Starting phenix.real_space_refine on Wed May 6 05:52:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ve_76074/05_2026/11ve_76074.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ve_76074/05_2026/11ve_76074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11ve_76074/05_2026/11ve_76074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ve_76074/05_2026/11ve_76074.map" model { file = "/net/cci-nas-00/data/ceres_data/11ve_76074/05_2026/11ve_76074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ve_76074/05_2026/11ve_76074.cif" } resolution = 3.85 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= 0.029 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 27 5.49 5 S 151 5.16 5 C 22136 2.51 5 N 6270 2.21 5 O 6796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35382 Number of models: 1 Model: "" Number of chains: 17 Chain: "G" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4397 Classifications: {'peptide': 553} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 522} Chain breaks: 1 Chain: "M" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1025 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 112} Chain: "O" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 861 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 94} Chain: "P" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 2 Chain: "A" Number of atoms: 5201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5201 Classifications: {'peptide': 728} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 40, 'TRANS': 687} Chain breaks: 2 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 692 Unresolved non-hydrogen dihedrals: 431 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 16, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 6, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 310 Chain: "B" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4300 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 519} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5176 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 685} Chain breaks: 3 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 16, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 4, 'PHE:plan': 6, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 314 Chain: "D" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4201 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 521} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 9, 'ASP:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 95 Chain: "E" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4268 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 519} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "F" Number of atoms: 5195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5195 Classifications: {'peptide': 727} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 547 Unresolved non-hydrogen angles: 693 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 16, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 6, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 313 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 884 SG CYS G 130 100.922 88.390 134.093 1.00 28.04 S ATOM 943 SG CYS G 138 102.904 85.612 132.339 1.00 12.28 S ATOM 966 SG CYS G 141 104.318 89.021 132.636 1.00 27.02 S ATOM 1383 SG CYS G 194 126.108 101.694 92.049 1.00485.39 S ATOM 1468 SG CYS G 205 125.825 99.155 89.054 1.00447.95 S ATOM 1490 SG CYS G 208 123.284 102.120 89.514 1.00424.08 S Time building chain proxies: 8.87, per 1000 atoms: 0.25 Number of scatterers: 35382 At special positions: 0 Unit cell: (199.462, 175.822, 178.777, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 151 16.00 P 27 15.00 O 6796 8.00 N 6270 7.00 C 22136 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=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 701 " pdb="ZN ZN G 701 " - pdb=" NE2 HIS G 140 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 138 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 141 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 130 " pdb=" ZN G 702 " pdb="ZN ZN G 702 " - pdb=" ND1 HIS G 197 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 208 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 194 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 205 " Number of angles added : 6 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8784 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 34 sheets defined 52.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'G' and resid 25 through 38 Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 108 through 116 Processing helix chain 'G' and resid 138 through 142 removed outlier: 3.879A pdb=" N VAL G 142 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 155 removed outlier: 3.747A pdb=" N LEU G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 172 Processing helix chain 'G' and resid 231 through 236 Processing helix chain 'G' and resid 238 through 245 Processing helix chain 'G' and resid 291 through 304 removed outlier: 4.078A pdb=" N VAL G 295 " --> pdb=" O PRO G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 351 Processing helix chain 'G' and resid 388 through 397 Processing helix chain 'G' and resid 484 through 495 Processing helix chain 'G' and resid 500 through 505 removed outlier: 3.584A pdb=" N SER G 505 " --> pdb=" O LEU G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 516 removed outlier: 3.521A pdb=" N LEU G 510 " --> pdb=" O ASP G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 535 removed outlier: 4.330A pdb=" N LEU G 528 " --> pdb=" O SER G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 545 removed outlier: 4.006A pdb=" N ALA G 540 " --> pdb=" O ASN G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 560 removed outlier: 4.338A pdb=" N ALA G 550 " --> pdb=" O SER G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 566 through 570 removed outlier: 3.693A pdb=" N GLY G 570 " --> pdb=" O HIS G 567 " (cutoff:3.500A) Processing helix chain 'M' and resid 530 through 561 Processing helix chain 'M' and resid 595 through 605 removed outlier: 3.758A pdb=" N VAL M 599 " --> pdb=" O LYS M 595 " (cutoff:3.500A) Processing helix chain 'M' and resid 625 through 627 No H-bonds generated for 'chain 'M' and resid 625 through 627' Processing helix chain 'O' and resid 548 through 559 removed outlier: 4.296A pdb=" N GLN O 559 " --> pdb=" O LEU O 555 " (cutoff:3.500A) Processing helix chain 'O' and resid 595 through 605 removed outlier: 4.370A pdb=" N VAL O 599 " --> pdb=" O LYS O 595 " (cutoff:3.500A) Processing helix chain 'O' and resid 609 through 611 No H-bonds generated for 'chain 'O' and resid 609 through 611' Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 91 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.540A pdb=" N LEU A 140 " --> pdb=" O PRO A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 200 removed outlier: 3.768A pdb=" N GLU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 removed outlier: 6.025A pdb=" N ASP A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.524A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.710A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.644A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 296 removed outlier: 3.573A pdb=" N SER A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.956A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 437 through 444 removed outlier: 3.948A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.516A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.508A pdb=" N GLY A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.906A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.704A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.769A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.914A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 553 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 616 removed outlier: 4.166A pdb=" N ASN A 616 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.584A pdb=" N ILE A 633 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 removed outlier: 3.845A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 3.580A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 715 Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.654A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 760 removed outlier: 3.545A pdb=" N GLN A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 199 removed outlier: 3.609A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.594A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.661A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.731A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 319 through 335 removed outlier: 3.972A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.854A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.751A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.045A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 4.189A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 554 removed outlier: 3.882A pdb=" N LEU B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.899A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 Processing helix chain 'B' and resid 599 through 610 Processing helix chain 'B' and resid 612 through 615 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 652 through 661 Processing helix chain 'B' and resid 671 