Starting phenix.real_space_refine on Fri Sep 11 16:09:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w2x_21533/09_2026/6w2x_21533.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w2x_21533/09_2026/6w2x_21533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w2x_21533/09_2026/6w2x_21533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w2x_21533/09_2026/6w2x_21533.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6w2x_21533/09_2026/6w2x_21533.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w2x_21533/09_2026/6w2x_21533.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w2x_21533/09_2026/6w2x_21533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w2x_21533/09_2026/6w2x_21533.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 46 5.16 5 Cl 2 4.86 5 C 6455 2.51 5 N 1620 2.21 5 O 1733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4934 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 676, 4920 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 477 Unresolved non-hydrogen angles: 587 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 13, 'ASP:plan': 15, 'GLN:plan1': 10, 'PHE:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 7, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 304 Conformer: "B" Number of residues, atoms: 676, 4920 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 477 Unresolved non-hydrogen angles: 587 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 13, 'ASP:plan': 15, 'GLN:plan1': 10, 'PHE:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 7, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 304 bond proxies already assigned to first conformer: 5027 Chain: "B" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 4724 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 27, 'TRANS': 641} Chain breaks: 4 Unresolved non-hydrogen bonds: 599 Unresolved non-hydrogen angles: 729 Unresolved non-hydrogen dihedrals: 482 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 12, 'ASP:plan': 20, 'GLN:plan1': 8, 'ASN:plan1': 13, 'TYR:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 331 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 1, 'L9Q': 1, 'NAG': 2, 'SGG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATRP A 278 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 278 " occ=0.50 residue: pdb=" N L9Q A 905 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q A 905 " occ=0.99 residue: pdb=" N L9Q B1003 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q B1003 " occ=0.99 Time building chain proxies: 3.04, per 1000 atoms: 0.31 Number of scatterers: 9860 At special positions: 0 Unit cell: (137.188, 99.6957, 174.681, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 46 16.00 P 3 15.00 Mg 1 11.99 O 1733 8.00 N 1620 7.00 C 6455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 129 " distance=2.05 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 644 " distance=1.76 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " 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 BETA1-3 " NAG D 1 " - " NAG D 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 901 " - " ASN A 397 " " NAG A 902 " - " ASN A 365 " " NAG C 1 " - " ASN A 323 " " NAG D 1 " - " ASN B 404 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 704.3 milliseconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 54.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.677A pdb=" N VAL A 75 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.664A pdb=" N ALA A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 140 removed outlier: 3.788A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.535A pdb=" N SER A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 removed outlier: 3.583A pdb=" N LYS A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.650A pdb=" N VAL A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.050A pdb=" N CYS A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.860A pdb=" N GLU A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 368 removed outlier: 3.642A pdb=" N ALA A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 473 through 499 removed outlier: 4.109A pdb=" N SER A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.849A pdb=" N SER A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 526 Processing helix chain 'A' and resid 527 through 532 removed outlier: 4.175A pdb=" N GLY A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 532' Processing helix chain 'A' and resid 542 through 576 removed outlier: 3.995A pdb=" N CYS A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE A 568 " --> pdb=" O MET A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 615 removed outlier: 3.735A pdb=" N LEU A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 595 " --> pdb=" O TRP A 591 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 674 removed outlier: 4.309A pdb=" N TRP A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU A 663 