Starting phenix.real_space_refine on Tue Jul 29 10:36:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uo8_20822/07_2025/6uo8_20822.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uo8_20822/07_2025/6uo8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6uo8_20822/07_2025/6uo8_20822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uo8_20822/07_2025/6uo8_20822.map" model { file = "/net/cci-nas-00/data/ceres_data/6uo8_20822/07_2025/6uo8_20822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uo8_20822/07_2025/6uo8_20822.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 2, 'GLU:plan': 2, '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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.14, per 1000 atoms: 0.65 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: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.47 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: 3.65 Time building geometry restraints manager: 3.31 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 - 20.75: 6319 20.75 - 41.50: 434 41.50 - 62.25: 51 62.25 - 83.00: 19 83.00 - 103.76: 6 Dihedral angle restraints: 6829 sinusoidal: 2797 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 6826 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.770 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 14.261 103.756 4210 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.001 TRP A 728 HIS 0.009 0.001 HIS A 689 PHE 0.018 0.002 PHE A 584 TYR 0.015 0.001 TYR A 615 ARG 0.002 0.000 ARG A 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 9) link_NAG-ASN : angle 4.55877 ( 27) link_BETA1-4 : bond 0.01657 ( 4) link_BETA1-4 : angle 7.25389 ( 12) hydrogen bonds : bond 0.10708 ( 489) hydrogen bonds : angle 5.57784 ( 1455) SS BOND : bond 0.00450 ( 7) SS BOND : angle 1.53637 ( 14) covalent geometry : bond 0.00428 (11212) covalent geometry : angle 0.76092 (15234) *********************** 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 : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7440 (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: 0.1838 time to fit residues: 42.5301 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 : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.0060 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 189 GLN A 422 HIS A 630 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 257 GLN B 343 ASN B 383 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090711 restraints weight = 25887.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.093137 restraints weight = 12848.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094688 restraints weight = 8285.386| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11232 Z= 0.171 Angle : 0.647 12.474 15287 Z= 0.323 Chirality : 0.046 0.325 1762 Planarity : 0.004 0.044 1904 Dihedral : 7.997 67.439 1788 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.05 % Allowed : 14.07 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.22), residues: 1377 helix: -0.19 (0.20), residues: 663 sheet: -1.43 (0.35), residues: 231 loop : -3.57 (0.23), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 686 HIS 0.006 0.001 HIS A 802 PHE 0.013 0.001 PHE A 786 TYR 0.010 0.001 TYR A 615 ARG 0.002 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 9) link_NAG-ASN : angle 3.82198 ( 27) link_BETA1-4 : bond 0.01460 ( 4) link_BETA1-4 : angle 5.25902 ( 12) hydrogen bonds : bond 0.04749 ( 489) hydrogen bonds : angle 4.48162 ( 1455) SS BOND : bond 0.00459 ( 7) SS BOND : angle 1.26616 ( 14) covalent geometry : bond 0.00388 (11212) covalent geometry : angle 0.60861 (15234) *********************** 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 150 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 CYS cc_start: 0.4781 (OUTLIER) cc_final: 0.4380 (p) REVERT: A 327 GLU cc_start: 0.8748 (pp20) cc_final: 0.8528 (pp20) REVERT: A 357 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8572 (tp-100) REVERT: A 639 LEU cc_start: 0.8641 (tt) cc_final: 0.8360 (tt) REVERT: A 672 LEU cc_start: 0.8776 (tt) cc_final: 0.8511 (tt) REVERT: A 687 TRP cc_start: 0.6840 (m100) cc_final: 0.6583 (m100) REVERT: A 807 MET cc_start: 0.7813 (mtm) cc_final: 0.7139 (mtm) REVERT: B 531 TYR cc_start: 0.8030 (m-10) cc_final: 0.7784 (m-10) REVERT: B 702 MET cc_start: 0.8220 (tpp) cc_final: 0.7960 (tpp) outliers start: 23 outliers final: 13 residues processed: 142 average time/residue: 0.1870 time to fit residues: 40.8038 Evaluate side-chains 123 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 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 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 727 VAL Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 65 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN A 577 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** 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 = 0.3582 r_free = 0.3582 target = 0.113137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.088237 restraints weight = 26184.