Starting phenix.real_space_refine on Fri Sep 11 19:40:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uo8_20822/09_2026/6uo8_20822.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uo8_20822/09_2026/6uo8_20822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uo8_20822/09_2026/6uo8_20822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uo8_20822/09_2026/6uo8_20822.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uo8_20822/09_2026/6uo8_20822.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uo8_20822/09_2026/6uo8_20822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uo8_20822/09_2026/6uo8_20822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uo8_20822/09_2026/6uo8_20822.map" } resolution = 3.63 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= -0.004 sd= 0.066 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 1 5.49 5 S 58 5.16 5 C 7057 2.51 5 N 1817 2.21 5 O 2025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10958 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5378 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 5370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5370 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 28, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {'NAG': 2, 'QD7': 1, 'QDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.69, per 1000 atoms: 0.25 Number of scatterers: 10958 At special positions: 0 Unit cell: (82.6537, 109.921, 172.976, 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 58 16.00 P 1 15.00 O 2025 8.00 N 1817 7.00 C 7057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.04 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1002 " - " ASN A 514 " " NAG A1005 " - " ASN A 502 " " NAG B 903 " - " ASN B 298 " " NAG B 904 " - " ASN B 453 " " NAG B 905 " - " ASN B 389 " " NAG B 906 " - " ASN B 90 " " NAG C 1 " - " ASN A 482 " " NAG D 1 " - " ASN A 440 " " NAG E 1 " - " ASN B 404 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 587.0 milliseconds 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 50.8% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 184 through 200 Proline residue: A 190 - end of helix removed outlier: 4.365A pdb=" N GLU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP A 198 " --> pdb=" O MET A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.594A pdb=" N TYR A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 removed outlier: 4.040A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.606A pdb=" N SER A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A 276 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 removed outlier: 3.952A pdb=" N LEU A 292 " --> pdb=" O SER A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.904A pdb=" N LYS A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 330 removed outlier: 3.875A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 removed outlier: 3.763A pdb=" N GLY A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 368 through 379 removed outlier: 4.002A pdb=" N ARG A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.915A pdb=" N GLU A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 466 through 485 removed outlier: 3.829A pdb=" N ALA A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TRP A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 515 removed outlier: 3.653A pdb=" N SER A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.063A pdb=" N GLY A 571 " --> pdb=" O TRP A 568 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 572' Processing helix chain 'A' and resid 589 through 616 removed outlier: 3.900A pdb=" N SER A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.829A pdb=" N LEU A 649 " --> pdb=" O PHE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 691 removed outlier: 3.812A pdb=" N PHE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER A 675 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 731 removed outlier: 3.560A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 790 removed outlier: 3.684A pdb=" N LEU A 780 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 824 removed outlier: 3.717A pdb=" N ALA A 804 " --> pdb=" O ASN A 800 " (cutoff:3.500A) Proline residue: A 821 - end of helix removed outlier: 4.041A pdb=" N MET A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 854 removed outlier: 3.701A pdb=" N ALA A 837 " --> pdb=" O ALA A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 862 Processing helix chain 'B' and resid 71 through 90 Proline residue: B 79 - end of helix removed outlier: 4.284A pdb=" N GLU B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.696A pdb=" N LEU B 163 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 165' Processing