc_start: 0.8245 (m-10) cc_final: 0.7436 (m-90) REVERT: A 641 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6895 (mtt180) REVERT: A 662 ASP cc_start: 0.9205 (t0) cc_final: 0.8924 (t0) REVERT: C 326 HIS cc_start: 0.7233 (m-70) cc_final: 0.6668 (t-90) REVERT: C 352 GLU cc_start: 0.8770 (pt0) cc_final: 0.8317 (pm20) REVERT: C 368 MET cc_start: 0.9354 (ptm) cc_final: 0.8940 (ptm) REVERT: C 541 TRP cc_start: 0.6682 (OUTLIER) cc_final: 0.6354 (m100) REVERT: C 558 GLN cc_start: 0.9136 (mt0) cc_final: 0.8541 (mt0) REVERT: D 203 ARG cc_start: 0.8768 (tmm160) cc_final: 0.8451 (ptt90) REVERT: D 208 LEU cc_start: 0.9261 (mt) cc_final: 0.8765 (tp) REVERT: D 328 ILE cc_start: 0.9163 (mp) cc_final: 0.8609 (mm) REVERT: D 368 MET cc_start: 0.9219 (ptm) cc_final: 0.8731 (ptm) REVERT: D 389 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: D 390 MET cc_start: 0.7062 (mmm) cc_final: 0.6350 (mmm) REVERT: D 393 TYR cc_start: 0.7324 (m-80) cc_final: 0.7103 (m-80) REVERT: D 478 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8358 (tm-30) REVERT: D 488 LEU cc_start: 0.9020 (tt) cc_final: 0.8469 (mm) REVERT: D 541 TRP cc_start: 0.7145 (OUTLIER) cc_final: 0.6925 (m100) REVERT: D 546 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6106 (pm20) REVERT: D 591 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8421 (tm-30) REVERT: D 613 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7034 (mtp85) REVERT: D 648 HIS cc_start: 0.7984 (m-70) cc_final: 0.7310 (m170) REVERT: D 676 GLU cc_start: 0.8915 (tp30) cc_final: 0.8602 (tp30) REVERT: D 677 ASN cc_start: 0.9036 (m-40) cc_final: 0.8700 (m-40) REVERT: D 687 TYR cc_start: 0.8390 (t80) cc_final: 0.7819 (t80) REVERT: E 203 ARG cc_start: 0.8619 (tmm160) cc_final: 0.8251 (ppt170) REVERT: E 314 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8879 (tp) REVERT: E 318 MET cc_start: 0.8679 (mmm) cc_final: 0.8374 (mmm) REVERT: E 439 GLU cc_start: 0.8346 (mp0) cc_final: 0.8086 (mp0) REVERT: E 466 TRP cc_start: 0.8244 (m-10) cc_final: 0.7420 (m-90) REVERT: E 541 TRP cc_start: 0.7510 (OUTLIER) cc_final: 0.7280 (m100) REVERT: E 546 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6292 (pm20) REVERT: E 641 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6548 (mtp85) REVERT: E 645 LEU cc_start: 0.9270 (mm) cc_final: 0.8947 (mm) REVERT: F 205 MET cc_start: 0.9417 (ppp) cc_final: 0.8764 (ppp) REVERT: F 368 MET cc_start: 0.9346 (ptm) cc_final: 0.8934 (ptm) REVERT: F 389 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8897 (pm20) REVERT: F 393 TYR cc_start: 0.7213 (m-80) cc_final: 0.6951 (m-80) REVERT: F 466 TRP cc_start: 0.8439 (m-10) cc_final: 0.7808 (m-90) REVERT: F 541 TRP cc_start: 0.6664 (OUTLIER) cc_final: 0.6293 (m100) REVERT: F 558 GLN cc_start: 0.9154 (mt0) cc_final: 0.8537 (mt0) REVERT: G 203 ARG cc_start: 0.8766 (tmm160) cc_final: 0.8456 (ptt90) REVERT: G 208 LEU cc_start: 0.9266 (mt) cc_final: 0.8775 (tp) REVERT: G 328 ILE cc_start: 0.9154 (mp) cc_final: 0.8597 (mm) REVERT: G 368 MET cc_start: 0.9216 (ptm) cc_final: 0.8724 (ptm) REVERT: G 389 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8671 (pm20) REVERT: G 390 MET cc_start: 0.7072 (mmm) cc_final: 0.6628 (mmm) REVERT: G 467 ASP cc_start: 0.8576 (m-30) cc_final: 0.8339 (p0) REVERT: G 478 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8413 (tm-30) REVERT: G 591 GLN cc_start: 0.8668 (tp40) cc_final: 0.8396 (tm-30) REVERT: G 613 ARG cc_start: 0.7849 (mtt180) cc_final: 0.6976 (mtp85) REVERT: G 677 ASN cc_start: 0.9048 (m-40) cc_final: 0.8706 (t0) REVERT: G 687 TYR cc_start: 0.8376 (t80) cc_final: 0.7813 (t80) outliers start: 117 outliers final: 76 residues processed: 636 average time/residue: 0.1350 time to fit residues: 145.4368 Evaluate side-chains 626 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 537 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 389 GLU 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 641 ARG Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 199 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 389 GLU 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 541 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 612 ASN 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 386 PHE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 454 LEU 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 546 GLU Chi-restraints excluded: chain D residue 586 GLU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 