through 677 removed outlier: 3.613A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 715 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.999A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 760 removed outlier: 3.664A pdb=" N GLU B 756 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 189 through 199 Processing helix chain 'C' and resid 200 through 201 No H-bonds generated for 'chain 'C' and resid 200 through 201' Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.819A pdb=" N MET C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.827A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.778A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.703A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.804A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.758A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 427 removed outlier: 3.586A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'C' and resid 437 through 443 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 removed outlier: 4.121A pdb=" N GLN C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.886A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 550 through 550 No H-bonds generated for 'chain 'C' and resid 550 through 550' Processing helix chain 'C' and resid 555 through 556 No H-bonds generated for 'chain 'C' and resid 555 through 556' Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.531A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 583 removed outlier: 3.781A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 652 through 662 Processing helix chain 'C' and resid 671 through 677 Processing helix chain 'C' and resid 683 through 714 Processing helix chain 'C' and resid 732 through 738 removed outlier: 3.806A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 741 No H-bonds generated for 'chain 'C' and resid 739 through 741' Processing helix chain 'C' and resid 748 through 758 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.804A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.046A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 295 removed outlier: 3.584A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.891A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 335 Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 428 Processing helix chain 'D' and resid 437 through 444 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.925A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.106A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.947A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS D 529 " --> pdb=" O THR D 525 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 553 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.945A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 585 removed outlier: 3.724A pdb=" N ALA D 585 " --> pdb=" O ILE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 removed outlier: 3.849A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 652 through 662 Processing helix chain 'D' and resid 671 through 678 Processing helix chain 'D' and resid 683 through 715 Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.661A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 760 Processing helix chain 'E' and resid 194 through 198 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.633A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.131A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.703A pdb=" N ASN E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 262 " --> pdb=" O VAL E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 removed outlier: 3.891A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 297 removed outlier: 3.944A pdb=" N ALA E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.975A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.989A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.662A pdb=" N SER E 352 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.534A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 424 Processing helix chain 'E' and resid 425 through 430 removed outlier: 5.732A pdb=" N ASP E 428 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 429 " --> pdb=" O LYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.566A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.987A pdb=" N ILE E 479 " --> pdb=" O THR E 475 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY E 480 " --> pdb=" O TRP E 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 475 through 480' Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.780A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.978A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 544 through 553 Processing helix chain 'E' and resid 554 through 557 removed outlier: 6.196A pdb=" N ALA E 557 " --> pdb=" O GLU E 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 554 through 557' Processing helix chain 'E' and resid 558 through 569 removed outlier: 4.011A pdb=" N ILE E 562 " --> pdb=" O ASN E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 582 Processing helix chain 'E' and resid 598 through 611 removed outlier: 4.009A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET E 611 " --> pdb=" O GLU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 615 removed outlier: 3.544A pdb=" N LYS E 615 " --> pdb=" O SER E 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 612 through 615' Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 651 through 661 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.572A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 709 Processing helix chain 'E' and resid 709 through 716 removed outlier: 3.546A pdb=" N ASN E 716 " --> pdb=" O GLU E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 742 removed outlier: 4.310A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 760 Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 120 through 124 removed outlier: 4.136A pdb=" N VAL F 123 " --> pdb=" O ASP F 120 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU F 124 " --> pdb=" O ASP F 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 120 through 124' Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.560A pdb=" N VAL F 133 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 199 removed outlier: 3.657A pdb=" N ASP F 193 " --> pdb=" O ILE F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.788A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.495A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.807A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.925A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.645A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.808A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 427 removed outlier: 3.683A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 430 No H-bonds generated for 'chain 'F' and resid 428 through 430' Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.561A pdb=" N ASN F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.094A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.966A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 544 through 553 removed outlier: 3.902A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 569 removed outlier: 3.855A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 583 Processing helix chain 'F' and resid 598 through 611 removed outlier: 3.763A pdb=" N THR F 606 " --> pdb=" O ASN F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 616 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 652 through 662 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.713A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 715 removed outlier: 3.782A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR F 715 " --> pdb=" O ARG F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 741 removed outlier: 3.917A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 760 Processing sheet with id=AA1, first strand: chain 'G' and resid 16 through 21 removed outlier: 8.754A pdb=" N LEU G 75 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG G 8 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 162 through 163 removed outlier: 5.830A pdb=" N MET G 162 " --> pdb=" O ARG G 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 225 through 228 removed outlier: 5.387A pdb=" N ILE G 266 " --> pdb=" O HIS G 259 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N HIS G 259 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA G 268 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N THR G 257 " --> pdb=" O ALA G 268 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL G 270 " --> pdb=" O ARG G 255 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG G 255 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY G 254 " --> pdb=" O LYS G 307 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS G 307 " --> pdb=" O GLY G 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 278 through 280 Processing sheet with id=AA5, first strand: chain 'G' and resid 317 through 319 Processing sheet with id=AA6, first strand: chain 'G' and resid 400 through 402 Processing sheet with id=AA7, first strand: chain 'G' and resid 425 through 429 Processing sheet with id=AA8, first strand: chain 'M' and resid 585 through 591 removed outlier: 3.729A pdb=" N GLU M 642 " --> pdb=" O LYS M 575 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG M 577 " --> pdb=" O GLU M 642 