helix chain 'B' and resid 182 through 191 removed outlier: 3.698A pdb=" N LEU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 219 removed outlier: 4.075A pdb=" N VAL B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 238 removed outlier: 3.946A pdb=" N THR B 238 " --> pdb=" O ASP B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 238' Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 256 through 270 removed outlier: 3.612A pdb=" N ALA B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU B 269 " --> pdb=" O CYS B 265 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.858A pdb=" N ALA B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.616A pdb=" N ARG B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 removed outlier: 3.915A pdb=" N ILE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 384 Processing helix chain 'B' and resid 392 through 405 removed outlier: 3.824A pdb=" N ALA B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 506 removed outlier: 3.579A pdb=" N ASN B 506 " --> pdb=" O PHE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 538 removed outlier: 3.784A pdb=" N ALA B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 582 removed outlier: 3.710A pdb=" N CYS B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 557 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRP B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 582 " --> pdb=" O VAL B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 614 removed outlier: 3.669A pdb=" N LEU B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 680 removed outlier: 3.944A pdb=" N ASN B 680 " --> pdb=" O TRP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 711 removed outlier: 3.819A pdb=" N ILE B 701 " --> pdb=" O TYR B 697 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 708 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 750 removed outlier: 3.590A pdb=" N LEU B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 731 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 741 " --> pdb=" O CYS B 737 " (cutoff:3.500A) Proline residue: B 742 - end of helix removed outlier: 3.521A pdb=" N THR B 746 " --> pdb=" O PRO B 742 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 217 removed outlier: 8.930A pdb=" N LYS A 239 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR A 171 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE A 241 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE A 240 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU A 265 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.475A pdb=" N ILE A 309 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE A 339 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N PHE A 343 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN A 313 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.475A pdb=" N ILE A 309 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE A 339 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A 361 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A 393 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR A 425 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N HIS A 422 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 542 " --> pdb=" O HIS A 422 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 537 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYR A 552 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 583 Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 104 removed outlier: 6.212A pdb=" N LEU B 56 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ARG B 102 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 58 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N TYR B 104 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLY B 60 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N MET B 129 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER B 57 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N PHE B 131 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N MET B 59 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 231 removed outlier: 7.657A pdb=" N VAL B 198 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 229 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR B 200 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER B 231 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B 202 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP B 279 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL B 317 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE B 281 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N PHE B 319 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE B 426 