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 709 removed outlier: 3.635A pdb=" N VAL A 697 " --> pdb=" O TYR A 693 " (cutoff:3.500A) Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 714 through 733 removed outlier: 4.583A pdb=" N ALA A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA A 723 " --> pdb=" O PHE A 719 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 746 removed outlier: 3.883A pdb=" N MET A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 109 through 123 removed outlier: 4.153A pdb=" N ALA B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.519A pdb=" N THR B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.736A pdb=" N LYS B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 removed outlier: 4.310A pdb=" N VAL B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 removed outlier: 3.614A pdb=" N ASN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 271 removed outlier: 3.821A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.651A pdb=" N ARG B 340 " --> pdb=" O GLN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 378 removed outlier: 3.586A pdb=" N ASP B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 404 removed outlier: 3.761A pdb=" N GLY B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 506 removed outlier: 3.975A pdb=" N ILE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.531A pdb=" N SER B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 539 removed outlier: 3.641A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 584 removed outlier: 3.564A pdb=" N PHE B 549 " --> pdb=" O SER B 545 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 619 removed outlier: 3.671A pdb=" N LEU B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 598 " --> pdb=" O ASP B 594 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 608 " --> pdb=" O MET B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 678 Processing helix chain 'B' and resid 688 through 713 removed outlier: 3.628A pdb=" N PHE B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 750 removed outlier: 4.049A pdb=" N GLN B 720 " --> pdb=" O GLN B 716 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 741 " --> pdb=" O CYS B 737 " (cutoff:3.500A) Proline residue: B 742 - end of helix removed outlier: 3.909A pdb=" N LEU B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 100 removed outlier: 4.837A pdb=" N ILE A 124 " --> pdb=" O TYR A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 226 removed outlier: 6.069A pdb=" N ILE A 192 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE A 222 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 226 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE A 244 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 248 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP A 273 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR A 308 " --> pdb=" O TRP A 273 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU A 275 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N ILE A 310 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 307 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 444 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.926A pdb=" N PHE A 401 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 467 removed outlier: 6.347A pdb=" N ILE A 464 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN A 640 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR A 466 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N GLU A 642 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 622 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 104 Processing sheet with id=AA6, first strand: chain 'B' and resid 197 through 203 removed outlier: 6.774A pdb=" N VAL B 198 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 228 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 200 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 250 through 252 removed outlier: 6.924A pdb=" N TRP B 279 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N VAL B 317 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR B 314 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 431 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 426 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU B 441 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE B 428 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 448 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB1, first strand: chain 'B' and resid 622 through 627 510 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1515 1.32 - 1.45: 2997 1.45 - 1.59: 5509 1.59 - 1.72: 4 1.72 - 1.86: 72 Bond restraints: 10097 Sorted by residual: bond pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta sigma weight residual 1.454 1.500 -0.046 1.17e-02 7.31e+03 1.52e+01 bond pdb=" CA SER A 149 " pdb=" CB SER A 149 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.55e-02 4.16e+03 1.40e+01 bond