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 622 through 623 removed outlier: 3.711A pdb=" N ARG M 622 " --> pdb=" O SER M 617 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 585 through 591 removed outlier: 9.176A pdb=" N GLU O 642 " --> pdb=" O VAL O 573 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS O 575 " --> pdb=" O GLU O 642 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU O 644 " --> pdb=" O LYS O 575 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG O 577 " --> pdb=" O LEU O 644 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU O 646 " --> pdb=" O ARG O 577 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG O 579 " --> pdb=" O LEU O 646 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N ALA O 648 " --> pdb=" O ARG O 579 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.825A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 114 through 118 removed outlier: 7.038A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AB5, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.431A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 619 through 623 removed outlier: 3.535A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 541 through 543 removed outlier: 6.583A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.452A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.541A pdb=" N ILE B 540 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AC2, first strand: chain 'C' and resid 66 through 70 Processing sheet with id=AC3, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.958A pdb=" N GLY C 111 " --> pdb=" O ILE C 175 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 114 through 118 removed outlier: 7.243A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.759A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 541 through 543 removed outlier: 3.531A pdb=" N ASP C 577 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 265 through 270 removed outlier: 3.679A pdb=" N ILE D 301 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 538 through 543 removed outlier: 5.985A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.489A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 538 through 543 removed outlier: 3.636A pdb=" N ILE E 540 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 29 through 30 removed outlier: 5.873A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 66 through 70 Processing sheet with id=AD4, first strand: chain 'F' and resid 110 through 111 Processing sheet with id=AD5, first strand: chain 'F' and resid 117 through 118 Processing sheet with id=AD6, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.751A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 541 through 543 removed outlier: 6.415A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1578 hydrogen bonds defined for protein. 4398 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: 8.28 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12123 1.34 - 1.46: 6871 1.46 - 1.58: 16710 1.58 - 1.70: 38 1.70 - 1.82: 248 Bond restraints: 35990 Sorted by residual: bond pdb=" CB PRO A 571 " pdb=" CG PRO A 571 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.13e+00 bond pdb=" CA ILE P 271 " pdb=" CB ILE P 271 " ideal model delta sigma weight residual 1.531 1.550 -0.019 1.16e-02 7.43e+03 2.74e+00 bond pdb=" CB MET E 608 " pdb=" CG MET E 608 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.68e+00 bond pdb=" C SER C 171 " pdb=" N PRO C 172 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.30e-02 5.92e+03 1.96e+00 bond pdb=" CG ARG G 131 " pdb=" CD ARG G 131 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 ... (remaining 35985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 48253 2.84 - 5.67: 499 5.67 - 8.51: 53 8.51 - 11.34: 11 11.34 - 14.18: 2 Bond angle restraints: 48818 Sorted by residual: angle pdb=" CA MET A 740 " pdb=" CB MET A 740 " pdb=" CG MET A 740 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 angle pdb=" CG ARG G 131 " pdb=" CD ARG G 131 " pdb=" NE ARG G 131 " ideal model delta sigma weight residual 112.00 121.18 -9.18 2.20e+00 2.07e-01 1.74e+01 angle pdb=" CA LEU E 639 " pdb=" CB LEU E 639 " pdb=" CG LEU E 639 " ideal model delta sigma weight residual 116.30 130.48 -14.18 3.50e+00 8.16e-02 1.64e+01 angle pdb=" CA ARG E 487 " pdb=" CB ARG E 487 " pdb=" CG ARG E 487 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CB MET G 227 " pdb=" CG MET G 227 " pdb=" SD MET G 227 " ideal model delta sigma weight residual 112.70 124.10 -11.40 3.00e+00 1.11e-01 1.44e+01 ... (remaining 48813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.91: 21013 29.91 - 59.81: 1117 59.81 - 89.72: 97 89.72 - 119.62: 3 119.62 - 149.53: 4 Dihedral angle restraints: 22234 sinusoidal: 8754 harmonic: 13480 Sorted by residual: dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 89.53 -149.53 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PB ADP D 902 " pdb=" PA ADP D 902 " ideal model delta sinusoidal sigma weight residual 300.00 155.76 144.23 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP D 901 " pdb=" O3A ADP D 901 " pdb=" PB ADP D 901 " pdb=" PA ADP D 901 " ideal model delta sinusoidal sigma weight residual 300.00 173.65 126.34 1 2.00e+01 2.50e-03 3.82e+01 ... (remaining 22231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4474 0.056 - 0.112: 956 0.112 - 0.168: 105 0.168 - 0.224: 5 0.224 - 0.280: 1 Chirality restraints: 5541 Sorted by residual: chirality pdb=" CG LEU D 657 " pdb=" CB LEU D 657 " pdb=" CD1 LEU D 657 " pdb=" CD2 LEU D 657 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CG LEU B 657 " pdb=" CB LEU B 657 " pdb=" CD1 LEU B 657 " pdb=" CD2 LEU B 657 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PRO A 571 " pdb=" N PRO A 571 " pdb=" C PRO A 571 " pdb=" CB PRO A 571 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 5538 not shown) Planarity restraints: 6453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 570 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO A 571 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 476 " 0.024 2.00e-02 2.50e+03 2.22e-02 1.24e+01 pdb=" CG TRP A 476 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 476 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 476 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 476 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 476 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 476 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 476 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 476 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 476 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 136 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO C 137 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 137 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 137 " 0.030 5.00e-02 4.00e+02 ... (remaining 6450 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 16077 2.95 - 3.43: 39009 3.43 - 3.92: 58221 3.92 - 4.41: 66367 4.41 - 4.90: 102753 Nonbonded interactions: 282427 Sorted by model distance: nonbonded pdb=" O GLU G 149 " pdb=" OE1 GLU G 149 " model vdw 2.457 3.040 nonbonded pdb=" O2' ADP C 902 " pdb=" O3' ADP C 902 " model vdw 2.492 2.432 nonbonded pdb=" O2' ADP F 901 " pdb=" O3' ADP F 901 " model vdw 2.492 2.432 nonbonded pdb=" O2' ADP A 902 " pdb=" O3' ADP A 902 " model vdw 2.493 2.432 nonbonded pdb=" O2' ADP D 901 " pdb=" O3' ADP D 901 " model vdw 2.493 2.432 ... (remaining 282422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 550 or resid 555 through 567 or (r \ esid 568 through 570 and (name N or name CA or name C or name O or name CB )) or \ resid 571 through 715 or resid 725 through 761 or resid 902)) selection = (chain 'C' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 715 or resid 725 through 761 or re \ sid 902)) selection = (chain 'F' and (resid 14 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 550 or resid 555 through 567 or \ (resid 568 through 570 and (name N or name CA or name C or name O or name CB )) \ or resid 571 through 715 or resid 725 through 761 or resid 902)) } ncs_group { reference = (chain 'B' and ((resid 194 through 201 and (name N or name CA or name C or name \ O or name CB )) or resid 202 through 553 or (resid 554 through 570 and (name N o \ r name CA or name C or name O or name CB )) or resid 571 or (resid 572 and (name \ N or name CA or name C or name O or name CB )) or resid 573 through 577 or (res \ id 578 and (name N or name CA or name C or name O or name CB )) or resid 579 or \ (resid 580 through 581 and (name N or name CA or name C or name O or name CB )) \ or resid 582 or (resid 598 through 600 and (name N or name CA or name C or name \ O or name CB )) or resid 601 through 715 or resid 725 through 761 or resid 902)) \ selection = (chain 'D' and (resid 194 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 582 or resid 598 through 761 o \ r resid 902)) selection = (chain 'E' and (resid 194 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 553 or (resid 554 through 570 \ and (name N or name CA or name C or name O or name CB )) or resid 571 or (resid \ 572 and (name N or name CA or name C or name O or name CB )) or resid 573 throug \ h 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) or \ resid 579 or (resid 580 through 581 and (name N or name CA or name C or name O o \ r name CB )) or resid 582 or (resid 