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090603 restraints weight = 13125.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092114 restraints weight = 8521.373| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11232 Z= 0.198 Angle : 0.663 11.557 15287 Z= 0.332 Chirality : 0.046 0.322 1762 Planarity : 0.004 0.055 1904 Dihedral : 7.451 68.102 1788 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.67 % Allowed : 15.05 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.22), residues: 1377 helix: 0.30 (0.21), residues: 657 sheet: -1.31 (0.35), residues: 230 loop : -3.51 (0.23), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 615 HIS 0.010 0.001 HIS A 689 PHE 0.017 0.002 PHE A 682 TYR 0.012 0.001 TYR B 564 ARG 0.003 0.000 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 9) link_NAG-ASN : angle 3.88594 ( 27) link_BETA1-4 : bond 0.01359 ( 4) link_BETA1-4 : angle 4.95629 ( 12) hydrogen bonds : bond 0.05005 ( 489) hydrogen bonds : angle 4.48379 ( 1455) SS BOND : bond 0.00365 ( 7) SS BOND : angle 1.60766 ( 14) covalent geometry : bond 0.00453 (11212) covalent geometry : angle 0.62653 (15234) *********************** 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 145 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 357 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8538 (tp-100) REVERT: A 639 LEU cc_start: 0.8678 (tt) cc_final: 0.8470 (tt) REVERT: A 687 TRP cc_start: 0.6833 (m100) cc_final: 0.6580 (m100) REVERT: A 807 MET cc_start: 0.7826 (mtm) cc_final: 0.7071 (mtm) REVERT: B 519 MET cc_start: 0.6631 (mtt) cc_final: 0.6035 (mtp) REVERT: B 531 TYR cc_start: 0.8142 (m-10) cc_final: 0.7903 (m-10) REVERT: B 702 MET cc_start: 0.8229 (tpp) cc_final: 0.7787 (tpp) outliers start: 30 outliers final: 19 residues processed: 135 average time/residue: 0.1796 time to fit residues: 38.8479 Evaluate side-chains 127 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 530 SER 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 822 VAL Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain B residue 58 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 35 optimal weight: 0.0040 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3620 r_free = 0.3620 target = 0.115656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.090967 restraints weight = 25416.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.093350 restraints weight = 12618.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094901 restraints weight = 8162.110| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1378 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= 0.112 Angle : 0.601 10.966 15287 Z= 0.295 Chirality : 0.044 0.310 1762 Planarity : 0.004 0.042 1904 Dihedral : 6.672 66.578 1788 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.51 % Allowed : 16.92 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.23), residues: 1377 helix: 0.64 (0.21), residues: 663 sheet: -1.07 (0.36), residues: 220 loop : -3.32 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 615 HIS 0.009 0.001 HIS A 689 PHE 0.017 0.001 PHE A 682 TYR 0.009 0.001 TYR B 564 ARG 0.002 0.000 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 9) link_NAG-ASN : angle 3.77886 ( 27) link_BETA1-4 : bond 0.01385 ( 4) link_BETA1-4 : angle 4.61247 ( 12) hydrogen bonds : bond 0.04174 ( 489) hydrogen bonds : angle 4.14213 ( 1455) SS BOND : bond 0.00364 ( 7) SS BOND : angle 1.80266 ( 14) covalent geometry : bond 0.00240 (11212) covalent geometry : angle 0.56288 (15234) *********************** 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 140 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 357 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8500 (tp-100) REVERT: A 687 TRP cc_start: 0.6840 (m100) cc_final: 0.6595 (m100) REVERT: A 807 MET cc_start: 0.7741 (mtm) cc_final: 0.7002 (mtm) REVERT: B 519 MET cc_start: 0.6633 (mtt) cc_final: 0.6344 (mtp) REVERT: B 702 MET cc_start: 0.8078 (tpp) cc_final: 0.7655 (tpp) outliers start: 17 outliers final: 12 residues processed: 136 average time/residue: 0.1800 time to fit residues: 38.5359 Evaluate side-chains 125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 477 LEU 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 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 568 PHE Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 2 optimal weight: 0.0010 chunk 65 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 overall best weight: 2.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** 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 = 0.3575 r_free = 0.3575 target = 0.112627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.087953 restraints weight = 25692.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.090277 restraints weight = 12957.