pdb=" CA SER A 152 " pdb=" CB SER A 152 " ideal model delta sigma weight residual 1.531 1.476 0.055 1.52e-02 4.33e+03 1.30e+01 bond pdb=" C11 L9Q A 905 " pdb=" O3 L9Q A 905 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 L9Q B1003 " pdb=" O3 L9Q B1003 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 10092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 13534 2.21 - 4.41: 237 4.41 - 6.62: 32 6.62 - 8.83: 11 8.83 - 11.03: 5 Bond angle restraints: 13819 Sorted by residual: angle pdb=" CA SER A 149 " pdb=" C SER A 149 " pdb=" O SER A 149 " ideal model delta sigma weight residual 120.80 115.94 4.86 1.11e+00 8.12e-01 1.92e+01 angle pdb=" C HIS A 643 " pdb=" CA HIS A 643 " pdb=" CB HIS A 643 " ideal model delta sigma weight residual 110.22 103.70 6.52 1.67e+00 3.59e-01 1.52e+01 angle pdb=" CA HIS B 652 " pdb=" C HIS B 652 " pdb=" O HIS B 652 " ideal model delta sigma weight residual 122.63 117.70 4.93 1.29e+00 6.01e-01 1.46e+01 angle pdb=" O3P L9Q A 905 " pdb=" P L9Q A 905 " pdb=" O4P L9Q A 905 " ideal model delta sigma weight residual 98.21 109.24 -11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O3P L9Q B1003 " pdb=" P L9Q B1003 " pdb=" O4P L9Q B1003 " ideal model delta sigma weight residual 98.21 109.24 -11.03 3.00e+00 1.11e-01 1.35e+01 ... (remaining 13814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 5460 22.34 - 44.68: 296 44.68 - 67.02: 19 67.02 - 89.36: 2 89.36 - 111.70: 2 Dihedral angle restraints: 5779 sinusoidal: 1872 harmonic: 3907 Sorted by residual: dihedral pdb=" CB CYS B 553 " pdb=" SG CYS B 553 " pdb=" SG CYS B 648 " pdb=" CB CYS B 648 " ideal model delta sinusoidal sigma weight residual 93.00 138.87 -45.87 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CB CYS A 103 " pdb=" SG CYS A 103 " pdb=" SG CYS A 129 " pdb=" CB CYS A 129 " ideal model delta sinusoidal sigma weight residual -86.00 -128.95 42.95 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CB CYS A 546 " pdb=" SG CYS A 546 " pdb=" SG CYS A 644 " pdb=" CB CYS A 644 " ideal model delta sinusoidal sigma weight residual 93.00 135.62 -42.62 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 5776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1597 0.101 - 0.202: 56 0.202 - 0.303: 2 0.303 - 0.404: 0 0.404 - 0.505: 3 Chirality restraints: 1658 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.90 0.50 2.00e-02 2.50e+03 6.38e+02 chirality pdb=" C1 NAG D 2 " pdb=" O3 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.88 0.48 2.00e-02 2.50e+03 5.74e+02 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 397 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 1655 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 152 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C SER A 152 " 0.067 2.00e-02 2.50e+03 pdb=" O SER A 152 " -0.026 2.00e-02 2.50e+03 pdb=" N SER A 153 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 148 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C LEU A 148 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A 148 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A 149 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 703 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.92e+00 pdb=" N PRO A 704 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 704 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 704 " -0.041 5.00e-02 4.00e+02 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 56 2.61 - 3.18: 8750 3.18 - 3.75: 13380 3.75 - 4.33: 17819 4.33 - 4.90: 30180 Nonbonded interactions: 70185 Sorted by model distance: nonbonded pdb=" O4 NAG D 1 " pdb=" N2 NAG D 2 " model vdw 2.034 3.120 nonbonded pdb=" OD1 ASN A 694 " pdb=" N VAL A 695 " model vdw 2.095 3.120 nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.183 3.040 nonbonded pdb=" O GLY A 151 " pdb=" O10 SGG A 906 " model vdw 2.220 3.040 nonbonded pdb=" O GLU A 309 " pdb=" OG1 THR A 420 " model vdw 2.236 3.040 ... (remaining 70180 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 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.130 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.300 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.006 0.270 10108 Z= 0.277 Angle : 0.858 31.480 13847 Z= 0.412 Chirality : 0.048 0.505 1658 Planarity : 0.004 0.075 1716 Dihedral : 13.017 111.696 3244 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.21), residues: 1330 helix: -1.16 (0.19), residues: 662 sheet: -1.62 (0.38), residues: 205 loop : -4.30 (0.21), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 TYR 0.014 0.001 TYR B 171 PHE 0.013 0.001 PHE A 624 TRP 0.006 0.001 TRP A 143 HIS 0.003 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.24 (10097) covalent geometry : angle 0.75166 / 0.39 (13819) SS BOND : bond 0.12088 / 5.76 ( 5) SS BOND : angle 5.15632 / 2.14 ( 10) hydrogen bonds : bond 0.18158 / 11.78 ( 510) hydrogen bonds : angle 6.09670 / 4.26 ( 1512) link_BETA1-3 : bond 0.00905 / 0.48 ( 1) link_BETA1-3 : angle 18.45321 / 10.76 ( 3) link_BETA1-4 : bond 0.00988 / 0.52 ( 1) link_BETA1-4 : angle 17.09346 / 9.66 ( 3) link_NAG-ASN : bond 0.00285 / 0.14 ( 4) link_NAG-ASN : angle 4.35505 / 2.