598 through 600 and (name N or name CA or na \ me C or name O or name CB )) or resid 601 through 715 or resid 725 through 761 o \ r resid 902)) } ncs_group { reference = (chain 'M' and resid 547 through 650) selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 38.100 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.003 0.088 35998 Z= 0.123 Angle : 0.687 14.176 48824 Z= 0.335 Chirality : 0.045 0.280 5541 Planarity : 0.005 0.114 6453 Dihedral : 17.206 149.530 13450 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 3.26 % Allowed : 22.82 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % 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 are not related in a simple way. whole: -0.18 (0.13), residues: 4611 helix: 0.79 (0.12), residues: 1953 sheet: -1.11 (0.23), residues: 554 loop : -0.63 (0.15), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 638 TYR 0.025 0.002 TYR G 47 PHE 0.022 0.001 PHE C 736 TRP 0.059 0.002 TRP A 476 HIS 0.009 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00262 (35990) covalent geometry : angle 0.68601 (48818) hydrogen bonds : bond 0.14467 ( 1578) hydrogen bonds : angle 6.32658 ( 4398) metal coordination : bond 0.02230 ( 8) metal coordination : angle 3.50066 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 205 time to evaluate : 0.959 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: G 1 MET cc_start: 0.6985 (mtt) cc_final: 0.5577 (ttm) REVERT: G 249 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5863 (t80) REVERT: G 425 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7190 (t80) REVERT: A 285 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8678 (t0) REVERT: A 423 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9112 (tp) REVERT: A 437 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7488 (pt) REVERT: A 551 TRP cc_start: 0.4708 (OUTLIER) cc_final: 0.3849 (m100) REVERT: A 563 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8844 (t80) REVERT: B 427 MET cc_start: 0.8310 (tpp) cc_final: 0.7672 (tpp) REVERT: B 608 MET cc_start: 0.9266 (ppp) cc_final: 0.9022 (ppp) REVERT: B 651 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8657 (ptpp) REVERT: B 690 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9235 (tp) REVERT: B 712 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.9074 (pt0) REVERT: C 442 MET cc_start: 0.8740 (tpp) cc_final: 0.8388 (tpp) REVERT: C 508 MET cc_start: 0.5842 (tpt) cc_final: 0.4824 (tpp) REVERT: C 608 MET cc_start: 0.8591 (tmm) cc_final: 0.8353 (tmm) REVERT: C 672 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8267 (mp) REVERT: D 277 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8811 (ptpt) REVERT: D 427 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8005 (tpp) REVERT: D 508 MET cc_start: 0.5643 (tpp) cc_final: 0.5266 (tpp) REVERT: D 611 MET cc_start: 0.6818 (mtt) cc_final: 0.6599 (mtt) REVERT: E 211 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8646 (mtmm) REVERT: E 275 MET cc_start: 0.8678 (tpp) cc_final: 0.8425 (mpp) REVERT: E 515 LEU cc_start: 0.9624 (mt) cc_final: 0.8838 (tp) REVERT: F 678 MET cc_start: 0.9061 (mpp) cc_final: 0.8840 (mpp) outliers start: 114 outliers final: 63 residues processed: 307 average time/residue: 0.1985 time to fit residues: 102.6197 Evaluate side-chains 242 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 165 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 425 PHE Chi-restraints excluded: chain O residue 578 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 574 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.0470 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 40.0000 overall best weight: 4.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 536 GLN P 298 GLN A 538 ASN E 285 ASN F 558 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.056808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036628 restraints weight = 253459.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.037585 restraints weight = 147352.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038224 restraints weight = 105008.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.038636 restraints weight = 84596.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.038881 restraints weight = 73560.784| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 35998 Z= 0.231 Angle : 0.688 11.493 48824 Z= 0.337 Chirality : 0.044 0.216 5541 Planarity : 0.005 0.112 6453 Dihedral : 9.777 151.932 5325 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.38 % Favored : 93.52 % Rotamer: Outliers : 5.26 % Allowed : 22.28 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % 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 are not related in a simple way. whole: -0.05 (0.13), residues: 4611 helix: 0.94 (0.12), residues: 2003 sheet: -1.18 (0.23), residues: 551 loop : -0.59 (0.15), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 349 TYR 0.024 0.002 TYR D 755 PHE 0.025 0.001 PHE C 736 TRP 0.039 0.002 TRP A 476 HIS 0.009 0.001 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.00486 (35990) covalent geometry : angle 0.68748 (48818) hydrogen bonds : bond 0.03936 ( 1578) hydrogen bonds : angle 5.28803 ( 4398) metal coordination : bond 0.01898 ( 8) metal coordination : angle 3.11777 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 165 time to evaluate : 1.620 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: G 1 MET cc_start: 0.7429 (mtt) cc_final: 0.6614 (ttm) REVERT: G 116 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.9023 (mtmt) REVERT: G 249 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6453 (t80) REVERT: A 219 MET cc_start: 0.9207 (ttm) cc_final: 0.8885 (ttp) REVERT: A 285 ASN cc_start: 0.9753 (OUTLIER) cc_final: 0.9417 (t0) REVERT: A 454 TRP cc_start: 0.9444 (OUTLIER) cc_final: 0.9152 (t-100) REVERT: A 508 MET cc_start: 0.8258 (tpp) cc_final: 0.7925 (tpp) REVERT: A 551 TRP cc_start: 0.5598 (OUTLIER) cc_final: 0.4269 (m100) REVERT: A 556 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: A 563 PHE cc_start: 0.9638 (OUTLIER) cc_final: 0.9154 (t80) REVERT: A 672 LEU cc_start: 0.9122 (mp) cc_final: 0.8879 (tt) REVERT: B 608 MET cc_start: 0.9426 (ppp) cc_final: 0.9027 (ppp) REVERT: C 275 MET cc_start: 0.8985 (tpp) cc_final: 0.8643 (mpp) REVERT: C 417 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: C 442 MET cc_start: 0.9302 (tpp) cc_final: 0.8938 (tpp) REVERT: C 449 MET cc_start: 0.9067 (mmm) cc_final: 0.8671 (mmm) REVERT: C 508 MET cc_start: 0.6928 (tpt) cc_final: 0.5942 (tpp) REVERT: D 387 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8906 (t0) REVERT: D 388 MET cc_start: 0.8994 (mtm) cc_final: 0.8748 (mtt) REVERT: D 427 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8444 (tpp) REVERT: D 608 MET cc_start: 0.9478 (ppp) cc_final: 0.9272 (ppp) REVERT: D 731 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8406 (tt) REVERT: E 515 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.8674 (tp) REVERT: F 283 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8992 (mp0) REVERT: F 319 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: F 427 MET cc_start: 0.9303 (ppp) cc_final: 0.9095 (ppp) REVERT: F 508 MET cc_start: 0.8273 (tpp) cc_final: 0.7429 (tpp) REVERT: F 524 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8680 (mttp) REVERT: F 558 ASN cc_start: 0.9372 (OUTLIER) cc_final: 0.8978 (p0) REVERT: F 560 ARG cc_start: 0.9594 (OUTLIER) cc_final: 0.9046 (ptp-170) REVERT: F 678 MET cc_start: 0.9376 (mpp) cc_final: 0.9021 (mpp) outliers start: 184 outliers final: 106 residues processed: 342 average time/residue: 0.1903 time to fit residues: 111.7631 Evaluate side-chains 274 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 151 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain M residue 536 GLN Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 454 TRP Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 285 ASN Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 524 LYS Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 558 ASN Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 247 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 16 optimal weight: 40.0000 chunk 373 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 385 optimal weight: 5.9990 chunk 429 optimal weight: 0.9980 chunk 426 optimal weight: 1.9990 chunk 424 optimal weight: 0.1980 chunk 456 optimal weight: 10.0000 chunk 405 optimal weight: 50.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN B 624 ASN E 285 ASN ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 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 = 0.3601 r_free = 0.3601 target = 0.057762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037576 restraints weight = 248399.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.038535 restraints weight = 144522.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039190 restraints weight = 102119.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.039626 restraints weight = 81892.