Starting phenix.real_space_refine on Wed Nov 19 05:52:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cud_7620/11_2025/6cud_7620_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cud_7620/11_2025/6cud_7620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cud_7620/11_2025/6cud_7620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cud_7620/11_2025/6cud_7620.map" model { file = "/net/cci-nas-00/data/ceres_data/6cud_7620/11_2025/6cud_7620_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cud_7620/11_2025/6cud_7620_neut.cif" } resolution = 3.3 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= -0.003 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 104 5.16 5 C 13844 2.51 5 N 3484 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21028 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5196 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 22, 'TRANS': 681} Chain breaks: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 38, 'ARG:plan': 6, 'ASP:plan': 25, 'ASN:plan1': 9, 'TYR:plan': 3, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 333 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'6OE': 1, 'FGJ': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 4.37, per 1000 atoms: 0.21 Number of scatterers: 21028 At special positions: 0 Unit cell: (123.51, 123.51, 148.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 4 15.00 O 3592 8.00 N 3484 7.00 C 13844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 184 " distance=2.05 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 184 " distance=2.05 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 184 " distance=2.05 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 184 " distance=2.05 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 Links applied NAG-ASN " NAG A 903 " - " ASN A 404 " " NAG B 903 " - " ASN B 404 " " NAG C 903 " - " ASN C 404 " " NAG D 903 " - " ASN D 404 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 870.9 milliseconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 removed outlier: 3.953A pdb=" N ALA A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.718A pdb=" N MET A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 50 " --> pdb=" O MET A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.658A pdb=" N LEU A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.633A pdb=" N LEU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 103 through 111 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.513A pdb=" N ALA A 116 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.632A pdb=" N HIS A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.746A pdb=" N HIS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 removed outlier: 3.628A pdb=" N HIS A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 4.516A pdb=" N SER A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.920A pdb=" N THR A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.556A pdb=" N TYR A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 3.717A pdb=" N VAL A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.956A pdb=" N LYS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.683A pdb=" N VAL A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 4.185A pdb=" N GLN A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 4.132A pdb=" N GLU A 331 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 332 " --> pdb=" O LEU A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 333 through 347 Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.923A pdb=" N ILE A 357 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.629A pdb=" N LYS A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 392 Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.445A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 448 removed outlier: 3.544A pdb=" N MET A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.756A pdb=" N GLN A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 493 removed outlier: 3.812A pdb=" N VAL A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.577A pdb=" N TYR A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.523A pdb=" N VAL A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 544 removed outlier: 3.967A pdb=" N ILE A 541 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 542 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 587 removed outlier: 3.779A pdb=" N GLN A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 590 No H-bonds generated for 'chain 'A' and resid 588 through 590' Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 618 through 622 removed outlier: 3.947A pdb=" N SER A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 665 removed outlier: 3.524A pdb=" N GLU A 632 " --> pdb=" O HIS A 628 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.904A pdb=" N LYS A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 786 removed outlier: 3.889A pdb=" N GLU A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.929A pdb=" N GLU A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 38 removed outlier: 3.953A pdb=" N ALA B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 50 removed outlier: 3.717A pdb=" N MET B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.658A pdb=" N LEU B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 82 removed outlier: 3.634A pdb=" N LEU B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 103 through 111 Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.513A pdb=" N ALA B 116 " --> pdb=" O HIS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.632A pdb=" N HIS B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.745A