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 LEU cc_start: 0.8261 (tp) cc_final: 0.7171 (mp) REVERT: B 666 LEU cc_start: 0.8603 (mt) cc_final: 0.8364 (mp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0980 time to fit residues: 20.2655 Evaluate side-chains 88 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 159 ASN B 180 ASN B 192 HIS B 278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.154709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132827 restraints weight = 21585.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130409 restraints weight = 27233.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128341 restraints weight = 23185.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128347 restraints weight = 24923.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128236 restraints weight = 17846.589| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10108 Z= 0.248 Angle : 0.759 9.820 13847 Z= 0.383 Chirality : 0.049 0.319 1658 Planarity : 0.005 0.057 1716 Dihedral : 7.747 99.235 1490 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.27 % Allowed : 12.80 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.23), residues: 1330 helix: -0.03 (0.20), residues: 675 sheet: -1.54 (0.36), residues: 229 loop : -3.57 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 416 TYR 0.021 0.002 TYR B 273 PHE 0.021 0.002 PHE B 582 TRP 0.019 0.002 TRP A 273 HIS 0.011 0.002 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (10097) covalent geometry : angle 0.74830 / 0.38 (13819) SS BOND : bond 0.00507 / 0.25 ( 5) SS BOND : angle 1.43109 / 0.76 ( 10) hydrogen bonds : bond 0.06976 / 4.78 ( 510) hydrogen bonds : angle 4.63321 / 3.29 ( 1512) link_BETA1-3 : bond 0.01610 / 0.85 ( 1) link_BETA1-3 : angle 4.41666 / 2.36 ( 3) link_BETA1-4 : bond 0.00200 / 0.11 ( 1) link_BETA1-4 : angle 1.08485 / 0.49 ( 3) link_NAG-ASN : bond 0.00634 / 0.31 ( 4) link_NAG-ASN : angle 3.59814 / 1.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.392 Fit side-chains REVERT: B 91 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7908 (tt0) outliers start: 11 outliers final: 5 residues processed: 102 average time/residue: 0.0748 time to fit residues: 12.1020 Evaluate side-chains 87 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain B residue 128 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 80 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 127 optimal weight: 0.0980 chunk 101 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 67 optimal weight: 0.0370 chunk 41 optimal weight: 4.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.157960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137029 restraints weight = 20589.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133111 restraints weight = 23551.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131384 restraints weight = 24224.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131229 restraints weight = 22521.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131005 restraints weight = 17367.710| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10108 Z= 0.123 Angle : 0.588 8.940 13847 Z= 0.290 Chirality : 0.043 0.291 1658 Planarity : 0.004 0.050 1716 Dihedral : 6.815 78.099 1490 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.38 % Allowed : 16.26 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.24), residues: 1330 helix: 0.60 (0.21), residues: 676 sheet: -0.88 (0.38), residues: 212 loop : -3.13 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.024 0.001 TYR B 273 PHE 0.018 0.001 PHE B 582 TRP 0.013 0.001 TRP B 279 HIS 0.004 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (10097) covalent geometry : angle 0.57660 / 0.29 (13819) SS BOND : bond 0.00157 / 0.09 ( 5) SS BOND : angle 0.73978 / 0.40 ( 10) hydrogen bonds : bond 0.05232 / 3.55 ( 510) hydrogen bonds : angle 4.20839 / 2.99 ( 1512) link_BETA1-3 : bond 0.00943 / 0.50 ( 1) link_BETA1-3 : angle 4.26140 / 2.27 ( 3) link_BETA1-4 : bond 0.00371 / 0.20 ( 1) link_BETA1-4 : angle 1.17272 / 0.64 ( 3) link_NAG-ASN : bond 0.00457 / 0.23 ( 4) link_NAG-ASN : angle 3.21209 / 1.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.383 Fit side-chains REVERT: B 91 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7751 (tt0) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 0.0825 time to fit residues: 12.7127 Evaluate side-chains 88 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 365 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132331 restraints weight = 19866.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129892 restraints weight = 27258.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128573 restraints weight = 22290.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.128991 restraints weight = 22292.