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091790 restraints weight = 8455.529| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1586 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= 0.203 Angle : 0.664 11.134 15287 Z= 0.330 Chirality : 0.046 0.314 1762 Planarity : 0.004 0.044 1904 Dihedral : 6.914 68.966 1788 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.67 % Allowed : 18.52 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.23), residues: 1377 helix: 0.72 (0.21), residues: 658 sheet: -1.16 (0.36), residues: 222 loop : -3.31 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 615 HIS 0.009 0.001 HIS A 689 PHE 0.017 0.002 PHE A 682 TYR 0.013 0.001 TYR B 564 ARG 0.002 0.000 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 9) link_NAG-ASN : angle 3.83827 ( 27) link_BETA1-4 : bond 0.01344 ( 4) link_BETA1-4 : angle 4.53083 ( 12) hydrogen bonds : bond 0.04928 ( 489) hydrogen bonds : angle 4.42053 ( 1455) SS BOND : bond 0.00396 ( 7) SS BOND : angle 2.92725 ( 14) covalent geometry : bond 0.00467 (11212) covalent geometry : angle 0.62582 (15234) *********************** 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: 30 poor density : 116 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8506 (tp-100) REVERT: A 687 TRP cc_start: 0.6834 (m100) cc_final: 0.6576 (m100) REVERT: A 807 MET cc_start: 0.7857 (mtm) cc_final: 0.7093 (mtm) REVERT: B 103 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8705 (mp) REVERT: B 519 MET cc_start: 0.6692 (mtt) cc_final: 0.6375 (mtp) REVERT: B 702 MET cc_start: 0.8202 (tpp) cc_final: 0.7759 (tpp) outliers start: 30 outliers final: 23 residues processed: 134 average time/residue: 0.1684 time to fit residues: 35.9587 Evaluate side-chains 133 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 477 LEU 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 737 THR Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 851 VAL 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 186 ILE 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 727 VAL 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 81 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3621 r_free = 0.3621 target = 0.115686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.090978 restraints weight = 25824.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.093404 restraints weight = 12798.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094958 restraints weight = 8235.265| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 11232 Z= 0.108 Angle : 0.599 10.674 15287 Z= 0.294 Chirality : 0.044 0.305 1762 Planarity : 0.004 0.036 1904 Dihedral : 6.310 67.421 1788 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.05 % Allowed : 19.41 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.23), residues: 1377 helix: 0.92 (0.21), residues: 662 sheet: -0.74 (0.37), residues: 212 loop : -3.19 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 615 HIS 0.009 0.001 HIS A 689 PHE 0.014 0.001 PHE B 319 TYR 0.008 0.001 TYR B 564 ARG 0.002 0.000 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 9) link_NAG-ASN : angle 3.74359 ( 27) link_BETA1-4 : bond 0.01271 ( 4) link_BETA1-4 : angle 4.26198 ( 12) hydrogen bonds : bond 0.03963 ( 489) hydrogen bonds : angle 4.05869 ( 1455) SS BOND : bond 0.00133 ( 7) SS BOND : angle 1.90152 ( 14) covalent geometry : bond 0.00236 (11212) covalent geometry : angle 0.56326 (15234) *********************** 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: 23 poor density : 122 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8351 (tm-30) REVERT: A 357 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8504 (tp-100) REVERT: A 687 TRP cc_start: 0.6788 (m100) cc_final: 0.6528 (m100) REVERT: A 807 MET cc_start: 0.7771 (mtm) cc_final: 0.7040 (mtm) REVERT: B 702 MET cc_start: 0.8000 (tpp) cc_final: 0.7578 (tpp) outliers start: 23 outliers final: 15 residues processed: 138 average time/residue: 0.1700 time to fit residues: 37.3820 Evaluate side-chains 125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 477 LEU 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 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 439 VAL Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 625 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 115 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 53 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 121 optimal weight: 30.0000 chunk 90 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3593 r_free = 0.3593 target = 0.113881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089095 restraints weight = 26180.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.091482 restraints weight = 13092.