pdb=" N HIS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.627A pdb=" N HIS B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 4.517A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.920A pdb=" N THR B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 264 removed outlier: 3.555A pdb=" N TYR B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 258 " --> pdb=" O CYS B 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.717A pdb=" N VAL B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.957A pdb=" N LYS B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.683A pdb=" N VAL B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.185A pdb=" N GLN B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 4.131A pdb=" N GLU B 331 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 332 " --> pdb=" O LEU B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 332' Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.924A pdb=" N ILE B 357 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.628A pdb=" N LYS B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 392 Processing helix chain 'B' and resid 414 through 421 removed outlier: 4.444A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 448 removed outlier: 3.544A pdb=" N MET B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 428 " --> pdb=" O TRP B 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.755A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 493 removed outlier: 3.813A pdb=" N VAL B 459 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.577A pdb=" N TYR B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 521 through 537 removed outlier: 3.523A pdb=" N VAL B 534 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 544 removed outlier: 3.967A pdb=" N ILE B 541 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 542 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 587 removed outlier: 3.779A pdb=" N GLN B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 566 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 590 No H-bonds generated for 'chain 'B' and resid 588 through 590' Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 618 through 622 removed outlier: 3.947A pdb=" N SER B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 665 removed outlier: 3.524A pdb=" N GLU B 632 " --> pdb=" O HIS B 628 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 647 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.904A pdb=" N LYS B 679 " --> pdb=" O PHE B 675 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 786 removed outlier: 3.888A pdb=" N GLU B 786 " --> pdb=" O LYS B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 806 removed outlier: 3.930A pdb=" N GLU B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 38 removed outlier: 3.954A pdb=" N ALA C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 50 removed outlier: 3.718A pdb=" N MET C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.657A pdb=" N LEU C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 82 removed outlier: 3.634A pdb=" N LEU C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 112 through 117 removed outlier: 3.514A pdb=" N ALA C 116 " --> pdb=" O HIS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.632A pdb=" N HIS C 165 " --> pdb=" O TYR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 193 removed outlier: 3.746A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 210 removed outlier: 3.628A pdb=" N HIS C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 4.516A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 241 removed outlier: 3.920A pdb=" N THR C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.556A pdb=" N TYR C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 258 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 275 removed outlier: 3.717A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.956A pdb=" N LYS C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.683A pdb=" N VAL C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 4.185A pdb=" N GLN C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 removed outlier: 4.133A pdb=" N GLU C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN C 332 " --> pdb=" O LEU C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 332' Processing helix chain 'C' and resid 333 through 347 Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.924A pdb=" N ILE C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 361 through 366 removed outlier: 3.628A pdb=" N LYS C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 392 Processing helix chain 'C' and resid 414 through 421 removed outlier: 4.444A pdb=" N LYS C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 448 removed outlier: 3.545A pdb=" N MET C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 428 " --> pdb=" O TRP C 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 455 removed outlier: 3.755A pdb=" N GLN C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 493 removed outlier: 3.813A pdb=" N VAL C 459 " --> pdb=" O GLN C 455 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.578A pdb=" N TYR C 509 " --> pdb=" O PRO C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 521 through 537 removed outlier: 3.524A pdb=" N VAL C 534 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 544 removed outlier: 3.967A pdb=" N ILE C 541 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 542 " --> pdb=" O SER C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 587 removed outlier: 3.779A pdb=" N GLN C 555 " --> pdb=" O PHE C 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 