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039904 restraints weight = 70956.630| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 35998 Z= 0.119 Angle : 0.634 11.599 48824 Z= 0.302 Chirality : 0.044 0.237 5541 Planarity : 0.004 0.110 6453 Dihedral : 9.394 151.289 5280 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.88 % Rotamer: Outliers : 4.26 % Allowed : 23.02 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % 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 are not related in a simple way. whole: 0.07 (0.13), residues: 4611 helix: 1.09 (0.12), residues: 2025 sheet: -1.04 (0.22), residues: 585 loop : -0.61 (0.15), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 239 TYR 0.022 0.002 TYR D 755 PHE 0.026 0.001 PHE G 500 TRP 0.018 0.001 TRP A 476 HIS 0.006 0.001 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00261 (35990) covalent geometry : angle 0.63338 (48818) hydrogen bonds : bond 0.03327 ( 1578) hydrogen bonds : angle 4.87564 ( 4398) metal coordination : bond 0.01785 ( 8) metal coordination : angle 2.45700 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 168 time to evaluate : 1.893 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: G 1 MET cc_start: 0.7400 (mtt) cc_final: 0.6459 (ttm) REVERT: G 116 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8991 (mtmt) REVERT: G 249 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6385 (t80) REVERT: A 219 MET cc_start: 0.9207 (ttm) cc_final: 0.8902 (ttp) REVERT: A 285 ASN cc_start: 0.9747 (OUTLIER) cc_final: 0.9386 (t0) REVERT: A 401 ASN cc_start: 0.9648 (OUTLIER) cc_final: 0.9130 (m-40) REVERT: A 442 MET cc_start: 0.9493 (mtm) cc_final: 0.9263 (ptp) REVERT: A 454 TRP cc_start: 0.9418 (OUTLIER) cc_final: 0.9008 (t-100) REVERT: A 551 TRP cc_start: 0.5508 (OUTLIER) cc_final: 0.4193 (m100) REVERT: A 563 PHE cc_start: 0.9632 (OUTLIER) cc_final: 0.9115 (t80) REVERT: A 608 MET cc_start: 0.8521 (ppp) cc_final: 0.7916 (ppp) REVERT: B 608 MET cc_start: 0.9503 (ppp) cc_final: 0.9069 (ppp) REVERT: C 275 MET cc_start: 0.9196 (tpp) cc_final: 0.8823 (mpp) REVERT: C 442 MET cc_start: 0.9255 (tpp) cc_final: 0.8958 (tpp) REVERT: C 449 MET cc_start: 0.9065 (mmm) cc_final: 0.8717 (mmm) REVERT: C 508 MET cc_start: 0.6740 (tpt) cc_final: 0.5890 (tpp) REVERT: C 578 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: C 608 MET cc_start: 0.9585 (tmm) cc_final: 0.9286 (ppp) REVERT: D 218 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8796 (tm-30) REVERT: D 387 ASN cc_start: 0.9085 (OUTLIER) cc_final: 0.8836 (t0) REVERT: D 388 MET cc_start: 0.8914 (mtm) cc_final: 0.8578 (mtt) REVERT: D 427 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8567 (tpp) REVERT: D 550 MET cc_start: 0.6928 (mmm) cc_final: 0.6478 (tmm) REVERT: D 740 MET cc_start: 0.9159 (tpp) cc_final: 0.8814 (tmm) REVERT: E 211 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9215 (mtmm) REVERT: E 335 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9198 (mm) REVERT: E 515 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.8650 (tp) REVERT: F 283 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8946 (mp0) REVERT: F 319 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: F 390 LEU cc_start: 0.9291 (pt) cc_final: 0.9075 (pp) REVERT: F 449 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8078 (tmm) REVERT: F 508 MET cc_start: 0.8397 (tpp) cc_final: 0.7569 (tpp) REVERT: F 540 ILE cc_start: 0.9372 (mt) cc_final: 0.9086 (mp) REVERT: F 555 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8455 (p) REVERT: F 678 MET cc_start: 0.9360 (mpp) cc_final: 0.8909 (mpp) outliers start: 149 outliers final: 83 residues processed: 308 average time/residue: 0.1897 time to fit residues: 100.1171 Evaluate side-chains 260 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 159 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain M residue 639 PHE Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 454 TRP Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 449 MET Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 68 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 355 optimal weight: 8.9990 chunk 374 optimal weight: 3.9990 chunk 422 optimal weight: 0.9990 chunk 364 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 293 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 419 GLN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.057475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.039573 restraints weight = 250383.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.039092 restraints weight = 129614.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.039171 restraints weight = 120842.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.039281 restraints weight = 105000.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039354 restraints weight = 90991.248| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 35998 Z= 0.138 Angle : 0.625 11.721 48824 Z= 0.298 Chirality : 0.043 0.196 5541 Planarity : 0.004 0.108 6453 Dihedral : 9.257 152.018 5262 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.07 % Favored : 93.86 % Rotamer: Outliers : 4.23 % Allowed : 23.31 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % 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 are not related in a simple way. whole: 0.18 (0.13), residues: 4611 helix: 1.22 (0.12), residues: 2023 sheet: -1.04 (0.22), residues: 584 loop : -0.58 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 638 TYR 0.020 0.001 TYR D 755 PHE 0.020 0.001 PHE C 736 TRP 0.014 0.001 TRP A 476 HIS 0.006 0.001 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.00299 (35990) covalent geometry : angle 0.62501 (48818) hydrogen bonds : bond 0.03115 ( 1578) hydrogen bonds : angle 4.76135 ( 4398) metal coordination : bond 0.01616 ( 8) metal coordination : angle 2.20764 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 162 time to evaluate : 1.241 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: G 1 MET cc_start: 0.7293 (mtt) cc_final: 0.6055 (ttm) REVERT: G 116 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9007 (mtmt) REVERT: G 249 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6350 (t80) REVERT: A 205 ASP cc_start: 0.9278 (OUTLIER) cc_final: 0.8859 (t0) REVERT: A 219 MET cc_start: 0.9208 (ttm) cc_final: 0.8898 (ttp) REVERT: A 285 ASN cc_start: 0.9755 (OUTLIER) cc_final: 0.9389 (t0) REVERT: A 454 TRP cc_start: 0.9422 (OUTLIER) cc_final: 0.9031 (t-100) REVERT: A 551 TRP cc_start: 0.5797 (OUTLIER) cc_final: 0.4360 (m100) REVERT: A 556 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8561 (tp30) REVERT: A 563 PHE cc_start: 0.9572 (OUTLIER) cc_final: 0.9076 (t80) REVERT: A 608 MET cc_start: 0.8572 (ppp) cc_final: 0.8319 (ppp) REVERT: B 560 ARG cc_start: 0.9625 (ttm170) cc_final: 0.9285 (ttp80) REVERT: B 651 LYS cc_start: 0.9618 (OUTLIER) cc_final: 0.9330 (ptpp) REVERT: C 442 MET cc_start: 0.9287 (tpp) cc_final: 0.9010 (tpt) REVERT: C 449 MET cc_start: 0.9122 (mmm) cc_final: 0.8707 (mmm) REVERT: C 508 MET cc_start: 0.7471 (tpt) cc_final: 0.6817 (tpp) REVERT: C 578 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: D 218 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8797 (tm-30) REVERT: D 349 ARG cc_start: 0.8778 (tpp-160) cc_final: 0.8548 (tpp-160) REVERT: D 387 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8796 (t0) REVERT: D 427 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8906 (tpp) REVERT: D 550 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6376 (tmm) REVERT: E 211 LYS cc_start: 0.9575 (OUTLIER) cc_final: 0.9277 (mtmm) REVERT: E 380 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9353 (mm) REVERT: E 515 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.8829 (tp) REVERT: F 283 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8954 (mp0) REVERT: F 319 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: F 508 MET cc_start: 0.8527 (tpp) cc_final: 0.7947 (tpp) REVERT: F 678 MET cc_start: 0.9405 (mpp) cc_final: 0.8953 (mpp) outliers start: 148 outliers final: 101 residues processed: 303 average time/residue: 0.1955 time to fit residues: 100.3831 Evaluate side-chains 279 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 159 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain M residue 639 PHE Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 454 TRP Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 90 optimal weight: 0.5980 chunk 322 optimal weight: 9.9990 chunk 339 optimal weight: 6.9990 chunk 21 optimal weight: 30.0000 chunk 185 optimal weight: 9.9990 chunk 389 optimal weight: 0.0050 chunk 110 optimal weight: 0.7980 chunk 403 optimal weight: 50.0000 chunk 303 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 overall best weight: 3.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 458 GLN D 387 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN F 558 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.056917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036790 restraints weight = 252251.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.037727 restraints weight = 147277.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038361 restraints weight = 105135.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.038779 restraints weight = 84285.