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 441 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE B 428 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 416 through 418 removed outlier: 4.827A pdb=" N VAL B 416 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 474 removed outlier: 6.461A pdb=" N LEU B 471 " --> pdb=" O ARG B 642 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 644 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN B 473 " --> pdb=" O LEU B 644 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1455 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: 1.90 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3418 1.34 - 1.46: 2515 1.46 - 1.58: 5184 1.58 - 1.70: 1 1.70 - 1.82: 94 Bond restraints: 11212 Sorted by residual: bond pdb=" C21 QDA A1009 " pdb=" C22 QDA A1009 " ideal model delta sigma weight residual 1.546 1.452 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C09 QDA A1009 " pdb=" C10 QDA A1009 " ideal model delta sigma weight residual 1.546 1.459 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CAG QD7 A1001 " pdb=" PAE QD7 A1001 " ideal model delta sigma weight residual 1.830 1.776 0.054 2.00e-02 2.50e+03 7.30e+00 bond pdb=" C1 NAG B 903 " pdb=" O5 NAG B 903 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" C04 QDA A1009 " pdb=" N02 QDA A1009 " ideal model delta sigma weight residual 1.396 1.444 -0.048 2.00e-02 2.50e+03 5.86e+00 ... (remaining 11207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 15002 2.57 - 5.13: 192 5.13 - 7.70: 33 7.70 - 10.27: 6 10.27 - 12.83: 1 Bond angle restraints: 15234 Sorted by residual: angle pdb=" CA CYS A 220 " pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " ideal model delta sigma weight residual 114.40 127.23 -12.83 2.30e+00 1.89e-01 3.11e+01 angle pdb=" C LYS A 219 " pdb=" N CYS A 220 " pdb=" CA CYS A 220 " ideal model delta sigma weight residual 122.82 129.51 -6.69 1.42e+00 4.96e-01 2.22e+01 angle pdb=" N VAL B 544 " pdb=" CA VAL B 544 " pdb=" C VAL B 544 " ideal model delta sigma weight residual 113.53 108.97 4.56 9.80e-01 1.04e+00 2.16e+01 angle pdb=" C SER B 300 " pdb=" N ARG B 301 " pdb=" CA ARG B 301 " ideal model delta sigma weight residual 125.02 131.39 -6.37 1.76e+00 3.23e-01 1.31e+01 angle pdb=" C ILE B 512 " pdb=" N LYS B 513 " pdb=" CA LYS B 513 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 ... (remaining 15229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5925 17.20 - 34.40: 494 34.40 - 51.60: 101 51.60 - 68.79: 17 68.79 - 85.99: 9 Dihedral angle restraints: 6546 sinusoidal: 2514 harmonic: 4032 Sorted by residual: dihedral pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " pdb=" SG CYS B 266 " pdb=" CB CYS B 266 " ideal model delta sinusoidal sigma weight residual -86.00 -20.11 -65.89 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CA VAL A 691 " pdb=" C VAL A 691 " pdb=" N PHE A 692 " pdb=" CA PHE A 692 " ideal model delta harmonic sigma weight residual 180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CB CYS A 663 " pdb=" SG CYS A 663 " pdb=" SG CYS A 761 " pdb=" CB CYS A 761 " ideal model delta sinusoidal sigma weight residual 93.00 131.89 -38.89 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 6543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1637 0.097 - 0.194: 117 0.194 - 0.290: 6 0.290 - 0.387: 1 0.387 - 0.484: 1 Chirality restraints: 1762 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 440 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C1 NAG B 903 " pdb=" ND2 ASN B 298 " pdb=" C2 NAG B 903 " pdb=" O5 NAG B 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C1 NAG B 905 " pdb=" ND2 ASN B 389 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1759 not shown) Planarity restraints: 1913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 QDA A1009 " -0.001 2.00e-02 2.50e+03 3.32e-02 2.76e+01 pdb=" C05 QDA A1009 " -0.000 2.00e-02 2.50e+03 pdb=" C13 QDA A1009 " -0.005 2.00e-02 2.50e+03 pdb=" C17 QDA A1009 " 0.014 2.00e-02 2.50e+03 pdb=" N02 QDA A1009 " -0.075 2.00e-02 2.50e+03 pdb=" N06 QDA A1009 " 0.054 2.00e-02 2.50e+03 pdb=" N12 QDA A1009 " -0.009 2.00e-02 2.50e+03 pdb=" N16 QDA A1009 " 0.010 2.00e-02 2.50e+03 pdb=" N18 QDA A1009 " 0.038 2.00e-02 2.50e+03 pdb=" S14 QDA A1009 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 294 " 0.036 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO A 295 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 755 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO A 756 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 756 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 756 " -0.029 5.00e-02 4.00e+02 ... (remaining 1910 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3204 