556 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 557 " --> pdb=" O PRO C 553 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE C 566 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 571 " --> pdb=" O LYS C 567 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 590 No H-bonds generated for 'chain 'C' and resid 588 through 590' Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 618 through 622 removed outlier: 3.947A pdb=" N SER C 621 " --> pdb=" O GLU C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 665 removed outlier: 3.524A pdb=" N GLU C 632 " --> pdb=" O HIS C 628 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 647 " --> pdb=" O ASN C 643 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 661 " --> pdb=" O MET C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 686 removed outlier: 3.904A pdb=" N LYS C 679 " --> pdb=" O PHE C 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 786 removed outlier: 3.889A pdb=" N GLU C 786 " --> pdb=" O LYS C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 806 removed outlier: 3.929A pdb=" N GLU C 791 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.953A pdb=" N ALA D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.718A pdb=" N MET D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER D 50 " --> pdb=" O MET D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.658A pdb=" N LEU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 82 removed outlier: 3.634A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 103 through 111 Processing helix chain 'D' and resid 112 through 117 removed outlier: 3.514A pdb=" N ALA D 116 " --> pdb=" O HIS D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.632A pdb=" N HIS D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 193 removed outlier: 3.746A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 210 removed outlier: 3.627A pdb=" N HIS D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 4.516A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 241 removed outlier: 3.921A pdb=" N THR D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 264 removed outlier: 3.556A pdb=" N TYR D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 258 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 removed outlier: 3.717A pdb=" N VAL D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 removed outlier: 3.956A pdb=" N LYS D 302 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.683A pdb=" N VAL D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 4.185A pdb=" N GLN D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 removed outlier: 4.132A pdb=" N GLU D 331 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN D 332 " --> pdb=" O LEU D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 332' Processing helix chain 'D' and resid 333 through 347 Processing helix chain 'D' and resid 350 through 357 removed outlier: 3.923A pdb=" N ILE D 357 " --> pdb=" O ILE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.628A pdb=" N LYS D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 392 Processing helix chain 'D' and resid 414 through 421 removed outlier: 4.444A pdb=" N LYS D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 448 removed outlier: 3.544A pdb=" N MET D 427 " --> pdb=" O THR D 423 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 428 " --> pdb=" O TRP D 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 434 " --> pdb=" O MET D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.756A pdb=" N GLN D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 493 removed outlier: 3.813A pdb=" N VAL D 459 " --> pdb=" O GLN D 455 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA D 482 " --> pdb=" O ALA D 478 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 removed outlier: 3.578A pdb=" N TYR D 509 " --> pdb=" O PRO D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'D' and resid 521 through 537 removed outlier: 3.523A pdb=" N VAL D 534 " --> pdb=" O TYR D 530 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 544 removed outlier: 3.967A pdb=" N ILE D 541 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 542 " --> pdb=" O SER D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 587 removed outlier: 3.779A pdb=" N GLN D 555 " --> pdb=" O PHE D 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 556 " --> pdb=" O GLY D 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 557 " --> pdb=" O PRO D 553 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE D 566 " --> pdb=" O VAL D 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 571 " --> pdb=" O LYS D 567 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 590 No H-bonds generated for 'chain 'D' and resid 588 through 590' Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 618 through 622 removed outlier: 3.947A pdb=" N SER D 621 " --> pdb=" O GLU D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 665 removed outlier: 3.524A pdb=" N GLU D 632 " --> pdb=" O HIS D 628 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 647 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 661 " --> pdb=" O MET D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 686 removed outlier: 3.904A pdb=" N LYS D 679 " --> pdb=" O PHE D 675 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR D 684 " --> pdb=" O LEU D 680 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP D 686 " --> pdb=" O LEU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 786 removed outlier: 3.888A pdb=" N GLU D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 806 removed outlier: 3.930A pdb=" N GLU