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.039038 restraints weight = 73308.329| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 35998 Z= 0.179 Angle : 0.641 12.001 48824 Z= 0.308 Chirality : 0.043 0.207 5541 Planarity : 0.004 0.107 6453 Dihedral : 9.261 153.156 5257 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 4.43 % Allowed : 23.82 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % 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 are not related in a simple way. whole: 0.18 (0.13), residues: 4611 helix: 1.23 (0.12), residues: 2028 sheet: -1.14 (0.22), residues: 578 loop : -0.56 (0.15), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 349 TYR 0.020 0.002 TYR D 755 PHE 0.023 0.001 PHE O 600 TRP 0.025 0.002 TRP O 610 HIS 0.006 0.001 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.00381 (35990) covalent geometry : angle 0.64071 (48818) hydrogen bonds : bond 0.03132 ( 1578) hydrogen bonds : angle 4.79020 ( 4398) metal coordination : bond 0.01609 ( 8) metal coordination : angle 2.21289 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 159 time to evaluate : 1.293 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: G 1 MET cc_start: 0.7425 (mtt) cc_final: 0.6532 (ttm) REVERT: G 116 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9025 (mtmt) REVERT: G 249 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6424 (t80) REVERT: G 435 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8934 (tp30) REVERT: M 639 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: A 205 ASP cc_start: 0.9270 (OUTLIER) cc_final: 0.8910 (t0) REVERT: A 219 MET cc_start: 0.9259 (ttm) cc_final: 0.8959 (ttp) REVERT: A 285 ASN cc_start: 0.9762 (OUTLIER) cc_final: 0.9398 (t0) REVERT: A 454 TRP cc_start: 0.9428 (OUTLIER) cc_final: 0.9025 (t-100) REVERT: A 551 TRP cc_start: 0.5845 (OUTLIER) cc_final: 0.4949 (m100) REVERT: A 563 PHE cc_start: 0.9585 (OUTLIER) cc_final: 0.9094 (t80) REVERT: B 560 ARG cc_start: 0.9608 (ttm170) cc_final: 0.9277 (ttp80) REVERT: B 608 MET cc_start: 0.9439 (ppp) cc_final: 0.8902 (ppp) REVERT: B 651 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9208 (ptpp) REVERT: C 442 MET cc_start: 0.9109 (tpp) cc_final: 0.8696 (tpt) REVERT: C 449 MET cc_start: 0.9164 (mmm) cc_final: 0.8819 (mmm) REVERT: C 508 MET cc_start: 0.7456 (tpt) cc_final: 0.6875 (tpp) REVERT: C 578 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: C 608 MET cc_start: 0.9482 (tmm) cc_final: 0.9271 (ppp) REVERT: C 672 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8834 (mp) REVERT: D 218 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.8804 (tm-30) REVERT: D 388 MET cc_start: 0.8795 (mtm) cc_final: 0.8561 (mtp) REVERT: D 427 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8551 (tpp) REVERT: D 550 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6354 (tmm) REVERT: D 740 MET cc_start: 0.9180 (tpp) cc_final: 0.8832 (tmm) REVERT: E 515 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.8891 (tp) REVERT: E 608 MET cc_start: 0.8613 (tmm) cc_final: 0.8326 (tmm) REVERT: F 244 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: F 319 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: F 388 MET cc_start: 0.9274 (mtp) cc_final: 0.8768 (mtt) REVERT: F 508 MET cc_start: 0.8566 (tpp) cc_final: 0.7960 (tpp) REVERT: F 678 MET cc_start: 0.9366 (mpp) cc_final: 0.8995 (mpp) outliers start: 155 outliers final: 108 residues processed: 304 average time/residue: 0.2011 time to fit residues: 102.3240 Evaluate side-chains 276 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 150 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 435 GLU Chi-restraints excluded: chain M residue 639 PHE Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 454 TRP Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 393 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 425 optimal weight: 2.9990 chunk 345 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 313 optimal weight: 0.9980 chunk 347 optimal weight: 6.9990 chunk 439 optimal weight: 1.9990 chunk 433 optimal weight: 3.9990 chunk 372 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.057510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037294 restraints weight = 250630.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038289 restraints weight = 145323.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038940 restraints weight = 102985.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039349 restraints weight = 82650.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.039627 restraints weight = 71777.680| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 35998 Z= 0.123 Angle : 0.630 12.299 48824 Z= 0.299 Chirality : 0.043 0.383 5541 Planarity : 0.004 0.105 6453 Dihedral : 9.137 152.404 5254 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.93 % Rotamer: Outliers : 4.09 % Allowed : 24.05 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4611 helix: 1.29 (0.12), residues: 2025 sheet: -1.01 (0.22), residues: 586 loop : -0.52 (0.15), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 338 TYR 0.032 0.001 TYR D 203 PHE 0.033 0.001 PHE O 600 TRP 0.012 0.001 TRP A 476 HIS 0.005 0.001 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00269 (35990) covalent geometry : angle 0.62992 (48818) hydrogen bonds : bond 0.02922 ( 1578) hydrogen bonds : angle 4.63254 ( 4398) metal coordination : bond 0.01381 ( 8) metal coordination : angle 2.14341 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 165 time to evaluate : 1.460 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: G 1 MET cc_start: 0.7749 (mtt) cc_final: 0.7005 (ttm) REVERT: G 116 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9026 (mtmt) REVERT: G 249 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6380 (t80) REVERT: M 639 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: A 205 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8872 (t0) REVERT: A 219 MET cc_start: 0.9250 (ttm) cc_final: 0.8945 (ttp) REVERT: A 285 ASN cc_start: 0.9761 (OUTLIER) cc_final: 0.9382 (t0) REVERT: A 449 MET cc_start: 0.8929 (tmm) cc_final: 0.8489 (tpp) REVERT: A 454 TRP cc_start: 0.9397 (OUTLIER) cc_final: 0.8962 (t-100) REVERT: A 551 TRP cc_start: 0.5846 (OUTLIER) cc_final: 0.4948 (m100) REVERT: A 563 PHE cc_start: 0.9572 (OUTLIER) cc_final: 0.9043 (t80) REVERT: B 275 MET cc_start: 0.9606 (OUTLIER) cc_final: 0.9403 (mmt) REVERT: B 560 ARG cc_start: 0.9589 (ttm170) cc_final: 0.9271 (ttp80) REVERT: B 651 LYS cc_start: 0.9545 (OUTLIER) cc_final: 0.9241 (ptpp) REVERT: C 244 TYR cc_start: 0.8948 (p90) cc_final: 0.8220 (p90) REVERT: C 442 MET cc_start: 0.9043 (tpp) cc_final: 0.8663 (tpt) REVERT: C 449 MET cc_start: 0.9185 (mmm) cc_final: 0.8809 (mmm) REVERT: C 508 MET cc_start: 0.7485 (tpt) cc_final: 0.7050 (tpp) REVERT: C 578 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: C 608 MET cc_start: 0.9503 (tmm) cc_final: 0.9284 (ppp) REVERT: D 218 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8781 (tm-30) REVERT: D 388 MET cc_start: 0.8910 (mtm) cc_final: 0.8639 (mtp) REVERT: D 427 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8613 (tpp) REVERT: D 508 MET cc_start: 0.7315 (tpp) cc_final: 0.6370 (tpp) REVERT: D 550 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6028 (tmm) REVERT: E 211 LYS cc_start: 0.9584 (OUTLIER) cc_final: 0.9300 (mtmm) REVERT: E 515 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8393 (tt) REVERT: E 608 MET cc_start: 0.8623 (tmm) cc_final: 0.8397 (tmm) REVERT: F 244 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: F 283 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8933 (mp0) REVERT: F 319 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: F 388 MET cc_start: 0.9251 (mtp) cc_final: 0.8676 (mtt) REVERT: F 508 MET cc_start: 0.8608 (tpp) cc_final: 0.8008 (tpp) REVERT: F 560 ARG cc_start: 0.9477 (OUTLIER) cc_final: 0.9018 (ptp90) REVERT: F 678 MET cc_start: 0.9340 (mpp) cc_final: 0.8945 (mpp) outliers start: 143 outliers final: 95 residues processed: 297 average time/residue: 0.2070 time to fit residues: 104.1019 Evaluate side-chains 269 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 154 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain M residue 639 PHE Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 454 TRP Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 161 optimal weight: 5.9990 chunk 337 optimal weight: 7.9990 chunk 288 optimal weight: 0.0970 chunk 35 optimal weight: 9.9990 chunk 414 optimal weight: 0.6980 chunk 296 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 429 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.058057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.037984 restraints weight = 246402.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039007 restraints weight = 143083.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039637 restraints weight = 100999.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.040084 restraints weight = 80969.