2.81 - 3.33: 9611 3.33 - 3.86: 16653 3.86 - 4.38: 17692 4.38 - 4.90: 31645 Nonbonded interactions: 78805 Sorted by model distance: nonbonded pdb=" OG1 THR B 329 " pdb=" O PHE B 409 " model vdw 2.290 3.040 nonbonded pdb=" NH1 ARG B 422 " pdb=" O MET B 423 " model vdw 2.320 3.120 nonbonded pdb=" OG SER A 247 " pdb=" OG SER A 271 " model vdw 2.321 3.040 nonbonded pdb=" O SER B 288 " pdb=" OG SER B 288 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR B 268 " pdb=" ND2 ASN B 306 " model vdw 2.345 3.120 ... (remaining 78800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 : 0.004 0.094 11232 Z= 0.209 Angle : 0.811 17.172 15287 Z= 0.417 Chirality : 0.052 0.484 1762 Planarity : 0.006 0.053 1904 Dihedral : 13.488 85.993 3927 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % 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: -3.75 (0.19), residues: 1377 helix: -1.69 (0.17), residues: 658 sheet: -1.78 (0.35), residues: 219 loop : -3.83 (0.21), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.015 0.001 TYR A 615 PHE 0.018 0.002 PHE A 584 TRP 0.019 0.001 TRP A 728 HIS 0.009 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (11212) covalent geometry : angle 0.76092 / 0.41 (15234) SS BOND : bond 0.00450 / 0.24 ( 7) SS BOND : angle 1.53637 / 0.84 ( 14) hydrogen bonds : bond 0.10708 / 7.10 ( 489) hydrogen bonds : angle 5.57784 / 3.92 ( 1455) link_BETA1-4 : bond 0.01657 / 0.82 ( 4) link_BETA1-4 : angle 7.25389 / 3.50 ( 12) link_NAG-ASN : bond 0.00777 / 0.29 ( 9) link_NAG-ASN : angle 4.55877 / 2.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7439 (mtp-110) REVERT: A 639 LEU cc_start: 0.8560 (tt) cc_final: 0.8235 (tt) REVERT: A 672 LEU cc_start: 0.8783 (tt) cc_final: 0.8581 (tt) REVERT: A 687 TRP cc_start: 0.6841 (m100) cc_final: 0.6541 (m100) REVERT: A 807 MET cc_start: 0.7761 (mtm) cc_final: 0.7416 (mtp) REVERT: B 147 GLN cc_start: 0.8994 (pt0) cc_final: 0.8676 (tm-30) REVERT: B 519 MET cc_start: 0.6703 (mtt) cc_final: 0.6488 (mtp) REVERT: B 531 TYR cc_start: 0.7989 (m-10) cc_final: 0.7747 (m-10) REVERT: B 702 MET cc_start: 0.8121 (tpp) cc_final: 0.7616 (tpp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0843 time to fit residues: 19.9237 Evaluate side-chains 125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.0370 chunk 55 optimal weight: 4.9990 overall best weight: 0.9418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 189 GLN A 422 HIS A 630 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 257 GLN B 343 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.092296 restraints weight = 25566.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094692 restraints weight = 12754.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096287 restraints weight = 8283.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097293 restraints weight = 6281.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097862 restraints weight = 5279.592| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11232 Z= 0.118 Angle : 0.610 12.246 15287 Z= 0.302 Chirality : 0.044 0.333 1762 Planarity : 0.004 0.042 1904 Dihedral : 5.087 66.090 1505 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.42 % Allowed : 12.91 % Favored : 85.66 % 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: -2.39 (0.22), residues: 1377 helix: -0.25 (0.20), residues: 663 sheet: -1.39 (0.35), residues: 229 loop : -3.58 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 714 TYR 0.013 0.001 TYR A 615 PHE 0.013 0.001 PHE A 786 TRP 0.014 0.001 TRP A 686 HIS 0.005 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (11212) covalent geometry : angle 0.57249 / 0.29 (15234) SS BOND : bond 0.00332 / 0.17 ( 7) SS BOND : angle 1.10455 / 0.60 ( 14) hydrogen bonds : bond 0.04250 / 2.94 ( 489) hydrogen bonds : angle 4.36243 / 3.05 ( 1455) link_BETA1-4 : bond 0.01486 / 0.73 ( 4) link_BETA1-4 : angle 5.18456 / 2.54 ( 12) link_NAG-ASN : bond 0.00730 / 0.33 ( 9) link_NAG-ASN : angle 3.60859 / 2.35 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 CYS cc_start: 0.4457 (OUTLIER) cc_final: 0.3922 (p) REVERT: A 329 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7352 (mtp-110) REVERT: A 639 LEU cc_start: 0.8597 (tt) cc_final: 0.8292 (tt) REVERT: A 672 LEU cc_start: 0.8808 (tt) cc_final: 0.8542 (tt) REVERT: A 687 TRP cc_start: 0.6780 (m100) cc_final: 0.6496 (m100) REVERT: A 807 MET cc_start: 0.7748 (mtm) cc_final: 0.7414 (mtp) REVERT: B 62 MET cc_start: 0.8266 (ptm) cc_final: 0.8043 (ptp) REVERT: B 147 GLN cc_start: 0.8974 (pt0) cc_final: 0.8729 (tm-30) REVERT: B 702 MET cc_start: 0.8131 (tpp) cc_final: 0.7860 (tpp) outliers start: 16 outliers final: 7 residues processed: 143 average time/residue: 0.0849 time to fit residues: 18.9597 Evaluate side-chains 126 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 70 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.117576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092498 restraints weight = 26398.