D 791 " --> pdb=" O VAL D 787 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3816 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: 3.48 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3334 1.32 - 1.45: 5818 1.45 - 1.57: 12168 1.57 - 1.69: 8 1.69 - 1.81: 176 Bond restraints: 21504 Sorted by residual: bond pdb=" C ILE C 40 " pdb=" N PRO C 41 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.20e-02 6.94e+03 1.73e+01 bond pdb=" C ILE D 40 " pdb=" N PRO D 41 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.68e+01 bond pdb=" C ILE A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.68e+01 bond pdb=" C ILE B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.67e+01 bond pdb=" N TYR C 410 " pdb=" CA TYR C 410 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.48e+01 ... (remaining 21499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 27711 2.31 - 4.63: 1401 4.63 - 6.94: 108 6.94 - 9.26: 48 9.26 - 11.57: 20 Bond angle restraints: 29288 Sorted by residual: angle pdb=" N LEU D 217 " pdb=" CA LEU D 217 " pdb=" C LEU D 217 " ideal model delta sigma weight residual 113.17 121.07 -7.90 1.26e+00 6.30e-01 3.93e+01 angle pdb=" N LEU B 217 " pdb=" CA LEU B 217 " pdb=" C LEU B 217 " ideal model delta sigma weight residual 113.17 121.07 -7.90 1.26e+00 6.30e-01 3.93e+01 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 113.17 121.05 -7.88 1.26e+00 6.30e-01 3.91e+01 angle pdb=" N LEU C 217 " pdb=" CA LEU C 217 " pdb=" C LEU C 217 " ideal model delta sigma weight residual 113.17 121.01 -7.84 1.26e+00 6.30e-01 3.87e+01 angle pdb=" N SER D 216 " pdb=" CA SER D 216 " pdb=" C SER D 216 " ideal model delta sigma weight residual 111.36 117.42 -6.06 1.09e+00 8.42e-01 3.09e+01 ... (remaining 29283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.33: 12432 31.33 - 62.67: 232 62.67 - 94.00: 40 94.00 - 125.34: 0 125.34 - 156.67: 24 Dihedral angle restraints: 12728 sinusoidal: 4412 harmonic: 8316 Sorted by residual: dihedral pdb=" CD ARG A 540 " pdb=" NE ARG A 540 " pdb=" CZ ARG A 540 " pdb=" NH1 ARG A 540 " ideal model delta sinusoidal sigma weight residual 0.00 -67.50 67.50 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CD ARG B 540 " pdb=" NE ARG B 540 " pdb=" CZ ARG B 540 " pdb=" NH1 ARG B 540 " ideal model delta sinusoidal sigma weight residual 0.00 -67.49 67.49 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CD ARG D 540 " pdb=" NE ARG D 540 " pdb=" CZ ARG D 540 " pdb=" NH1 ARG D 540 " ideal model delta sinusoidal sigma weight residual 0.00 -67.45 67.45 1 1.00e+01 1.00e-02 5.92e+01 ... (remaining 12725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2636 0.060 - 0.121: 668 0.121 - 0.181: 133 0.181 - 0.241: 23 0.241 - 0.302: 16 Chirality restraints: 3476 Sorted by residual: chirality pdb=" CA SER B 218 " pdb=" N SER B 218 " pdb=" C SER B 218 " pdb=" CB SER B 218 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA SER A 218 " pdb=" N SER A 218 " pdb=" C SER A 218 " pdb=" CB SER A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA SER C 218 " pdb=" N SER C 218 " pdb=" C SER C 218 " pdb=" CB SER C 218 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 3473 not shown) Planarity restraints: 3620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 540 " -1.013 9.50e-02 1.11e+02 4.54e-01 1.25e+02 pdb=" NE ARG B 540 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG B 540 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 540 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 540 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 540 " -1.013 9.50e-02 1.11e+02 4.54e-01 1.24e+02 pdb=" NE ARG C 540 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 540 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 540 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 540 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 540 " -1.013 9.50e-02 1.11e+02 4.54e-01 1.24e+02 pdb=" NE ARG A 540 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 540 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 540 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 540 " -0.023 2.00e-02 2.50e+03 ... (remaining 3617 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 972 2.72 - 3.26: 20716 3.26 - 3.81: 31253 3.81 - 4.35: 37160 4.35 - 4.90: 64535 Nonbonded interactions: 154636 Sorted by model distance: nonbonded pdb=" OD1 ASP B 92 " pdb=" NH2 ARG B 144 " model vdw 2.171 3.120 nonbonded pdb=" OD1 ASP A 92 " pdb=" NH2 ARG A 144 " model vdw 2.172 3.120 nonbonded pdb=" OD1 ASP C 92 " pdb=" NH2 ARG C 144 " model vdw 2.172 3.120 nonbonded pdb=" OD1 ASP D 92 " pdb=" NH2 ARG D 144 " model vdw 2.172 3.120 nonbonded pdb=" OE1 GLU B 440 " pdb=" OH TYR B 452 " model vdw 2.279 3.040 ... (remaining 154631 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.670 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 21512 Z= 0.418 Angle : 1.210 26.066 29308 Z= 0.733 Chirality : 0.059 0.302 3476 Planarity : 0.017 0.454 3616 Dihedral : 14.710 156.670 7324 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.49 % Rotamer: Outliers : 1.47 % Allowed : 5.53 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.04 (0.13), residues: 2792 helix: -1.63 (0.10), residues: 1948 sheet: None (None), residues: 0 loop : -2.59 (0.17), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 677 TYR 0.035 0.002 TYR B 636 PHE 0.031 0.002 PHE D 538 TRP 0.018 0.002 TRP D 611 HIS 0.006 0.002 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00675 (21504) covalent geometry : angle 1.13492 (29288) SS BOND : bond 0.01806 ( 4) SS BOND : angle 25.51011 ( 8) hydrogen bonds : bond 0.18691 ( 1284) hydrogen bonds : angle 5.68937 ( 3816) link_NAG-ASN : bond 0.00082 ( 4) link_NAG-ASN : angle 1.06919 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ASP cc_start: 0.7747 (m-30) cc_final: 0.7520 (m-30) REVERT: A 351 LEU cc_start: 0.7410 (mt) cc_final: 0.7055 (mt) REVERT: A 410 TYR cc_start: 0.5312 (OUTLIER) cc_final: 0.4272 (p90) REVERT: A 430 MET cc_start: 0.8349 (mmm) cc_final: 0.8100 (tpp) REVERT: A 521 ASP cc_start: 0.7881 (t0) cc_final: 0.7573 (t0) REVERT: B 246 ASP cc_start: 0.7717 (m-30) cc_final: 0.7506 (m-30) REVERT: B 351 LEU cc_start: 0.7448 (mt) cc_final: 0.7090 (mt) REVERT: B 410 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.4312 (p90) REVERT: B 430 MET cc_start: 0.8350 (mmm) cc_final: 0.8066 (tpp) REVERT: B 521 ASP cc_start: 0.8044 (t0) cc_final: 0.7662 (t0) REVERT: C 246 ASP cc_start: 0.7762 (m-30) cc_final: 0.7550 (m-30) REVERT: C 351 LEU cc_start: 0.7416 (mt) cc_final: 0.7051 (mt) REVERT: C 410 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.4327 (p90) REVERT: C 430 MET cc_start: 0.8352 (mmm) cc_final: 0.8093 (tpp) REVERT: C 521 ASP cc_start: 0.7909 (t0) cc_final: 0.7620 (t0) REVERT: D 351 LEU cc_start: 0.7426 (mt) cc_final: 0.7069 (mt) REVERT: D 410 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4347 (p90) REVERT: D 430 MET cc_start: 0.8367 (mmm) cc_final: 0.8094 (tpp) REVERT: D 521 ASP cc_start: 0.7882 (t0) cc_final: 0.7569 (t0) outliers start: 28 outliers final: 12 residues processed: 233 average time/residue: 0.1330 time to fit residues: 49.2329 Evaluate side-chains 171 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 445 TRP Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 445 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 198 HIS B 112 HIS B 198 HIS C 112 HIS C 198 HIS D 112 HIS D 198 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073008 restraints weight = 47179.879| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.93 r_work: 0.2922 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21512 Z= 0.152 Angle : 0.596 8.917 29308 Z= 0.312 Chirality : 0.039 0.122 3476 Planarity : 0.004 0.045 3616 Dihedral : 15.038 154.649 3296 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.13 % Rotamer: Outliers : 1.21 % Allowed : 8.95 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.15), residues: 2792 helix: 0.31 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : -2.10 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 330 TYR 0.017 0.002 TYR B 488 PHE 0.016 0.001 PHE A 181 TRP 0.012 0.001 TRP B 673 HIS 0.003 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00326 (21504) covalent geometry : angle 0.58952 (29288) SS BOND : bond 0.00720 ( 4) SS BOND : angle 5.24611 ( 8) hydrogen bonds : bond 0.06718 ( 1284) hydrogen bonds : angle 3.76332 ( 3816) link_NAG-ASN : bond 0.00113 ( 4) link_NAG-ASN : angle 1.07078 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7135 (mt) cc_final: 0.6813 (mt) REVERT: B 351 LEU cc_start: 0.7228 (mt) cc_final: 0.6906 (mt) REVERT: B 430 MET cc_start: 0.8426 (mmm) cc_final: 0.8225 (tpp) REVERT: B 521 ASP cc_start: 0.8018 (t0) cc_final: 0.7773 (t0) REVERT: C 351 LEU cc_start: 0.7112 (mt) cc_final: 0.6779 (mt) REVERT: C 521 ASP cc_start: 0.7953 (t0) cc_final: 0.7740 (t0) REVERT: D 351 LEU cc_start: 0.7119 (mt) cc_final: 0.6792 (mt) REVERT: D 521 ASP cc_start: 0.7960 (t0) cc_final: 0.7738 (t0) REVERT: D 583 MET cc_start: 0.9085 (mmm) cc_final: 0.8850 (mmt) outliers start: 23 outliers final: 23 residues processed: 193 average time/residue: 0.1249 time to fit residues: 39.4896 Evaluate side-chains 179 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 445 TRP Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 452 TYR Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 452 TYR Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 116 optimal weight: 20.0000 chunk 145 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 226 optimal weight: 0.7980 chunk 138 optimal weight: 30.0000 chunk 229 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 212 optimal weight: 0.0000 chunk 149 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.075861 restraints weight = 46586.260| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.88 r_work: 0.2972 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21512 Z= 0.110 Angle : 0.512 9.465 29308 Z= 0.259 Chirality : 0.038 0.119 3476 Planarity : 0.003 0.037 3616 Dihedral : 13.749 154.453 3288 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.58 % Favored : 96.28 % Rotamer: Outliers : 2.16 % Allowed : 10.05 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.16), residues: 2792 helix: 1.40 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -2.01 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 330 TYR 0.016 0.001 TYR B 636 PHE 0.012 0.001 PHE B 181 TRP 0.012 0.001 TRP A 356 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00222 (21504) covalent geometry : angle 0.50527 (29288) SS BOND : bond 0.00739 ( 4) SS BOND : angle 4.74906 ( 8) hydrogen bonds : bond 0.04609 ( 1284) hydrogen bonds : angle 3.12527 ( 3816) link_NAG-ASN : bond 0.00119 ( 4) link_NAG-ASN : angle 1.01657 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.691 Fit side-chains REVERT: A 194 ASP cc_start: 0.8074 (t0) cc_final: 0.7863 (t70) REVERT: A 351 LEU cc_start: 0.7257 (mt) cc_final: 0.7015 (mt) REVERT: A 583 MET cc_start: 0.9017 (mmt) cc_final: 0.8738 (mmt) REVERT: B 194 ASP cc_start: 0.8067 (t0) cc_final: 0.7819 (t70) REVERT: B 351 LEU cc_start: 0.7204 (mt) cc_final: 0.6871 (mt) REVERT: B 430 MET cc_start: 0.8182 (mmm) cc_final: 0.7788 (mmm) REVERT: B 572 PHE cc_start: 0.8297 (t80) cc_final: 0.8051 (t80) REVERT: C 194 ASP