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128323 restraints weight = 17477.460| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10108 Z= 0.152 Angle : 0.598 8.388 13847 Z= 0.297 Chirality : 0.044 0.247 1658 Planarity : 0.004 0.046 1716 Dihedral : 6.386 57.561 1490 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.61 % Allowed : 17.53 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.24), residues: 1330 helix: 0.78 (0.21), residues: 679 sheet: -0.80 (0.37), residues: 213 loop : -3.03 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 394 TYR 0.022 0.001 TYR B 273 PHE 0.025 0.001 PHE B 582 TRP 0.012 0.001 TRP B 279 HIS 0.006 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (10097) covalent geometry : angle 0.58868 / 0.30 (13819) SS BOND : bond 0.00280 / 0.14 ( 5) SS BOND : angle 0.97427 / 0.53 ( 10) hydrogen bonds : bond 0.05400 / 3.69 ( 510) hydrogen bonds : angle 4.12079 / 2.90 ( 1512) link_BETA1-3 : bond 0.00547 / 0.29 ( 1) link_BETA1-3 : angle 4.03891 / 2.15 ( 3) link_BETA1-4 : bond 0.00693 / 0.36 ( 1) link_BETA1-4 : angle 0.98309 / 0.54 ( 3) link_NAG-ASN : bond 0.00359 / 0.18 ( 4) link_NAG-ASN : angle 2.85751 / 1.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 508 SER cc_start: 0.6617 (t) cc_final: 0.6186 (p) REVERT: B 91 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7727 (tt0) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.0804 time to fit residues: 11.9513 Evaluate side-chains 90 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135762 restraints weight = 17114.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131216 restraints weight = 20302.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129752 restraints weight = 19464.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.129357 restraints weight = 18099.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128567 restraints weight = 17352.273| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10108 Z= 0.118 Angle : 0.544 7.511 13847 Z= 0.271 Chirality : 0.042 0.223 1658 Planarity : 0.004 0.044 1716 Dihedral : 5.946 54.742 1490 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.50 % Allowed : 19.03 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.24), residues: 1330 helix: 1.06 (0.21), residues: 678 sheet: -0.58 (0.38), residues: 213 loop : -2.83 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 394 TYR 0.028 0.001 TYR B 273 PHE 0.021 0.001 PHE B 582 TRP 0.014 0.001 TRP B 279 HIS 0.004 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10097) covalent geometry : angle 0.53612 / 0.27 (13819) SS BOND : bond 0.00170 / 0.09 ( 5) SS BOND : angle 0.72306 / 0.40 ( 10) hydrogen bonds : bond 0.04579 / 3.10 ( 510) hydrogen bonds : angle 3.94652 / 2.78 ( 1512) link_BETA1-3 : bond 0.00660 / 0.35 ( 1) link_BETA1-3 : angle 3.74329 / 1.99 ( 3) link_BETA1-4 : bond 0.00416 / 0.22 ( 1) link_BETA1-4 : angle 0.90037 / 0.49 ( 3) link_NAG-ASN : bond 0.00323 / 0.16 ( 4) link_NAG-ASN : angle 2.47942 / 1.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.394 Fit side-chains REVERT: A 508 SER cc_start: 0.6534 (t) cc_final: 0.6162 (p) outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.0796 time to fit residues: 12.0413 Evaluate side-chains 90 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 692 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 118 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 123 optimal weight: 0.1980 chunk 7 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133626 restraints weight = 15207.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129788 restraints weight = 21311.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127940 restraints weight = 20802.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127211 restraints weight = 20505.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126710 restraints weight = 18343.251| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10108 Z= 0.118 Angle : 0.541 7.276 13847 Z= 0.268 Chirality : 0.042 0.209 1658 Planarity : 0.004 0.043 1716 Dihedral : 5.713 52.940 1490 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.73 % Allowed : 19.84 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1330 helix: 1.20 (0.21), residues: 683 sheet: -0.42 (0.37), residues: 211 loop : -2.80 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 394 TYR 0.025 0.001 TYR B 663 PHE 0.020 0.001 PHE B 582 TRP 0.011 0.001 TRP B 279 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10097) covalent geometry : angle 0.53425 / 0.27 (13819) SS BOND : bond 0.00230 / 0.12 ( 5) SS BOND : angle 0.89725 / 0.49 ( 10) hydrogen bonds : bond 0.04513 / 3.08 ( 510) hydrogen bonds : angle 3.88433 / 2.73 ( 1512) link_BETA1-3 : bond 0.00771 / 0.41 ( 1) link_BETA1-3 : angle 3.45650 / 1.83 ( 3) link_BETA1-4 : bond 0.00380 / 0.20 ( 1) link_BETA1-4 : angle 0.79417 / 0.42 ( 3) link_NAG-ASN : bond 0.00277 / 0.14 ( 4) link_NAG-ASN : angle 2.35625 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.369 Fit side-chains REVERT: A 508 SER cc_start: 0.6505 (t) cc_final: 0.6095 (p) REVERT: B 163 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8459 (mp) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.0773 time to fit residues: 11.2738 Evaluate side-chains 90 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 117 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.157471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132222 restraints weight = 21680.