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094998 restraints weight = 12976.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096609 restraints weight = 8307.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097540 restraints weight = 6289.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098228 restraints weight = 5340.686| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11232 Z= 0.118 Angle : 0.600 11.033 15287 Z= 0.296 Chirality : 0.044 0.324 1762 Planarity : 0.004 0.043 1904 Dihedral : 4.905 66.097 1505 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.60 % Allowed : 14.16 % Favored : 84.24 % 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: -1.76 (0.23), residues: 1377 helix: 0.36 (0.21), residues: 662 sheet: -1.09 (0.36), residues: 225 loop : -3.41 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 714 TYR 0.011 0.001 TYR A 615 PHE 0.018 0.001 PHE A 682 TRP 0.020 0.001 TRP B 615 HIS 0.009 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (11212) covalent geometry : angle 0.56538 / 0.29 (15234) SS BOND : bond 0.00262 / 0.13 ( 7) SS BOND : angle 1.50774 / 0.82 ( 14) hydrogen bonds : bond 0.04105 / 2.85 ( 489) hydrogen bonds : angle 4.13543 / 2.89 ( 1455) link_BETA1-4 : bond 0.01347 / 0.66 ( 4) link_BETA1-4 : angle 4.73733 / 2.31 ( 12) link_NAG-ASN : bond 0.00663 / 0.29 ( 9) link_NAG-ASN : angle 3.50850 / 2.27 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 CYS cc_start: 0.4262 (OUTLIER) cc_final: 0.3905 (p) REVERT: A 328 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 329 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7505 (mtp-110) REVERT: A 672 LEU cc_start: 0.8830 (tt) cc_final: 0.8600 (tp) REVERT: A 687 TRP cc_start: 0.6811 (m100) cc_final: 0.6540 (m100) REVERT: A 807 MET cc_start: 0.7775 (mtm) cc_final: 0.7092 (mtm) REVERT: B 702 MET cc_start: 0.8173 (tpp) cc_final: 0.7699 (tpp) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 0.0845 time to fit residues: 18.1189 Evaluate side-chains 128 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 GLN A 577 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.113544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.088646 restraints weight = 26636.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.091036 restraints weight = 13185.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.092547 restraints weight = 8507.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093528 restraints weight = 6492.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094062 restraints weight = 5494.052| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11232 Z= 0.220 Angle : 0.686 10.998 15287 Z= 0.342 Chirality : 0.046 0.314 1762 Planarity : 0.004 0.050 1904 Dihedral : 5.195 68.298 1505 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.49 % Allowed : 15.76 % Favored : 81.75 % 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: -1.62 (0.23), residues: 1377 helix: 0.56 (0.21), residues: 659 sheet: -1.17 (0.36), residues: 230 loop : -3.39 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.013 0.002 TYR B 564 PHE 0.016 0.002 PHE A 586 TRP 0.038 0.002 TRP B 615 HIS 0.009 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (11212) covalent geometry : angle 0.65573 / 0.33 (15234) SS BOND : bond 0.00583 / 0.29 ( 7) SS BOND : angle 1.97566 / 1.07 ( 14) hydrogen bonds : bond 0.05139 / 3.58 ( 489) hydrogen bonds : angle 4.51004 / 3.17 ( 1455) link_BETA1-4 : bond 0.01275 / 0.62 ( 4) link_BETA1-4 : angle 4.56332 / 2.26 ( 12) link_NAG-ASN : bond 0.00549 / 0.22 ( 9) link_NAG-ASN : angle 3.56951 / 2.21 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7808 (mtp180) cc_final: 0.7476 (mtp-110) REVERT: A 687 TRP cc_start: 0.6818 (m100) cc_final: 0.6568 (m100) REVERT: A 807 MET cc_start: 0.7875 (mtm) cc_final: 0.7132 (mtm) REVERT: B 493 MET cc_start: 0.8160 (mmm) cc_final: 0.7820 (mmm) REVERT: B 519 MET cc_start: 0.6784 (mtt) cc_final: 0.6448 (mtp) REVERT: B 531 TYR cc_start: 0.7972 (m-10) cc_final: 0.7734 (m-10) REVERT: B 702 MET cc_start: 0.8222 (tpp) cc_final: 0.8006 (tpp) outliers start: 28 outliers final: 18 residues processed: 135 average time/residue: 0.0788 time to fit residues: 17.0254 Evaluate side-chains 124 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 66 optimal weight: 0.0770 chunk 95 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.091886 restraints weight = 25824.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.094297 restraints weight = 12849.