705 LEU 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 389 GLU 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 532 ILE Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 641 ARG Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 199 LEU 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 386 PHE 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 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 564 VAL 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 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 531 SER Chi-restraints excluded: chain G residue 546 GLU Chi-restraints excluded: chain G residue 586 GLU Chi-restraints excluded: chain G residue 637 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 81 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 228 optimal weight: 0.7980 chunk 275 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS E 648 HIS ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 698 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.120423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.098684 restraints weight = 60718.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.101938 restraints weight = 35332.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.104226 restraints weight = 23800.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105872 restraints weight = 17673.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107081 restraints weight = 14061.107| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23736 Z= 0.136 Angle : 0.725 10.320 32544 Z= 0.355 Chirality : 0.046 0.206 3966 Planarity : 0.006 0.067 4188 Dihedral : 11.487 172.869 3903 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.76 % Allowed : 28.95 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.14), residues: 3252 helix: -0.25 (0.13), residues: 1446 sheet: -0.80 (0.23), residues: 390 loop : -0.45 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 372 TYR 0.038 0.002 TYR G 393 PHE 0.022 0.002 PHE F 529 TRP 0.020 0.001 TRP C 466 HIS 0.005 0.001 HIS D 648 Details of bonding type rmsd covalent geometry : bond 0.00310 (23724) covalent geometry : angle 0.72549 (32544) hydrogen bonds : bond 0.04067 ( 990) hydrogen bonds : angle 5.50179 ( 2790) Misc. bond : bond 0.00247 ( 12) *********************** 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 682 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 561 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.8146 (mp) cc_final: 0.7945 (mp) REVERT: A 203 ARG cc_start: 0.8645 (tmm160) cc_final: 0.8289 (ppt170) REVERT: A 314 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9103 (tp) REVERT: A 439 GLU cc_start: 0.8364 (mp0) cc_final: 0.8114 (mp0) REVERT: A 466 TRP cc_start: 0.8239 (m-10) cc_final: 0.7388 (m-90) REVERT: A 613 ARG cc_start: 0.7785 (mtt180) cc_final: 0.6959 (ttm110) REVERT: A 645 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8900 (mm) REVERT: A 662 ASP cc_start: 0.9247 (t0) cc_final: 0.8964 (t0) REVERT: C 352 GLU cc_start: 0.8740 (pt0) cc_final: 0.8201 (pm20) REVERT: C 368 MET cc_start: 0.9389 (ptm) cc_final: 0.8976 (ptm) REVERT: C 389 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8743 (pm20) REVERT: C 390 MET cc_start: 0.7124 (mmm) cc_final: 0.5934 (mmm) REVERT: C 393 TYR cc_start: 0.7190 (m-80) cc_final: 0.6908 (m-80) REVERT: C 536 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8884 (tm-30) REVERT: C 541 TRP cc_start: 0.6611 (OUTLIER) cc_final: 0.6212 (m100) REVERT: C 558 GLN cc_start: 0.9170 (mt0) cc_final: 0.8564 (mt0) REVERT: C 648 HIS cc_start: 0.6896 (m-70) cc_final: 0.6608 (m170) REVERT: D 203 ARG cc_start: 0.8783 (tmm160) cc_final: 0.8581 (ptt90) REVERT: D 208 LEU cc_start: 0.9261 (mt) cc_final: 0.8812 (tp) REVERT: D 328 ILE cc_start: 0.9189 (mp) cc_final: 0.8662 (mm) REVERT: D 368 MET cc_start: 0.9248 (ptm) cc_final: 0.8747 (ptm) REVERT: D 389 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8548 (pm20) REVERT: D 390 MET cc_start: 0.7003 (mmm) cc_final: 0.6453 (mmm) REVERT: D 488 LEU cc_start: 0.9027 (tt) cc_final: 0.8502 (mm) REVERT: D 523 THR cc_start: 0.8705 (m) cc_final: 0.8319 (p) REVERT: D 541 TRP cc_start: 0.7161 (OUTLIER) cc_final: 0.6857 (m100) REVERT: D 591 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8498 (tm-30) REVERT: D 613 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7043 (mtp85) REVERT: D 648 HIS cc_start: 0.8175 (m-70) cc_final: 0.7276 (m170) REVERT: D 