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.040365 restraints weight = 70159.663| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 35998 Z= 0.102 Angle : 0.633 12.573 48824 Z= 0.296 Chirality : 0.043 0.286 5541 Planarity : 0.004 0.103 6453 Dihedral : 8.905 151.483 5254 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 3.40 % Allowed : 24.59 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 4611 helix: 1.32 (0.12), residues: 2026 sheet: -0.88 (0.22), residues: 580 loop : -0.47 (0.15), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 349 TYR 0.021 0.001 TYR D 203 PHE 0.046 0.001 PHE O 600 TRP 0.040 0.001 TRP A 476 HIS 0.005 0.001 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00225 (35990) covalent geometry : angle 0.63222 (48818) hydrogen bonds : bond 0.02771 ( 1578) hydrogen bonds : angle 4.49860 ( 4398) metal coordination : bond 0.01149 ( 8) metal coordination : angle 2.20744 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 170 time to evaluate : 1.357 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: G 1 MET cc_start: 0.7675 (mtt) cc_final: 0.6786 (ttm) REVERT: G 116 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8986 (mttt) REVERT: G 249 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6445 (t80) REVERT: G 318 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8793 (tt0) REVERT: M 639 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: A 205 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8882 (t0) REVERT: A 219 MET cc_start: 0.9252 (ttm) cc_final: 0.8944 (ttp) REVERT: A 285 ASN cc_start: 0.9758 (OUTLIER) cc_final: 0.9374 (t0) REVERT: A 449 MET cc_start: 0.8995 (tmm) cc_final: 0.8586 (tpp) REVERT: A 551 TRP cc_start: 0.6229 (OUTLIER) cc_final: 0.5132 (m100) REVERT: A 563 PHE cc_start: 0.9521 (OUTLIER) cc_final: 0.8854 (t80) REVERT: A 608 MET cc_start: 0.8669 (ppp) cc_final: 0.8156 (ppp) REVERT: B 336 LYS cc_start: 0.8794 (tppt) cc_final: 0.8438 (tppt) REVERT: B 442 MET cc_start: 0.9590 (ptp) cc_final: 0.8736 (ppp) REVERT: B 560 ARG cc_start: 0.9586 (ttm170) cc_final: 0.9251 (ttp80) REVERT: B 608 MET cc_start: 0.9529 (ppp) cc_final: 0.9292 (ppp) REVERT: B 651 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9173 (ptpp) REVERT: C 244 TYR cc_start: 0.8897 (p90) cc_final: 0.8195 (p90) REVERT: C 442 MET cc_start: 0.8901 (tpp) cc_final: 0.8632 (tpt) REVERT: C 449 MET cc_start: 0.9199 (mmm) cc_final: 0.8771 (mmm) REVERT: C 508 MET cc_start: 0.7400 (tpt) cc_final: 0.7040 (tpp) REVERT: C 564 ASP cc_start: 0.9012 (t0) cc_final: 0.8590 (p0) REVERT: C 578 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: C 608 MET cc_start: 0.9499 (tmm) cc_final: 0.9257 (ppp) REVERT: D 427 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.8664 (tpp) REVERT: D 550 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.5959 (tmm) REVERT: D 740 MET cc_start: 0.9184 (tpp) cc_final: 0.8848 (tmm) REVERT: E 211 LYS cc_start: 0.9581 (OUTLIER) cc_final: 0.9302 (mtmm) REVERT: E 515 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8810 (tt) REVERT: E 608 MET cc_start: 0.8646 (tmm) cc_final: 0.8152 (tmm) REVERT: F 244 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: F 283 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8937 (mp0) REVERT: F 319 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: F 508 MET cc_start: 0.8648 (tpp) cc_final: 0.8050 (tpp) REVERT: F 678 MET cc_start: 0.9328 (mpp) cc_final: 0.8902 (mpp) outliers start: 119 outliers final: 79 residues processed: 277 average time/residue: 0.2069 time to fit residues: 96.7181 Evaluate side-chains 255 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 159 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain M residue 637 LYS Chi-restraints excluded: chain M residue 639 PHE Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 618 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 712 GLU Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 30 optimal weight: 40.0000 chunk 397 optimal weight: 50.0000 chunk 375 optimal weight: 0.9990 chunk 381 optimal weight: 9.9990 chunk 355 optimal weight: 0.4980 chunk 175 optimal weight: 9.9990 chunk 376 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 283 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 447 optimal weight: 8.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.057346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.037078 restraints weight = 255537.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.038006 restraints weight = 143811.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.038672 restraints weight = 100957.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.039078 restraints weight = 80527.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039355 restraints weight = 70115.203| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35998 Z= 0.200 Angle : 0.669 13.638 48824 Z= 0.320 Chirality : 0.043 0.254 5541 Planarity : 0.004 0.100 6453 Dihedral : 9.056 154.188 5252 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 3.46 % Allowed : 24.79 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4611 helix: 1.31 (0.12), residues: 2027 sheet: -1.01 (0.22), residues: 589 loop : -0.48 (0.15), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 349 TYR 0.023 0.002 TYR D 203 PHE 0.013 0.001 PHE M 537 TRP 0.053 0.002 TRP O 610 HIS 0.005 0.001 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.00424 (35990) covalent geometry : angle 0.66860 (48818) hydrogen bonds : bond 0.03041 ( 1578) hydrogen bonds : angle 4.70394 ( 4398) metal coordination : bond 0.02136 ( 8) metal coordination : angle 3.04826 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 152 time to evaluate : 1.565 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: G 1 MET cc_start: 0.7700 (mtt) cc_final: 0.6895 (ttm) REVERT: G 116 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9022 (mtmt) REVERT: G 249 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6466 (t80) REVERT: G 318 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8832 (tt0) REVERT: M 639 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: A 205 ASP cc_start: 0.9265 (OUTLIER) cc_final: 0.8934 (t0) REVERT: A 219 MET cc_start: 0.9254 (ttm) cc_final: 0.8948 (ttp) REVERT: A 285 ASN cc_start: 0.9774 (OUTLIER) cc_final: 0.9417 (t0) REVERT: A 384 HIS cc_start: 0.9245 (OUTLIER) cc_final: 0.8715 (m-70) REVERT: A 449 MET cc_start: 0.8959 (tmm) cc_final: 0.8635 (tmm) REVERT: A 551 TRP cc_start: 0.6525 (OUTLIER) cc_final: 0.5755 (m100) REVERT: A 563 PHE cc_start: 0.9505 (OUTLIER) cc_final: 0.8798 (t80) REVERT: A 608 MET cc_start: 0.8581 (ppp) cc_final: 0.8074 (ppp) REVERT: B 275 MET cc_start: 0.9532 (mmp) cc_final: 0.9317 (mmt) REVERT: B 560 ARG cc_start: 0.9568 (ttm170) cc_final: 0.9268 (ttp80) REVERT: B 651 LYS cc_start: 0.9504 (OUTLIER) cc_final: 0.9180 (ptpp) REVERT: C 442 MET cc_start: 0.8904 (tpp) cc_final: 0.8654 (tpt) REVERT: C 508 MET cc_start: 0.7540 (tpt) cc_final: 0.7187 (tpp) REVERT: C 564 ASP cc_start: 0.9011 (t0) cc_final: 0.8571 (p0) REVERT: C 578 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: C 608 MET cc_start: 0.9475 (tmm) cc_final: 0.9197 (ppp) REVERT: D 427 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.8670 (tpp) REVERT: D 508 MET cc_start: 0.7416 (tpp) cc_final: 0.6357 (tpp) REVERT: D 550 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6314 (mmm) REVERT: E 427 MET cc_start: 0.8801 (mmm) cc_final: 0.8544 (mmm) REVERT: E 515 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8882 (tt) REVERT: E 608 MET cc_start: 0.8368 (tmm) cc_final: 0.8164 (tmm) REVERT: F 244 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: F 275 MET cc_start: 0.9053 (tpp) cc_final: 0.8812 (mmm) REVERT: F 319 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: F 508 MET cc_start: 0.8678 (tpp) cc_final: 0.8124 (tpp) REVERT: F 635 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8822 (mmt180) REVERT: F 678 MET cc_start: 0.9360 (mpp) cc_final: 0.8950 (mpp) outliers start: 121 outliers final: 95 residues processed: 266 average time/residue: 0.2028 time to fit residues: 92.0914 Evaluate side-chains 265 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 153 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain M residue 637 LYS Chi-restraints excluded: chain M residue 639 PHE Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 618 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 712 GLU Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 635 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 115 optimal weight: 0.3980 chunk 413 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 226 optimal weight: 30.0000 chunk 172 optimal weight: 0.2980 chunk 11 optimal weight: 7.9990 chunk 419 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 342 optimal weight: 0.1980 chunk 418 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.057978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039684 restraints weight = 246646.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.039537 restraints weight = 139798.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.039791 restraints weight = 109659.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.039927 restraints weight = 90440.