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095890 restraints weight = 8328.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096798 restraints weight = 6318.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097483 restraints weight = 5373.226| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11232 Z= 0.106 Angle : 0.606 9.763 15287 Z= 0.294 Chirality : 0.044 0.314 1762 Planarity : 0.004 0.037 1904 Dihedral : 4.822 64.751 1505 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.51 % Allowed : 17.81 % Favored : 80.68 % 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: -1.21 (0.23), residues: 1377 helix: 0.85 (0.21), residues: 664 sheet: -0.92 (0.37), residues: 221 loop : -3.16 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 622 TYR 0.009 0.001 TYR A 379 PHE 0.019 0.001 PHE A 682 TRP 0.039 0.001 TRP B 615 HIS 0.008 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (11212) covalent geometry : angle 0.57380 / 0.29 (15234) SS BOND : bond 0.00125 / 0.06 ( 7) SS BOND : angle 1.92902 / 1.05 ( 14) hydrogen bonds : bond 0.03900 / 2.73 ( 489) hydrogen bonds : angle 4.01947 / 2.81 ( 1455) link_BETA1-4 : bond 0.01296 / 0.64 ( 4) link_BETA1-4 : angle 4.22382 / 2.06 ( 12) link_NAG-ASN : bond 0.00702 / 0.31 ( 9) link_NAG-ASN : angle 3.46065 / 2.18 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 329 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7419 (mtp-110) REVERT: A 687 TRP cc_start: 0.6781 (m100) cc_final: 0.6546 (m100) REVERT: A 807 MET cc_start: 0.7746 (mtm) cc_final: 0.7034 (mtm) REVERT: B 519 MET cc_start: 0.6681 (mtt) cc_final: 0.6337 (mtp) REVERT: B 702 MET cc_start: 0.8059 (tpp) cc_final: 0.7615 (tpp) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.0798 time to fit residues: 18.3402 Evaluate side-chains 129 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 110 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.091970 restraints weight = 26315.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.094416 restraints weight = 12915.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095992 restraints weight = 8272.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096996 restraints weight = 6279.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097530 restraints weight = 5294.475| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11232 Z= 0.115 Angle : 0.603 9.104 15287 Z= 0.293 Chirality : 0.044 0.311 1762 Planarity : 0.004 0.035 1904 Dihedral : 4.689 64.347 1505 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.96 % Allowed : 18.52 % Favored : 79.52 % 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: -1.02 (0.23), residues: 1377 helix: 0.96 (0.21), residues: 668 sheet: -0.69 (0.37), residues: 224 loop : -3.11 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 622 TYR 0.008 0.001 TYR A 228 PHE 0.019 0.001 PHE B 117 TRP 0.019 0.001 TRP B 615 HIS 0.008 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (11212) covalent geometry : angle 0.57330 / 0.29 (15234) SS BOND : bond 0.00243 / 0.12 ( 7) SS BOND : angle 2.00772 / 1.09 ( 14) hydrogen bonds : bond 0.03929 / 2.74 ( 489) hydrogen bonds : angle 3.99587 / 2.80 ( 1455) link_BETA1-4 : bond 0.01184 / 0.58 ( 4) link_BETA1-4 : angle 3.94116 / 1.92 ( 12) link_NAG-ASN : bond 0.00614 / 0.26 ( 9) link_NAG-ASN : angle 3.36226 / 2.13 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8316 (tm-30) REVERT: A 329 ARG cc_start: 0.7764 (mtp180) cc_final: 0.7434 (mtp-110) REVERT: A 687 TRP cc_start: 0.6779 (m100) cc_final: 0.6528 (m100) REVERT: A 807 MET cc_start: 0.7817 (mtm) cc_final: 0.7122 (mtm) REVERT: B 702 MET cc_start: 0.8125 (tpp) cc_final: 0.7671 (tpp) outliers start: 22 outliers final: 18 residues processed: 137 average time/residue: 0.0816 time to fit residues: 17.8465 Evaluate side-chains 134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 53 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 631 ASN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.117616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092557 restraints weight = 26032.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095031 restraints weight = 12792.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096619 restraints weight = 8204.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097635 restraints weight = 6231.