677 ASN cc_start: 0.9018 (m-40) cc_final: 0.8744 (m-40) REVERT: D 687 TYR cc_start: 0.8406 (t80) cc_final: 0.7840 (t80) REVERT: E 203 ARG cc_start: 0.8617 (tmm160) cc_final: 0.8275 (ppt170) REVERT: E 314 LEU cc_start: 0.9371 (tp) cc_final: 0.9081 (tp) REVERT: E 439 GLU cc_start: 0.8332 (mp0) cc_final: 0.8093 (mp0) REVERT: E 466 TRP cc_start: 0.8200 (m-10) cc_final: 0.7316 (m-90) REVERT: E 541 TRP cc_start: 0.7324 (OUTLIER) cc_final: 0.6957 (m100) REVERT: E 613 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7447 (mtp85) REVERT: E 641 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6655 (mtp85) REVERT: E 645 LEU cc_start: 0.9248 (mm) cc_final: 0.8949 (mm) REVERT: F 205 MET cc_start: 0.9467 (ppp) cc_final: 0.8810 (ppp) REVERT: F 352 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: F 368 MET cc_start: 0.9351 (ptm) cc_final: 0.8972 (ptm) REVERT: F 389 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8897 (pm20) REVERT: F 517 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9123 (tt) REVERT: F 558 GLN cc_start: 0.9116 (mt0) cc_final: 0.8547 (mt0) REVERT: G 208 LEU cc_start: 0.9259 (mt) cc_final: 0.8821 (tp) REVERT: G 328 ILE cc_start: 0.9186 (mp) cc_final: 0.8659 (mm) REVERT: G 368 MET cc_start: 0.9273 (ptm) cc_final: 0.8782 (ptm) REVERT: G 389 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.9017 (pm20) REVERT: G 467 ASP cc_start: 0.8591 (m-30) cc_final: 0.8362 (p0) REVERT: G 478 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8475 (tm-30) REVERT: G 591 GLN cc_start: 0.8791 (tp40) cc_final: 0.8499 (tm-30) REVERT: G 613 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7020 (mtp85) REVERT: G 677 ASN cc_start: 0.9046 (m-40) cc_final: 0.8747 (m-40) REVERT: G 687 TYR cc_start: 0.8406 (t80) cc_final: 0.7834 (t80) outliers start: 121 outliers final: 85 residues processed: 639 average time/residue: 0.1359 time to fit residues: 146.7656 Evaluate side-chains 628 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 531 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 389 GLU 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 531 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 GLU 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 541 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 612 ASN 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 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 389 GLU 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 531 SER Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 586 GLU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 654 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 333 THR Chi-restraints excluded: chain E residue 389 GLU 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 465 HIS Chi-restraints excluded: chain E residue 492 VAL 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 586 GLU Chi-restraints excluded: chain E residue 641 ARG Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 199 LEU 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 352 GLU Chi-restraints excluded: chain F residue 389 GLU 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 465 HIS Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 586 GLU 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 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 389 GLU 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 531 SER Chi-restraints excluded: chain G residue 546 GLU Chi-restraints excluded: chain G residue 586 GLU Chi-restraints excluded: chain G residue 589 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 280 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 178 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS C 528 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.119612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098314 restraints weight = 61174.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.101517 restraints weight = 35472.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103778 restraints weight = 23888.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.105412 restraints weight = 17712.