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.131191 restraints weight = 27784.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.129207 restraints weight = 21510.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129873 restraints weight = 20567.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130165 restraints weight = 14443.771| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (14 function evaluations) r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10108 Z= 0.109 Angle : 0.534 11.407 13847 Z= 0.261 Chirality : 0.041 0.202 1658 Planarity : 0.004 0.041 1716 Dihedral : 5.581 53.488 1490 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.61 % Allowed : 20.30 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1330 helix: 1.33 (0.21), residues: 683 sheet: -0.41 (0.37), residues: 213 loop : -2.62 (0.25), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 394 TYR 0.028 0.001 TYR B 273 PHE 0.018 0.001 PHE B 582 TRP 0.012 0.001 TRP B 279 HIS 0.004 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (10097) covalent geometry : angle 0.52791 / 0.26 (13819) SS BOND : bond 0.00153 / 0.09 ( 5) SS BOND : angle 0.70182 / 0.39 ( 10) hydrogen bonds : bond 0.04143 / 2.81 ( 510) hydrogen bonds : angle 3.82325 / 2.69 ( 1512) link_BETA1-3 : bond 0.00766 / 0.40 ( 1) link_BETA1-3 : angle 3.30365 / 1.75 ( 3) link_BETA1-4 : bond 0.00421 / 0.22 ( 1) link_BETA1-4 : angle 0.84431 / 0.45 ( 3) link_NAG-ASN : bond 0.00315 / 0.16 ( 4) link_NAG-ASN : angle 2.15830 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.382 Fit side-chains REVERT: A 508 SER cc_start: 0.6408 (t) cc_final: 0.6020 (p) REVERT: B 280 ILE cc_start: 0.8184 (mm) cc_final: 0.7929 (mt) outliers start: 14 outliers final: 12 residues processed: 97 average time/residue: 0.0756 time to fit residues: 11.4356 Evaluate side-chains 94 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 78 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131334 restraints weight = 20235.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129550 restraints weight = 24746.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127261 restraints weight = 20053.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128296 restraints weight = 18234.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127627 restraints weight = 16114.214| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (18 function evaluations) r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10108 Z= 0.124 Angle : 0.545 8.253 13847 Z= 0.269 Chirality : 0.042 0.196 1658 Planarity : 0.004 0.039 1716 Dihedral : 5.632 54.398 1490 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.27 % Allowed : 20.99 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1330 helix: 1.37 (0.21), residues: 681 sheet: -0.36 (0.38), residues: 211 loop : -2.64 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.025 0.001 TYR B 273 PHE 0.018 0.001 PHE B 582 TRP 0.012 0.001 TRP B 279 HIS 0.004 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10097) covalent geometry : angle 0.53901 / 0.27 (13819) SS BOND : bond 0.00229 / 0.12 ( 5) SS BOND : angle 0.92799 / 0.51 ( 10) hydrogen bonds : bond 0.04572 / 3.11 ( 510) hydrogen bonds : angle 3.85817 / 2.71 ( 1512) link_BETA1-3 : bond 0.00725 / 0.38 ( 1) link_BETA1-3 : angle 3.18047 / 1.68 ( 3) link_BETA1-4 : bond 0.00355 / 0.19 ( 1) link_BETA1-4 : angle 0.82772 / 0.42 ( 3) link_NAG-ASN : bond 0.00257 / 0.13 ( 4) link_NAG-ASN : angle 2.13350 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.357 Fit side-chains REVERT: A 508 SER cc_start: 0.6394 (t) cc_final: 0.6045 (p) REVERT: B 163 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8506 (mp) REVERT: B 280 ILE cc_start: 0.8183 (mm) cc_final: 0.7916 (mt) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.0790 time to fit residues: 11.5408 Evaluate side-chains 91 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.154849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132038 restraints weight = 20110.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128102 restraints weight = 21861.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126180 restraints weight = 20414.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126224 restraints weight = 17601.