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098267 restraints weight = 5240.453| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 11232 Z= 0.106 Angle : 0.599 8.863 15287 Z= 0.291 Chirality : 0.044 0.313 1762 Planarity : 0.004 0.032 1904 Dihedral : 4.553 62.556 1505 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.05 % Allowed : 18.43 % Favored : 79.52 % 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: -0.92 (0.23), residues: 1377 helix: 1.05 (0.21), residues: 668 sheet: -0.58 (0.38), residues: 210 loop : -3.04 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 637 TYR 0.008 0.001 TYR B 564 PHE 0.024 0.001 PHE A 682 TRP 0.017 0.001 TRP B 615 HIS 0.007 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (11212) covalent geometry : angle 0.57117 / 0.28 (15234) SS BOND : bond 0.00151 / 0.07 ( 7) SS BOND : angle 1.83091 / 1.00 ( 14) hydrogen bonds : bond 0.03745 / 2.62 ( 489) hydrogen bonds : angle 3.91977 / 2.75 ( 1455) link_BETA1-4 : bond 0.01223 / 0.60 ( 4) link_BETA1-4 : angle 3.83216 / 1.86 ( 12) link_NAG-ASN : bond 0.00638 / 0.27 ( 9) link_NAG-ASN : angle 3.33376 / 2.11 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8310 (tm-30) REVERT: A 687 TRP cc_start: 0.6731 (m100) cc_final: 0.6494 (m100) REVERT: A 807 MET cc_start: 0.7799 (mtm) cc_final: 0.7120 (mtm) REVERT: B 637 ARG cc_start: 0.7470 (mmm160) cc_final: 0.6645 (mmm160) REVERT: B 702 MET cc_start: 0.8120 (tpp) cc_final: 0.7666 (tpp) outliers start: 23 outliers final: 15 residues processed: 140 average time/residue: 0.0782 time to fit residues: 17.4957 Evaluate side-chains 133 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 chunk 118 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 120 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.090888 restraints weight = 26230.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093277 restraints weight = 12854.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094818 restraints weight = 8267.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095806 restraints weight = 6288.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096456 restraints weight = 5301.414| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11232 Z= 0.148 Angle : 0.631 8.625 15287 Z= 0.309 Chirality : 0.045 0.310 1762 Planarity : 0.004 0.031 1904 Dihedral : 4.590 63.257 1505 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.87 % Allowed : 18.61 % Favored : 79.52 % 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: -0.88 (0.23), residues: 1377 helix: 1.10 (0.21), residues: 669 sheet: -0.62 (0.37), residues: 212 loop : -3.02 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 637 TYR 0.011 0.001 TYR B 564 PHE 0.021 0.001 PHE A 682 TRP 0.017 0.001 TRP B 615 HIS 0.007 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11212) covalent geometry : angle 0.60343 / 0.30 (15234) SS BOND : bond 0.00282 / 0.14 ( 7) SS BOND : angle 2.17256 / 1.27 ( 14) hydrogen bonds : bond 0.04227 / 2.97 ( 489) hydrogen bonds : angle 4.07331 / 2.86 ( 1455) link_BETA1-4 : bond 0.01189 / 0.58 ( 4) link_BETA1-4 : angle 3.80439 / 1.86 ( 12) link_NAG-ASN : bond 0.00566 / 0.23 ( 9) link_NAG-ASN : angle 3.33605 / 2.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.411 Fit side-chains REVERT: A 328 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 687 TRP cc_start: 0.6735 (m100) cc_final: 0.6486 (m100) REVERT: A 807 MET cc_start: 0.7851 (mtm) cc_final: 0.7164 (mtm) REVERT: B 103 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 702 MET cc_start: 0.8201 (tpp) cc_final: 0.7729 (tpp) outliers start: 21 outliers final: 18 residues processed: 131 average time/residue: 0.0740 time to fit residues: 16.1299 Evaluate side-chains 134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 56 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 125 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.116082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.091253 restraints weight = 26159.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.093661 restraints weight = 12896.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.095222 restraints weight = 8308.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096143 restraints weight = 6310.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096798 restraints weight = 5367.979| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11232 Z= 0.132 Angle : 0.628 9.206 15287 Z= 0.306 Chirality : 0.044 0.310 1762 Planarity : 0.004 0.032 1904 Dihedral : 4.567 62.617 1505 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.69 % Allowed : 19.15 % Favored : 79.16 % 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: -0.81 (0.23), residues: 1377 helix: 1.15 (0.21), residues: 669 sheet: -0.59 (0.37), residues: 212 loop : -3.00 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 637 TYR 0.010 0.001 TYR B 564 PHE 0.020 0.001 PHE A 682 TRP 0.019 0.001 TRP B 615 HIS 0.007 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11212) covalent geometry : angle 0.60006 / 0.30 (15234) SS BOND : bond 0.00305 / 0.16 ( 7) SS BOND : angle 2.20822 / 1.28 ( 14) hydrogen