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106585 restraints weight = 14072.395| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23736 Z= 0.137 Angle : 0.728 11.266 32544 Z= 0.357 Chirality : 0.046 0.198 3966 Planarity : 0.006 0.066 4188 Dihedral : 11.358 173.997 3900 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.10 % Allowed : 30.29 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 3252 helix: -0.25 (0.13), residues: 1482 sheet: -0.77 (0.23), residues: 390 loop : -0.40 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 455 TYR 0.037 0.002 TYR D 393 PHE 0.027 0.001 PHE G 386 TRP 0.019 0.002 TRP C 466 HIS 0.007 0.001 HIS D 648 Details of bonding type rmsd covalent geometry : bond 0.00312 (23724) covalent geometry : angle 0.72814 (32544) hydrogen bonds : bond 0.03985 ( 990) hydrogen bonds : angle 5.48020 ( 2790) Misc. bond : bond 0.00305 ( 12) *********************** 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 655 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 548 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8644 (tmm160) cc_final: 0.8295 (ppt170) REVERT: A 439 GLU cc_start: 0.8339 (mp0) cc_final: 0.8110 (mp0) REVERT: A 466 TRP cc_start: 0.8219 (m-10) cc_final: 0.7372 (m-90) REVERT: A 645 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8916 (mm) REVERT: A 662 ASP cc_start: 0.9299 (t0) cc_final: 0.8924 (t0) REVERT: C 352 GLU cc_start: 0.8718 (pt0) cc_final: 0.8035 (tm-30) REVERT: C 368 MET cc_start: 0.9377 (ptm) cc_final: 0.8954 (ptm) REVERT: C 389 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8872 (pm20) REVERT: C 390 MET cc_start: 0.7044 (mmm) cc_final: 0.6193 (mmm) REVERT: C 393 TYR cc_start: 0.7219 (m-80) cc_final: 0.7009 (m-80) REVERT: C 536 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8975 (tm-30) REVERT: C 541 TRP cc_start: 0.6577 (OUTLIER) cc_final: 0.6212 (m100) REVERT: C 558 GLN cc_start: 0.9117 (mt0) cc_final: 0.8561 (mt0) REVERT: C 648 HIS cc_start: 0.7044 (m-70) cc_final: 0.6731 (m170) REVERT: D 203 ARG cc_start: 0.8783 (tmm160) cc_final: 0.8578 (ptt90) REVERT: D 208 LEU cc_start: 0.9285 (mt) cc_final: 0.8859 (tp) REVERT: D 328 ILE cc_start: 0.9196 (mp) cc_final: 0.8673 (mm) REVERT: D 368 MET cc_start: 0.9246 (ptm) cc_final: 0.8785 (ptm) REVERT: D 478 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8459 (tm-30) REVERT: D 488 LEU cc_start: 0.9054 (tt) cc_final: 0.8521 (mm) REVERT: D 541 TRP cc_start: 0.6956 (OUTLIER) cc_final: 0.6648 (m100) REVERT: D 591 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8476 (tm-30) REVERT: D 613 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7041 (mtp85) REVERT: D 687 TYR cc_start: 0.8394 (t80) cc_final: 0.7846 (t80) REVERT: E 203 ARG cc_start: 0.8556 (tmm160) cc_final: 0.8173 (ppt170) REVERT: E 466 TRP cc_start: 0.8216 (m-10) cc_final: 0.7365 (m-90) REVERT: E 541 TRP cc_start: 0.7327 (OUTLIER) cc_final: 0.6875 (m100) REVERT: E 613 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7595 (mtp85) REVERT: E 641 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6627 (mtp85) REVERT: E 645 LEU cc_start: 0.9237 (mm) cc_final: 0.8936 (mm) REVERT: F 205 MET cc_start: 0.9464 (ppp) cc_final: 0.8809 (ppp) REVERT: F 352 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: F 368 MET cc_start: 0.9399 (ptm) cc_final: 0.9007 (ptm) REVERT: F 389 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8920 (pm20) REVERT: F 541 TRP cc_start: 0.6564 (OUTLIER) cc_final: 0.6124 (m100) REVERT: F 558 GLN cc_start: 0.9110 (mt0) cc_final: 0.8540 (mt0) REVERT: F 617 MET cc_start: 0.8826 (pmm) cc_final: 0.8317 (pmm) REVERT: G 208 LEU cc_start: 0.9304 (mt) cc_final: 0.8869 (tp) REVERT: G 328 ILE cc_start: 0.9196 (mp) cc_final: 0.8671 (mm) REVERT: G 368 MET cc_start: 0.9240 (ptm) cc_final: 0.8782 (ptm) REVERT: G 467 ASP cc_start: 0.8607 (m-30) cc_final: 0.8326 (p0) REVERT: G 478 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8510 (tm-30) REVERT: G 591 GLN cc_start: 0.8851 (tp40) cc_final: 0.8512 (tm-30) REVERT: G 613 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7008 (mtp85) REVERT: G 677 ASN cc_start: 0.9019 (m-40) cc_final: 0.8741 (m-40) REVERT: G 687 TYR cc_start: 0.8330 (t80) cc_final: 0.7792 (t80) outliers start: 107 outliers final: 78 residues processed: 621 average time/residue: 0.1257 time to fit residues: 132.3150 Evaluate side-chains 613 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 526 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 GLU 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 531 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 255 ILE 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 389 GLU 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 541 TRP Chi-restraints excluded: chain C residue 569 ILE 