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.093040 restraints weight = 8474.876| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11232 Z= 0.157 Angle : 0.628 9.847 15287 Z= 0.311 Chirality : 0.045 0.312 1762 Planarity : 0.004 0.038 1904 Dihedral : 6.493 68.664 1788 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.49 % Allowed : 19.32 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1377 helix: 0.94 (0.21), residues: 665 sheet: -0.75 (0.37), residues: 212 loop : -3.17 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 615 HIS 0.008 0.001 HIS A 689 PHE 0.021 0.001 PHE B 117 TYR 0.011 0.001 TYR B 564 ARG 0.001 0.000 ARG B 371 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 9) link_NAG-ASN : angle 3.75172 ( 27) link_BETA1-4 : bond 0.01277 ( 4) link_BETA1-4 : angle 4.17028 ( 12) hydrogen bonds : bond 0.04408 ( 489) hydrogen bonds : angle 4.22060 ( 1455) SS BOND : bond 0.00232 ( 7) SS BOND : angle 2.69153 ( 14) covalent geometry : bond 0.00360 (11212) covalent geometry : angle 0.59183 (15234) *********************** 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 144 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8379 (tm-30) REVERT: A 357 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8490 (tp-100) REVERT: A 527 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7895 (t80) REVERT: A 687 TRP cc_start: 0.6821 (m100) cc_final: 0.6550 (m100) REVERT: A 807 MET cc_start: 0.7810 (mtm) cc_final: 0.7075 (mtm) REVERT: B 702 MET cc_start: 0.8123 (tpp) cc_final: 0.7697 (tpp) outliers start: 28 outliers final: 20 residues processed: 134 average time/residue: 0.1824 time to fit residues: 38.8484 Evaluate side-chains 131 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 527 PHE 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 737 THR 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 218 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3596 r_free = 0.3596 target = 0.114047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089386 restraints weight = 25854.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091768 restraints weight = 12975.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093301 restraints weight = 8413.398| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11232 Z= 0.147 Angle : 0.641 10.066 15287 Z= 0.315 Chirality : 0.045 0.307 1762 Planarity : 0.004 0.037 1904 Dihedral : 6.464 68.704 1788 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.23 % Allowed : 20.12 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1377 helix: 0.97 (0.21), residues: 666 sheet: -0.76 (0.37), residues: 212 loop : -3.14 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 615 HIS 0.008 0.001 HIS A 689 PHE 0.031 0.001 PHE A 682 TYR 0.011 0.001 TYR B 564 ARG 0.007 0.000 ARG B 637 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 9) link_NAG-ASN : angle 3.74103 ( 27) link_BETA1-4 : bond 0.01295 ( 4) link_BETA1-4 : angle 4.11730 ( 12) hydrogen bonds : bond 0.04421 ( 489) hydrogen bonds : angle 4.21526 ( 1455) SS BOND : bond 0.00299 ( 7) SS BOND : angle 3.16890 ( 14) covalent geometry : bond 0.00335 (11212) covalent geometry : angle 0.60360 (15234) *********************** 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 141 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.165 Fit side-chains REVERT: A 328 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 357 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8511 (tp-100) REVERT: A 527 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7920 (t80) REVERT: A 687 TRP cc_start: 0.6753 (m100) cc_final: 0.6469 (m100) REVERT: A 807 MET cc_start: 0.7808 (mtm) cc_final: 0.7060 (mtm) REVERT: B 702 MET cc_start: 0.8116 (tpp) cc_final: 0.7697 (tpp) outliers start: 25 outliers final: 20 residues processed: 135 average time/residue: 0.1699 time to fit residues: 36.2166 Evaluate side-chains 130 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 527 PHE 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 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 186 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 525 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 87 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3633 r_free = 0.3633 target = 0.116483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.092020 restraints weight = 25604.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094437 restraints weight = 12607.