cc_start: 0.8106 (t0) cc_final: 0.7879 (t70) REVERT: C 351 LEU cc_start: 0.7293 (mt) cc_final: 0.7050 (mt) REVERT: C 572 PHE cc_start: 0.8279 (t80) cc_final: 0.8038 (t80) REVERT: C 583 MET cc_start: 0.9019 (mmt) cc_final: 0.8724 (mmt) REVERT: D 194 ASP cc_start: 0.8202 (t0) cc_final: 0.7989 (t70) REVERT: D 351 LEU cc_start: 0.7260 (mt) cc_final: 0.6932 (mt) REVERT: D 572 PHE cc_start: 0.8289 (t80) cc_final: 0.8039 (t80) outliers start: 41 outliers final: 20 residues processed: 207 average time/residue: 0.1181 time to fit residues: 41.5839 Evaluate side-chains 177 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 43 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 149 optimal weight: 0.3980 chunk 172 optimal weight: 0.0170 chunk 222 optimal weight: 0.5980 chunk 251 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 212 optimal weight: 0.0770 chunk 183 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076240 restraints weight = 46500.424| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.89 r_work: 0.2977 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21512 Z= 0.099 Angle : 0.495 9.462 29308 Z= 0.245 Chirality : 0.037 0.116 3476 Planarity : 0.003 0.036 3616 Dihedral : 13.121 155.066 3280 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Rotamer: Outliers : 2.32 % Allowed : 10.53 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.33 (0.16), residues: 2792 helix: 1.90 (0.12), residues: 1992 sheet: None (None), residues: 0 loop : -1.83 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 248 TYR 0.009 0.001 TYR D 639 PHE 0.015 0.001 PHE B 350 TRP 0.011 0.001 TRP A 356 HIS 0.002 0.000 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00201 (21504) covalent geometry : angle 0.48988 (29288) SS BOND : bond 0.00754 ( 4) SS BOND : angle 4.21928 ( 8) hydrogen bonds : bond 0.04185 ( 1284) hydrogen bonds : angle 2.97663 ( 3816) link_NAG-ASN : bond 0.00101 ( 4) link_NAG-ASN : angle 0.91074 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 194 ASP cc_start: 0.8081 (t0) cc_final: 0.7767 (t70) REVERT: A 430 MET cc_start: 0.7984 (tpp) cc_final: 0.7671 (tpp) REVERT: A 583 MET cc_start: 0.9038 (mmt) cc_final: 0.8752 (mmt) REVERT: B 194 ASP cc_start: 0.8108 (t0) cc_final: 0.7775 (t70) REVERT: B 351 LEU cc_start: 0.7281 (mt) cc_final: 0.7007 (mt) REVERT: B 430 MET cc_start: 0.8087 (mmm) cc_final: 0.7821 (mtt) REVERT: B 572 PHE cc_start: 0.8235 (t80) cc_final: 0.8004 (t80) REVERT: C 194 ASP cc_start: 0.8122 (t0) cc_final: 0.7801 (t70) REVERT: C 351 LEU cc_start: 0.7405 (mt) cc_final: 0.7203 (mt) REVERT: C 430 MET cc_start: 0.8017 (tpp) cc_final: 0.7692 (tpp) REVERT: C 564 ASP cc_start: 0.8251 (t0) cc_final: 0.8021 (t0) REVERT: C 583 MET cc_start: 0.9006 (mmt) cc_final: 0.8725 (mmt) REVERT: D 194 ASP cc_start: 0.8258 (t0) cc_final: 0.7955 (t70) REVERT: D 351 LEU cc_start: 0.7396 (mt) cc_final: 0.7194 (mt) REVERT: D 430 MET cc_start: 0.7982 (tpp) cc_final: 0.7656 (tpp) REVERT: D 564 ASP cc_start: 0.8312 (t0) cc_final: 0.8095 (t0) outliers start: 44 outliers final: 27 residues processed: 196 average time/residue: 0.1180 time to fit residues: 38.9260 Evaluate side-chains 181 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 69 optimal weight: 5.9990 chunk 229 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 247 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 156 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS D 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.099694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.074581 restraints weight = 46565.938| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.89 r_work: 0.2947 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21512 Z= 0.110 Angle : 0.490 7.448 29308 Z= 0.244 Chirality : 0.037 0.122 3476 Planarity : 0.003 0.056 3616 Dihedral : 12.848 155.961 3280 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 1.95 % Allowed : 11.84 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.17), residues: 2792 helix: 2.16 (0.12), residues: 2020 sheet: None (None), residues: 0 loop : -1.91 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 248 TYR 0.010 0.001 TYR C 636 PHE 0.014 0.001 PHE B 350 TRP 0.012 0.001 TRP A 356 HIS 0.006 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00243 (21504) covalent geometry : angle 0.48554 (29288) SS BOND : bond 0.00815 ( 4) SS BOND : angle 4.04908 ( 8) hydrogen bonds : bond 0.04381 ( 1284) hydrogen bonds : angle 2.96649 ( 3816) link_NAG-ASN : bond 0.00124 ( 4) link_NAG-ASN : angle 0.85221 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.782 Fit side-chains REVERT: A 194 ASP cc_start: 0.8105 (t0) cc_final: 0.7739 (t70) REVERT: B 194 ASP cc_start: 0.8206 (t0) cc_final: 0.7778 (t70) REVERT: B 351 LEU cc_start: 0.7289 (mt) cc_final: 0.7074 (mt) REVERT: B 430 MET cc_start: 0.8079 (mmm) cc_final: 0.7857 (mtt) REVERT: B 572 PHE cc_start: 0.8128 (t80) cc_final: 0.7896 (t80) REVERT: C 194 ASP cc_start: 0.8223 (t0) cc_final: 0.7792 (t70) REVERT: D 194 ASP cc_start: 0.8322 (t0) cc_final: 0.7877 (t70) outliers start: 37 outliers final: 32 residues processed: 180 average time/residue: 0.1104 time to fit residues: 34.0697 Evaluate side-chains 183 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Chi-restraints excluded: chain D residue 792 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 153 optimal weight: 0.0570 chunk 121 optimal weight: 0.4980 chunk 176 optimal weight: 0.2980 chunk 279 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075750 restraints weight = 46296.058| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.89 r_work: 0.2971 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21512 