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 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 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 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 586 GLU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 239 LEU 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 389 GLU 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 465 HIS Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 586 GLU Chi-restraints excluded: chain E residue 641 ARG Chi-restraints excluded: chain E residue 644 ILE 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 352 GLU Chi-restraints excluded: chain F residue 389 GLU 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 465 HIS Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 586 GLU 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 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR 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 586 GLU Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain G residue 612 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 272 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 189 optimal weight: 0.2980 chunk 172 optimal weight: 0.0770 chunk 79 optimal weight: 5.9990 chunk 235 optimal weight: 0.0670 chunk 38 optimal weight: 4.9990 chunk 311 optimal weight: 0.6980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS E 648 HIS ** G 685 ASN ** 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 = 0.3888 r_free = 0.3888 target = 0.121584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100213 restraints weight = 59865.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.103459 restraints weight = 34692.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.105771 restraints weight = 23311.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107452 restraints weight = 17242.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.108660 restraints weight = 13636.677| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23736 Z= 0.133 Angle : 0.750 11.919 32544 Z= 0.364 Chirality : 0.046 0.204 3966 Planarity : 0.005 0.064 4188 Dihedral : 11.199 174.453 3892 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.43 % Allowed : 31.10 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 3252 helix: -0.24 (0.13), residues: 1446 sheet: -0.69 (0.23), residues: 390 loop : -0.44 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 641 TYR 0.035 0.002 TYR D 393 PHE 0.026 0.001 PHE D 386 TRP 0.022 0.002 TRP C 466 HIS 0.003 0.001 HIS F 370 Details of bonding type rmsd covalent geometry : bond 0.00296 (23724) covalent geometry : angle 0.75013 (32544) hydrogen bonds : bond 0.03921 ( 990) hydrogen bonds : angle 5.44500 ( 2790) Misc. bond : bond 0.00423 ( 12) ********************** 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 651 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 558 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.8712 (tmm160) cc_final: 0.8347 (ppt170) REVERT: A 466 TRP cc_start: 0.8144 (m-10) cc_final: 0.7320 (m-90) REVERT: A 474 ASP cc_start: 0.9229 (p0) cc_final: 0.9015 (p0) REVERT: A 662 ASP cc_start: 0.9400 (t0) cc_final: 0.9033 (t0) REVERT: A 687 TYR cc_start: 0.8705 (t80) cc_final: 0.8228 (t80) REVERT: C 352 GLU cc_start: 0.8746 (pt0) cc_final: 0.7987 (tm-30) REVERT: C 353 ILE cc_start: 0.9095 (pt) cc_final: 0.8247 (pt) REVERT: C 368 MET cc_start: 0.9379 (ptm) cc_final: 0.9062 (ptm) REVERT: C 390 MET cc_start: 0.6748 (mmm) cc_final: 0.5641 (mmm) REVERT: C 393 TYR cc_start: 0.7273 (m-80) cc_final: 0.6990 (m-80) REVERT: C 536 GLU cc_start: 0.9264 (tm-30) cc_final: 0.9005 (tm-30) REVERT: C 541 TRP cc_start: 0.6587 (OUTLIER) cc_final: 0.6324 (m100) REVERT: C 558 GLN cc_start: 0.9117 (mt0) cc_final: 0.8507 (mt0) REVERT: C 594 THR cc_start: 0.9278 (t) cc_final: 0.9074 (p) REVERT: C 614 PRO cc_start: 0.8291 (Cg_exo) cc_final: 0.7864 (Cg_endo) REVERT: C 652 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8163 (mtt) REVERT: D 208 LEU cc_start: 0.9275 (mt) cc_final: 0.8848 (tp) REVERT: D 328 ILE cc_start: 0.9209 (mp) cc_final: 0.8680 (mm) REVERT: D 478 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8482 (tm-30) REVERT: D 488 LEU cc_start: 0.9071 (tt) cc_final: 0.8533 (mm) REVERT: D 591 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8441 (tm-30) REVERT: D 613 ARG cc_start: 0.7816 (mtt180) cc_final: 0.6969 (mtp85) REVERT: D 687 TYR cc_start: 0.8411 (t80) cc_final: 0.7854 (t80) REVERT: E 203 ARG cc_start: 0.8549 (tmm160) cc_final: 0.8161 (ppt170) REVERT: E 466 TRP cc_start: 0.8141 (m-10) cc_final: 0.7283 (m-90) REVERT: E 474 ASP cc_start: 0.9197 (p0) cc_final: 0.8959 (p0) REVERT: E 541 TRP cc_start: 0.7178 (OUTLIER) cc_final: 0.6849 (m100) REVERT: E 558 GLN cc_start: 0.9224 (mt0) cc_final: 0.8687 (mt0) REVERT: E 613 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7184 (mtp85) REVERT: E 645 LEU cc_start: 0.9232 (mm) cc_final: 0.8924 (mm) REVERT: F 205 MET cc_start: 0.9464 (ppp) cc_final: 0.8808 (ppp) REVERT: F 352 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: F 368 MET cc_start: 0.9389 (ptm) cc_final: 0.9003 (ptm) REVERT: F 541 TRP cc_start: 0.6503 (OUTLIER) cc_final: 0.6243 (m100) REVERT: F 558 GLN cc_start: 0.9127 (mt0) cc_final: 0.8515 (mt0) REVERT: F 617 MET cc_start: 0.8786 (pmm) cc_final: 0.8106 (pmm) REVERT: F 652 MET cc_start: 0.8352 (mmm) cc_final: 0.8050 (mmp) REVERT: G 208 LEU cc_start: 0.9308 (mt) cc_final: 0.8881 (tp) REVERT: G 328 ILE cc_start: 0.9206 (mp) cc_final: 0.8680 (mm) REVERT: G 368 MET cc_start: 0.9227 (ptm) cc_final: 0.8771 (ptm) REVERT: G 478 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8519 (tm-30) REVERT: G 591 GLN cc_start: 0.8721 (tp40) cc_final: 0.8465 (tm-30) REVERT: G 613 ARG cc_start: 0.7836 (mtt180) cc_final: 0.6998 (mtp85) REVERT: G 677 ASN cc_start: 0.9022 (m-40) cc_final: 0.8817 (m-40) REVERT: G 687 TYR cc_start: 0.8410 (t80) cc_final: 0.7846 (t80) outliers start: 93 outliers final: 71 residues processed: 620 average time/residue: 0.1164 time to fit residues: 123.6435 Evaluate side-chains 622 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 546 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 GLU 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 531 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 THR 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 386 PHE Chi-restraints excluded: chain C residue 389 GLU 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 541 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 652 MET 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 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 461 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 663 ILE 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 333 THR Chi-restraints excluded: chain E residue 389 GLU 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 465 HIS Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain E residue 692 ASP 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 352 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 541 TRP Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 586 GLU 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 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR 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 589 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 287 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 306 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS D 648 HIS ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.118822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097500 restraints weight = 61108.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.100659 restraints weight = 35810.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102890 restraints weight = 24269.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.104477 restraints weight = 18082.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.105653 restraints weight = 14484.774| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23736 Z= 0.151 Angle : 0.754 11.456 32544 Z= 0.372 Chirality : 0.046 0.200 3966 Planarity : 0.005 0.068 4188 Dihedral : 11.153 174.277 3892 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.95 % Allowed : 32.00 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 3252 helix: -0.12 (0.13), residues: 1500 sheet: -0.70 (0.24), residues: 390 loop : -0.31 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 641 TYR 0.035 0.002 TYR D 393 PHE 0.030 0.002 PHE G 386 TRP 0.022 0.002 TRP F 466 HIS 0.003 0.001 HIS F 648 Details of bonding type rmsd covalent geometry : bond 0.00349 (23724) covalent geometry : angle 0.75394 (32544) hydrogen bonds : bond 0.03990 ( 990) hydrogen bonds : angle 5.43177 ( 2790) Misc. bond : bond 0.00222 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4464.44 seconds wall clock time: 77 minutes 44.63 seconds (4664.63 seconds total)