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096019 restraints weight = 8055.983| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11232 Z= 0.107 Angle : 0.610 10.349 15287 Z= 0.297 Chirality : 0.044 0.310 1762 Planarity : 0.004 0.031 1904 Dihedral : 5.988 66.383 1788 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.78 % Allowed : 20.39 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1377 helix: 1.13 (0.21), residues: 666 sheet: -0.56 (0.38), residues: 210 loop : -3.02 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 615 HIS 0.008 0.001 HIS A 689 PHE 0.016 0.001 PHE B 572 TYR 0.013 0.001 TYR B 564 ARG 0.004 0.000 ARG B 637 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 9) link_NAG-ASN : angle 3.65455 ( 27) link_BETA1-4 : bond 0.01277 ( 4) link_BETA1-4 : angle 3.88631 ( 12) hydrogen bonds : bond 0.03799 ( 489) hydrogen bonds : angle 3.97687 ( 1455) SS BOND : bond 0.00131 ( 7) SS BOND : angle 1.89059 ( 14) covalent geometry : bond 0.00234 (11212) covalent geometry : angle 0.57806 (15234) *********************** 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 139 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.333 Fit side-chains REVERT: A 328 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8352 (tm-30) REVERT: A 357 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8503 (tp-100) REVERT: A 687 TRP cc_start: 0.6679 (m100) cc_final: 0.6431 (m100) REVERT: A 807 MET cc_start: 0.7777 (mtm) cc_final: 0.7062 (mtm) REVERT: B 702 MET cc_start: 0.8052 (tpp) cc_final: 0.7629 (tpp) outliers start: 20 outliers final: 17 residues processed: 135 average time/residue: 0.1820 time to fit residues: 38.5374 Evaluate side-chains 132 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 477 LEU 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 525 LEU 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 131 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3637 r_free = 0.3637 target = 0.115351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.090560 restraints weight = 26464.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.092949 restraints weight = 12993.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094503 restraints weight = 8364.227| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11232 Z= 0.159 Angle : 0.652 9.472 15287 Z= 0.321 Chirality : 0.045 0.308 1762 Planarity : 0.004 0.036 1904 Dihedral : 6.218 67.725 1788 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.69 % Allowed : 20.93 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1377 helix: 1.14 (0.21), residues: 665 sheet: -0.61 (0.37), residues: 212 loop : -3.04 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 615 HIS 0.007 0.001 HIS A 689 PHE 0.015 0.001 PHE B 117 TYR 0.012 0.001 TYR B 564 ARG 0.002 0.000 ARG B 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 9) link_NAG-ASN : angle 3.68002 ( 27) link_BETA1-4 : bond 0.01238 ( 4) link_BETA1-4 : angle 3.93836 ( 12) hydrogen bonds : bond 0.04231 ( 489) hydrogen bonds : angle 4.14385 ( 1455) SS BOND : bond 0.00294 ( 7) SS BOND : angle 2.74989 ( 14) covalent geometry : bond 0.00368 (11212) covalent geometry : angle 0.61931 (15234) ********************** 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: 19 poor density : 115 time to evaluate : 1.202 Fit side-chains REVERT: A 328 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8349 (tm-30) REVERT: A 357 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8476 (tp-100) REVERT: A 687 TRP cc_start: 0.6714 (m100) cc_final: 0.6484 (m100) REVERT: A 807 MET cc_start: 0.7854 (mtm) cc_final: 0.7135 (mtm) REVERT: B 702 MET cc_start: 0.8130 (tpp) cc_final: 0.7724 (tpp) outliers start: 19 outliers final: 19 residues processed: 129 average time/residue: 0.1600 time to fit residues: 33.5636 Evaluate side-chains 131 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 477 LEU 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 525 LEU 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 90 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 76 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3587 r_free = 0.3587 target = 0.113379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088841 restraints weight = 25835.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091206 restraints weight = 12906.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.092734 restraints weight = 8349.251| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11232 Z= 0.173 Angle : 0.678 10.269 15287 Z= 0.335 Chirality : 0.046 0.308 1762 Planarity : 0.004 0.042 1904 Dihedral : 6.486 69.696 1788 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.78 % Allowed : 21.10 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1377 helix: 1.07 (0.21), residues: 668 sheet: -0.68 (0.37), residues: 211 loop : -3.02 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 615 HIS 0.008 0.001 HIS A 689 PHE 0.016 0.001 PHE B 572 TYR 0.014 0.001 TYR B 564 ARG 0.002 0.000 ARG A 764 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 9) link_NAG-ASN : angle 3.75699 ( 27) link_BETA1-4 : bond 0.01224 ( 4) link_BETA1-4 : angle 3.93163 ( 12) hydrogen bonds : bond 0.04703 ( 489) hydrogen bonds : angle 4.30017 ( 1455) SS BOND : bond 0.00437 ( 7) SS BOND : angle 3.30864 ( 14) covalent geometry : bond 0.00401 (11212) covalent geometry : angle 0.64319 (15234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.37 seconds wall clock time: 63 minutes 5.15 seconds (3785.15 seconds total)