bonds : bond 0.04117 / 2.88 ( 489) hydrogen bonds : angle 4.02986 / 2.82 ( 1455) link_BETA1-4 : bond 0.01193 / 0.59 ( 4) link_BETA1-4 : angle 3.74423 / 1.83 ( 12) link_NAG-ASN : bond 0.00595 / 0.24 ( 9) link_NAG-ASN : angle 3.36526 / 2.09 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 687 TRP cc_start: 0.6707 (m100) cc_final: 0.6448 (m100) REVERT: A 807 MET cc_start: 0.7848 (mtm) cc_final: 0.7151 (mtm) REVERT: B 637 ARG cc_start: 0.7598 (mmm160) cc_final: 0.6976 (mmm160) REVERT: B 702 MET cc_start: 0.8154 (tpp) cc_final: 0.7730 (tpp) REVERT: B 730 PHE cc_start: 0.7778 (t80) cc_final: 0.7532 (t80) outliers start: 19 outliers final: 18 residues processed: 135 average time/residue: 0.0806 time to fit residues: 17.2932 Evaluate side-chains 136 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.113849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089183 restraints weight = 26469.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.091559 restraints weight = 13106.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.093093 restraints weight = 8428.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093963 restraints weight = 6407.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094636 restraints weight = 5462.932| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11232 Z= 0.190 Angle : 0.683 10.869 15287 Z= 0.337 Chirality : 0.046 0.307 1762 Planarity : 0.004 0.035 1904 Dihedral : 4.788 65.596 1505 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.60 % Allowed : 19.41 % Favored : 78.98 % 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: -0.83 (0.23), residues: 1377 helix: 1.14 (0.21), residues: 661 sheet: -0.38 (0.38), residues: 207 loop : -3.03 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 637 TYR 0.015 0.001 TYR B 564 PHE 0.019 0.002 PHE A 682 TRP 0.021 0.002 TRP B 615 HIS 0.007 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (11212) covalent geometry : angle 0.65524 / 0.33 (15234) SS BOND : bond 0.00459 / 0.23 ( 7) SS BOND : angle 2.77566 / 1.57 ( 14) hydrogen bonds : bond 0.04771 / 3.34 ( 489) hydrogen bonds : angle 4.27617 / 3.01 ( 1455) link_BETA1-4 : bond 0.01117 / 0.55 ( 4) link_BETA1-4 : angle 3.78573 / 1.88 ( 12) link_NAG-ASN : bond 0.00549 / 0.22 ( 9) link_NAG-ASN : angle 3.44111 / 2.10 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.426 Fit side-chains REVERT: A 328 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8511 (tm-30) REVERT: A 687 TRP cc_start: 0.6737 (m100) cc_final: 0.6492 (m100) REVERT: A 807 MET cc_start: 0.7868 (mtm) cc_final: 0.7133 (mtm) REVERT: B 519 MET cc_start: 0.6728 (mtt) cc_final: 0.6218 (mtp) REVERT: B 637 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7301 (mmm160) REVERT: B 702 MET cc_start: 0.8201 (tpp) cc_final: 0.7776 (tpp) REVERT: B 730 PHE cc_start: 0.7761 (t80) cc_final: 0.7549 (t80) outliers start: 18 outliers final: 16 residues processed: 130 average time/residue: 0.0761 time to fit residues: 16.2287 Evaluate side-chains 130 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 811 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.115989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.091549 restraints weight = 25922.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093977 restraints weight = 12590.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095568 restraints weight = 8022.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096464 restraints weight = 6041.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097139 restraints weight = 5113.955| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11232 Z= 0.121 Angle : 0.650 10.858 15287 Z= 0.314 Chirality : 0.044 0.308 1762 Planarity : 0.004 0.034 1904 Dihedral : 4.639 64.003 1505 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.78 % Allowed : 19.95 % Favored : 78.27 % 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: -0.72 (0.23), residues: 1377 helix: 1.21 (0.21), residues: 667 sheet: -0.48 (0.37), residues: 218 loop : -2.97 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 637 TYR 0.009 0.001 TYR B 564 PHE 0.018 0.001 PHE A 682 TRP 0.020 0.001 TRP B 615 HIS 0.008 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (11212) covalent geometry : angle 0.62071 / 0.31 (15234) SS BOND : bond 0.00170 / 0.09 ( 7) SS BOND : angle 2.84633 / 1.60 ( 14) hydrogen bonds : bond 0.04152 / 2.91 ( 489) hydrogen bonds : angle 4.04967 / 2.84 ( 1455) link_BETA1-4 : bond 0.01201 / 0.59 ( 4) link_BETA1-4 : angle 3.58316 / 1.75 ( 12) link_NAG-ASN : bond 0.00623 / 0.26 ( 9) link_NAG-ASN : angle 3.41250 / 2.10 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.65 seconds wall clock time: 33 minutes 59.62 seconds (2039.62 seconds total)