Z= 0.096 Angle : 0.470 7.330 29308 Z= 0.235 Chirality : 0.037 0.119 3476 Planarity : 0.003 0.035 3616 Dihedral : 12.615 155.419 3280 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.90 % Favored : 96.96 % Rotamer: Outliers : 2.53 % Allowed : 11.42 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.17), residues: 2792 helix: 2.39 (0.12), residues: 2020 sheet: None (None), residues: 0 loop : -1.86 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 248 TYR 0.008 0.001 TYR D 639 PHE 0.012 0.001 PHE B 350 TRP 0.035 0.001 TRP B 356 HIS 0.007 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00197 (21504) covalent geometry : angle 0.46522 (29288) SS BOND : bond 0.00833 ( 4) SS BOND : angle 3.91652 ( 8) hydrogen bonds : bond 0.03887 ( 1284) hydrogen bonds : angle 2.86445 ( 3816) link_NAG-ASN : bond 0.00138 ( 4) link_NAG-ASN : angle 0.85676 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.881 Fit side-chains REVERT: A 194 ASP cc_start: 0.8097 (t0) cc_final: 0.7672 (t70) REVERT: B 194 ASP cc_start: 0.8180 (t0) cc_final: 0.7732 (t70) REVERT: B 351 LEU cc_start: 0.7487 (mt) cc_final: 0.7259 (mt) REVERT: B 572 PHE cc_start: 0.8083 (t80) cc_final: 0.7848 (t80) REVERT: C 194 ASP cc_start: 0.8168 (t0) cc_final: 0.7717 (t70) REVERT: D 194 ASP cc_start: 0.8234 (t0) cc_final: 0.7799 (t70) REVERT: D 564 ASP cc_start: 0.8221 (t0) cc_final: 0.7999 (t0) outliers start: 48 outliers final: 30 residues processed: 188 average time/residue: 0.1116 time to fit residues: 36.5169 Evaluate side-chains 177 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 191 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 166 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 5 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.100853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.075710 restraints weight = 46645.893| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.90 r_work: 0.2971 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21512 Z= 0.095 Angle : 0.457 8.286 29308 Z= 0.230 Chirality : 0.037 0.121 3476 Planarity : 0.003 0.035 3616 Dihedral : 12.490 154.985 3280 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.22 % Favored : 96.63 % Rotamer: Outliers : 2.11 % Allowed : 12.68 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.12 (0.17), residues: 2792 helix: 2.52 (0.12), residues: 2024 sheet: None (None), residues: 0 loop : -1.83 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 330 TYR 0.009 0.001 TYR D 639 PHE 0.012 0.001 PHE B 350 TRP 0.035 0.001 TRP A 356 HIS 0.006 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00198 (21504) covalent geometry : angle 0.45256 (29288) SS BOND : bond 0.00830 ( 4) SS BOND : angle 3.79439 ( 8) hydrogen bonds : bond 0.03792 ( 1284) hydrogen bonds : angle 2.82344 ( 3816) link_NAG-ASN : bond 0.00132 ( 4) link_NAG-ASN : angle 0.83367 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.789 Fit side-chains REVERT: A 194 ASP cc_start: 0.8081 (t0) cc_final: 0.7638 (t70) REVERT: B 194 ASP cc_start: 0.8160 (t0) cc_final: 0.7705 (t70) REVERT: B 351 LEU cc_start: 0.7575 (mt) cc_final: 0.7343 (mt) REVERT: B 572 PHE cc_start: 0.8052 (t80) cc_final: 0.7812 (t80) REVERT: C 194 ASP cc_start: 0.8154 (t0) cc_final: 0.7704 (t70) REVERT: D 194 ASP cc_start: 0.8241 (t0) cc_final: 0.7801 (t70) outliers start: 40 outliers final: 33 residues processed: 179 average time/residue: 0.1099 time to fit residues: 34.0234 Evaluate side-chains 180 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 257 optimal weight: 0.0050 chunk 156 optimal weight: 0.2980 chunk 246 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 212 optimal weight: 0.0470 chunk 193 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS D 311 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076276 restraints weight = 46779.991| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.90 r_work: 0.2984 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21512 Z= 0.090 Angle : 0.449 8.886 29308 Z= 0.225 Chirality : 0.037 0.126 3476 Planarity : 0.003 0.035 3616 Dihedral : 12.316 154.082 3280 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 2.11 % Allowed : 13.37 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.30 (0.17), residues: 2792 helix: 2.66 (0.12), residues: 2020 sheet: None (None), residues: 0 loop : -1.78 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 248 TYR 0.009 0.001 TYR D 639 PHE 0.011 0.001 PHE B 350 TRP 0.033 0.001 TRP A 356 HIS 0.006 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00186 (21504) covalent geometry : angle 0.44498 (29288) SS BOND : bond 0.00824 ( 4) SS BOND : angle 3.74857 ( 8) hydrogen bonds : bond 0.03533 ( 1284) hydrogen bonds : angle 2.77116 ( 3816) link_NAG-ASN : bond 0.00142 ( 4) link_NAG-ASN : angle 0.85765 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.833 Fit side-chains REVERT: A 194 ASP cc_start: 0.8086 (t0) cc_final: 0.7639 (t70) REVERT: A 437 MET cc_start: 0.8477 (tpt) cc_final: 0.8150 (tpt) REVERT: A 583 MET cc_start: 0.9008 (mmt) cc_final: 0.8791 (mmt) REVERT: B 194 ASP cc_start: 0.8152 (t0) cc_final: 0.7685 (t70) REVERT: B 437 MET cc_start: 0.8507 (tpt) cc_final: 0.8194 (tpt) REVERT: B 572 PHE cc_start: 0.8007 (t80) cc_final: 0.7771 (t80) REVERT: C 194 ASP cc_start: 0.8110 (t0) cc_final: 0.7633 (t70) REVERT: C 437 MET cc_start: 0.8495 (tpt) cc_final: 0.8169 (tpt) REVERT: C 583 MET cc_start: 0.9015 (mmt) cc_final: 0.8797 (mmt) REVERT: D 194 ASP cc_start: 0.8210 (t0) cc_final: 0.7756 (t70) REVERT: D 437 MET cc_start: 0.8473 (tpt) cc_final: 0.8138 (tpt) outliers start: 40 outliers final: 30 residues processed: 178 average