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.039963 restraints weight = 83019.272| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 35998 Z= 0.103 Angle : 0.651 13.999 48824 Z= 0.302 Chirality : 0.043 0.254 5541 Planarity : 0.004 0.098 6453 Dihedral : 8.883 152.401 5250 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 3.12 % Allowed : 25.08 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 4611 helix: 1.35 (0.12), residues: 2021 sheet: -0.88 (0.22), residues: 587 loop : -0.43 (0.15), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 349 TYR 0.031 0.001 TYR O 613 PHE 0.018 0.001 PHE C 736 TRP 0.026 0.001 TRP O 610 HIS 0.004 0.001 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00229 (35990) covalent geometry : angle 0.65068 (48818) hydrogen bonds : bond 0.02762 ( 1578) hydrogen bonds : angle 4.48526 ( 4398) metal coordination : bond 0.01491 ( 8) metal coordination : angle 2.86017 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 163 time to evaluate : 1.410 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: G 1 MET cc_start: 0.7601 (mtt) cc_final: 0.6516 (ttm) REVERT: G 116 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8929 (mtmt) REVERT: G 249 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6436 (t80) REVERT: G 318 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8708 (tt0) REVERT: M 639 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: O 632 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8028 (t) REVERT: A 219 MET cc_start: 0.9253 (ttm) cc_final: 0.8948 (ttp) REVERT: A 285 ASN cc_start: 0.9765 (OUTLIER) cc_final: 0.9373 (t0) REVERT: A 449 MET cc_start: 0.9011 (tmm) cc_final: 0.8594 (tpp) REVERT: A 551 TRP cc_start: 0.6489 (OUTLIER) cc_final: 0.5581 (m100) REVERT: A 563 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.8733 (t80) REVERT: A 608 MET cc_start: 0.8713 (ppp) cc_final: 0.8159 (ppp) REVERT: B 336 LYS cc_start: 0.8868 (tppt) cc_final: 0.8516 (tppt) REVERT: B 442 MET cc_start: 0.9625 (ptp) cc_final: 0.8774 (ppp) REVERT: B 550 MET cc_start: 0.8522 (ptp) cc_final: 0.8206 (tpt) REVERT: B 560 ARG cc_start: 0.9609 (ttm170) cc_final: 0.9243 (ttp80) REVERT: B 608 MET cc_start: 0.9534 (ppp) cc_final: 0.9252 (ppp) REVERT: B 651 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9275 (ptpp) REVERT: C 449 MET cc_start: 0.9153 (mmm) cc_final: 0.8860 (mmm) REVERT: C 508 MET cc_start: 0.7462 (tpt) cc_final: 0.7152 (tpp) REVERT: C 564 ASP cc_start: 0.9101 (t0) cc_final: 0.8639 (p0) REVERT: C 578 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: C 608 MET cc_start: 0.9535 (tmm) cc_final: 0.9204 (tmm) REVERT: D 427 MET cc_start: 0.9454 (OUTLIER) cc_final: 0.8902 (tpp) REVERT: D 508 MET cc_start: 0.7564 (tpp) cc_final: 0.6554 (tpp) REVERT: D 728 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8030 (p) REVERT: D 740 MET cc_start: 0.9129 (tpp) cc_final: 0.8829 (ttt) REVERT: E 211 LYS cc_start: 0.9591 (OUTLIER) cc_final: 0.9324 (mtmm) REVERT: E 427 MET cc_start: 0.8864 (mmm) cc_final: 0.8629 (mmm) REVERT: E 515 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8828 (tt) REVERT: F 244 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: F 283 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8934 (mp0) REVERT: F 319 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: F 388 MET cc_start: 0.9208 (mtp) cc_final: 0.8648 (mtt) REVERT: F 508 MET cc_start: 0.8718 (tpp) cc_final: 0.7995 (tpp) REVERT: F 678 MET cc_start: 0.9376 (mpp) cc_final: 0.8924 (mpp) outliers start: 109 outliers final: 80 residues processed: 263 average time/residue: 0.2022 time to fit residues: 90.4643 Evaluate side-chains 253 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 156 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain M residue 637 LYS Chi-restraints excluded: chain M residue 639 PHE Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 618 THR Chi-restraints excluded: chain O residue 632 SER Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 351 optimal weight: 0.0770 chunk 439 optimal weight: 8.9990 chunk 262 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 404 optimal weight: 40.0000 chunk 201 optimal weight: 8.9990 chunk 414 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.057614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039133 restraints weight = 251093.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.039252 restraints weight = 136658.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039396 restraints weight = 107631.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.039470 restraints weight = 94466.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039502 restraints weight = 80018.459| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35998 Z= 0.124 Angle : 0.661 16.272 48824 Z= 0.308 Chirality : 0.043 0.244 5541 Planarity : 0.004 0.096 6453 Dihedral : 8.825 153.924 5248 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 3.06 % Allowed : 25.34 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4611 helix: 1.37 (0.12), residues: 2027 sheet: -0.90 (0.22), residues: 592 loop : -0.42 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 349 TYR 0.021 0.001 TYR D 203 PHE 0.017 0.001 PHE O 600 TRP 0.027 0.001 TRP O 610 HIS 0.004 0.001 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00274 (35990) covalent geometry : angle 0.66015 (48818) hydrogen bonds : bond 0.02822 ( 1578) hydrogen bonds : angle 4.52094 ( 4398) metal coordination : bond 0.01448 ( 8) metal coordination : angle 2.66885 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 157 time to evaluate : 1.420 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: G 1 MET cc_start: 0.7601 (mtt) cc_final: 0.6536 (ttm) REVERT: G 116 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.8973 (mtmt) REVERT: G 249 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.6466 (t80) REVERT: G 318 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: M 639 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: A 205 ASP cc_start: 0.9202 (OUTLIER) cc_final: 0.8941 (t0) REVERT: A 219 MET cc_start: 0.9218 (ttm) cc_final: 0.8920 (ttp) REVERT: A 285 ASN cc_start: 0.9773 (OUTLIER) cc_final: 0.9385 (t0) REVERT: A 449 MET cc_start: 0.8989 (tmm) cc_final: 0.8635 (tmm) REVERT: A 508 MET cc_start: 0.8361 (tpp) cc_final: 0.7883 (tpp) REVERT: A 551 TRP cc_start: 0.6526 (OUTLIER) cc_final: 0.5598 (m100) REVERT: A 563 PHE cc_start: 0.9463 (OUTLIER) cc_final: 0.8710 (t80) REVERT: A 608 MET cc_start: 0.8618 (ppp) cc_final: 0.8019 (ppp) REVERT: B 336 LYS cc_start: 0.8782 (tppt) cc_final: 0.8418 (tppt) REVERT: B 384 HIS cc_start: 0.9156 (OUTLIER) cc_final: 0.8769 (m-70) REVERT: B 442 MET cc_start: 0.9618 (ptp) cc_final: 0.8769 (ppp) REVERT: B 550 MET cc_start: 0.8647 (ptp) cc_final: 0.8355 (tpt) REVERT: B 560 ARG cc_start: 0.9597 (ttm170) cc_final: 0.9242 (ttp80) REVERT: B 608 MET cc_start: 0.9469 (ppp) cc_final: 0.9114 (ppp) REVERT: B 651 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9255 (ptpp) REVERT: C 449 MET cc_start: 0.9105 (mmm) cc_final: 0.8763 (mmm) REVERT: C 508 MET cc_start: 0.7469 (tpt) cc_final: 0.7167 (tpp) REVERT: C 578 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: C 608 MET cc_start: 0.9507 (tmm) cc_final: 0.9195 (tmm) REVERT: D 427 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8869 (tpp) REVERT: D 508 MET cc_start: 0.7504 (tpp) cc_final: 0.6528 (tpp) REVERT: D 728 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8088 (p) REVERT: D 740 MET cc_start: 0.9161 (tpp) cc_final: 0.8873 (ttt) REVERT: E 211 LYS cc_start: 0.9594 (OUTLIER) cc_final: 0.9320 (mtmm) REVERT: E 515 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8798 (tt) REVERT: F 244 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: F 283 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8928 (mp0) REVERT: F 319 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: F 508 MET cc_start: 0.8730 (tpp) cc_final: 0.8149 (tpp) REVERT: F 678 MET cc_start: 0.9372 (mpp) cc_final: 0.8927 (mpp) outliers start: 107 outliers final: 85 residues processed: 257 average time/residue: 0.1948 time to fit residues: 85.7269 Evaluate side-chains 257 residues out of total 4011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 154 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 147 PHE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 297 ASP Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 334 TYR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain M residue 637 LYS Chi-restraints excluded: chain M residue 639 PHE Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 618 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 201 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 379 optimal weight: 6.9990 chunk 426 optimal weight: 5.9990 chunk 170 optimal weight: 0.0050 chunk 18 optimal weight: 0.6980 chunk 304 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 314 optimal weight: 8.9990 chunk 7 optimal weight: 50.0000 chunk 110 optimal weight: 3.9990 overall best weight: 2.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.057346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038842 restraints weight = 251755.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038897 restraints weight = 143227.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.039149 restraints weight = 109311.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.039236 restraints weight = 99209.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.039273 restraints weight = 82812.034| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 35998 Z= 0.141 Angle : 0.661 14.514 48824 Z= 0.309 Chirality : 0.043 0.242 5541 Planarity : 0.004 0.094 6453 Dihedral : 8.847 154.694 5248 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.92 % Favored : 93.99 % Rotamer: Outliers : 3.15 % Allowed : 25.16 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4611 helix: 1.36 (0.12), residues: 2032 sheet: -0.93 (0.22), residues: 590 loop : -0.40 (0.15), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 638 TYR 0.021 0.001 TYR D 203 PHE 0.022 0.001 PHE M 537 TRP 0.024 0.001 TRP O 610 HIS 0.010 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00306 (35990) covalent geometry : angle 0.66034 (48818) hydrogen bonds : bond 0.02851 ( 1578) hydrogen bonds : angle 4.55196 ( 4398) metal coordination : bond 0.01472 ( 8) metal coordination : angle 2.60111 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7156.51 seconds wall clock time: 123 minutes 39.46 seconds (7419.46 seconds total)