time/residue: 0.1141 time to fit residues: 35.5924 Evaluate side-chains 172 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 205 optimal weight: 0.4980 chunk 240 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.074991 restraints weight = 46625.633| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.88 r_work: 0.2959 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21512 Z= 0.103 Angle : 0.458 9.125 29308 Z= 0.230 Chirality : 0.037 0.127 3476 Planarity : 0.003 0.035 3616 Dihedral : 12.253 154.310 3272 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.70 % Rotamer: Outliers : 2.05 % Allowed : 13.37 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.17), residues: 2792 helix: 2.71 (0.12), residues: 2016 sheet: None (None), residues: 0 loop : -1.74 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 330 TYR 0.009 0.001 TYR D 639 PHE 0.010 0.001 PHE B 350 TRP 0.028 0.001 TRP A 356 HIS 0.006 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00232 (21504) covalent geometry : angle 0.45330 (29288) SS BOND : bond 0.00855 ( 4) SS BOND : angle 3.69432 ( 8) hydrogen bonds : bond 0.03822 ( 1284) hydrogen bonds : angle 2.83379 ( 3816) link_NAG-ASN : bond 0.00138 ( 4) link_NAG-ASN : angle 0.84741 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.833 Fit side-chains REVERT: A 194 ASP cc_start: 0.8128 (t0) cc_final: 0.7681 (t70) REVERT: A 437 MET cc_start: 0.8480 (tpt) cc_final: 0.8147 (tpt) REVERT: B 194 ASP cc_start: 0.8195 (t0) cc_final: 0.7720 (t70) REVERT: B 437 MET cc_start: 0.8502 (tpt) cc_final: 0.8167 (tpt) REVERT: B 653 MET cc_start: 0.8367 (tpp) cc_final: 0.8147 (tpp) REVERT: C 194 ASP cc_start: 0.8166 (t0) cc_final: 0.7681 (t70) REVERT: C 437 MET cc_start: 0.8489 (tpt) cc_final: 0.8158 (tpt) REVERT: D 194 ASP cc_start: 0.8254 (t0) cc_final: 0.7809 (t70) REVERT: D 263 ASP cc_start: 0.9215 (t70) cc_final: 0.9005 (t0) REVERT: D 437 MET cc_start: 0.8466 (tpt) cc_final: 0.8128 (tpt) outliers start: 39 outliers final: 31 residues processed: 172 average time/residue: 0.1163 time to fit residues: 34.7828 Evaluate side-chains 175 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 116 optimal weight: 10.0000 chunk 276 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 187 optimal weight: 0.0970 chunk 124 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 199 optimal weight: 0.0670 chunk 132 optimal weight: 0.9980 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.100709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.075395 restraints weight = 46952.511| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.90 r_work: 0.2965 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21512 Z= 0.097 Angle : 0.446 9.598 29308 Z= 0.226 Chirality : 0.037 0.131 3476 Planarity : 0.003 0.035 3616 Dihedral : 12.197 154.062 3272 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.47 % Favored : 96.38 % Rotamer: Outliers : 2.00 % Allowed : 13.47 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.17), residues: 2792 helix: 2.75 (0.12), residues: 2020 sheet: None (None), residues: 0 loop : -1.70 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 330 TYR 0.009 0.001 TYR D 639 PHE 0.010 0.001 PHE B 350 TRP 0.043 0.001 TRP D 356 HIS 0.006 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00211 (21504) covalent geometry : angle 0.44190 (29288) SS BOND : bond 0.00830 ( 4) SS BOND : angle 3.68408 ( 8) hydrogen bonds : bond 0.03694 ( 1284) hydrogen bonds : angle 2.81036 ( 3816) link_NAG-ASN : bond 0.00139 ( 4) link_NAG-ASN : angle 0.86600 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.831 Fit side-chains REVERT: A 194 ASP cc_start: 0.8103 (t0) cc_final: 0.7660 (t70) REVERT: A 437 MET cc_start: 0.8484 (tpt) cc_final: 0.8157 (tpt) REVERT: B 194 ASP cc_start: 0.8168 (t0) cc_final: 0.7701 (t70) REVERT: B 437 MET cc_start: 0.8486 (tpt) cc_final: 0.8171 (tpt) REVERT: C 194 ASP cc_start: 0.8142 (t0) cc_final: 0.7666 (t70) REVERT: C 437 MET cc_start: 0.8486 (tpt) cc_final: 0.8174 (tpt) REVERT: D 194 ASP cc_start: 0.8232 (t0) cc_final: 0.7786 (t70) REVERT: D 263 ASP cc_start: 0.9223 (t70) cc_final: 0.9012 (t0) REVERT: D 437 MET cc_start: 0.8453 (tpt) cc_final: 0.8135 (tpt) outliers start: 38 outliers final: 33 residues processed: 169 average time/residue: 0.1169 time to fit residues: 34.1883 Evaluate side-chains 175 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 239 optimal weight: 0.0050 chunk 145 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.072735 restraints weight = 47196.908| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.90 r_work: 0.2911 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21512 Z= 0.140 Angle : 0.496 10.182 29308 Z= 0.252 Chirality : 0.038 0.136 3476 Planarity : 0.003 0.033 3616 Dihedral : 12.288 155.750 3272 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.76 % Favored : 96.10 % Rotamer: Outliers : 2.05 % Allowed : 13.42 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.17), residues: 2792 helix: 2.71 (0.12), residues: 1996 sheet: None (None), residues: 0 loop : -1.61 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 266 TYR 0.010 0.001 TYR D 639 PHE 0.011 0.001 PHE C 181 TRP 0.045 0.002 TRP B 356 HIS 0.006 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00331 (21504) covalent geometry : angle 0.49237 (29288) SS BOND : bond 0.00891 ( 4) SS BOND : angle 3.74970 ( 8) hydrogen bonds : bond 0.04763 ( 1284) hydrogen bonds : angle 3.02772 ( 3816) link_NAG-ASN : bond 0.00136 ( 4) link_NAG-ASN : angle 0.91609 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4027.35 seconds wall clock time: 69 minutes 51.20 seconds (4191.20 seconds total)