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125840 restraints weight = 14714.560| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10108 Z= 0.132 Angle : 0.552 8.806 13847 Z= 0.274 Chirality : 0.042 0.191 1658 Planarity : 0.004 0.041 1716 Dihedral : 5.683 55.551 1490 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.61 % Allowed : 21.22 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1330 helix: 1.36 (0.21), residues: 681 sheet: -0.39 (0.38), residues: 207 loop : -2.61 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.023 0.001 TYR B 273 PHE 0.016 0.001 PHE B 582 TRP 0.013 0.001 TRP B 279 HIS 0.005 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10097) covalent geometry : angle 0.54643 / 0.27 (13819) SS BOND : bond 0.00228 / 0.12 ( 5) SS BOND : angle 0.97047 / 0.54 ( 10) hydrogen bonds : bond 0.04733 / 3.22 ( 510) hydrogen bonds : angle 3.90425 / 2.74 ( 1512) link_BETA1-3 : bond 0.00555 / 0.29 ( 1) link_BETA1-3 : angle 3.16764 / 1.68 ( 3) link_BETA1-4 : bond 0.00386 / 0.20 ( 1) link_BETA1-4 : angle 0.78371 / 0.40 ( 3) link_NAG-ASN : bond 0.00281 / 0.14 ( 4) link_NAG-ASN : angle 2.12966 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.373 Fit side-chains REVERT: A 508 SER cc_start: 0.6365 (OUTLIER) cc_final: 0.6073 (p) REVERT: B 163 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 280 ILE cc_start: 0.8154 (mm) cc_final: 0.7884 (mt) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 0.0727 time to fit residues: 10.9408 Evaluate side-chains 95 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 105 optimal weight: 0.0870 chunk 55 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 83 optimal weight: 0.0070 chunk 18 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.157471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137247 restraints weight = 18951.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135099 restraints weight = 26503.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133765 restraints weight = 22325.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.133597 restraints weight = 22004.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132961 restraints weight = 19157.703| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10108 Z= 0.102 Angle : 0.518 8.724 13847 Z= 0.255 Chirality : 0.041 0.190 1658 Planarity : 0.004 0.036 1716 Dihedral : 5.400 55.113 1490 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.50 % Allowed : 21.34 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.24), residues: 1330 helix: 1.52 (0.21), residues: 681 sheet: -0.18 (0.38), residues: 205 loop : -2.58 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.026 0.001 TYR B 663 PHE 0.016 0.001 PHE B 582 TRP 0.013 0.001 TRP B 279 HIS 0.003 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (10097) covalent geometry : angle 0.51243 / 0.25 (13819) SS BOND : bond 0.00142 / 0.08 ( 5) SS BOND : angle 0.76544 / 0.43 ( 10) hydrogen bonds : bond 0.04000 / 2.72 ( 510) hydrogen bonds : angle 3.78041 / 2.65 ( 1512) link_BETA1-3 : bond 0.00709 / 0.37 ( 1) link_BETA1-3 : angle 3.07059 / 1.62 ( 3) link_BETA1-4 : bond 0.00441 / 0.23 ( 1) link_BETA1-4 : angle 0.85138 / 0.43 ( 3) link_NAG-ASN : bond 0.00301 / 0.15 ( 4) link_NAG-ASN : angle 1.96682 / 1.08 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.286 Fit side-chains REVERT: A 508 SER cc_start: 0.6253 (t) cc_final: 0.6032 (p) REVERT: B 163 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8444 (mp) REVERT: B 280 ILE cc_start: 0.8165 (mm) cc_final: 0.7895 (mt) outliers start: 13 outliers final: 12 residues processed: 96 average time/residue: 0.0715 time to fit residues: 10.8543 Evaluate side-chains 96 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 127 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133857 restraints weight = 16276.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.130141 restraints weight = 19475.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127505 restraints weight = 20497.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126909 restraints weight = 22671.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126144 restraints weight = 18385.742| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10108 Z= 0.134 Angle : 0.548 8.436 13847 Z= 0.272 Chirality : 0.042 0.184 1658 Planarity : 0.004 0.041 1716 Dihedral : 5.436 55.316 1490 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.61 % Allowed : 21.34 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1330 helix: 1.46 (0.21), residues: 681 sheet: -0.37 (0.38), residues: 209 loop : -2.57 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.026 0.001 TYR B 663 PHE 0.016 0.001 PHE B 582 TRP 0.012 0.001 TRP B 279 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (10097) covalent geometry : angle 0.54305 / 0.27 (13819) SS BOND : bond 0.00237 / 0.12 ( 5) SS BOND : angle 1.00088 / 0.56 ( 10) hydrogen bonds : bond 0.04637 / 3.16 ( 510) hydrogen bonds : angle 3.86229 / 2.72 ( 1512) link_BETA1-3 : bond 0.00724 / 0.38 ( 1) link_BETA1-3 : angle 2.95542 / 1.57 ( 3) link_BETA1-4 : bond 0.00411 / 0.22 ( 1) link_BETA1-4 : angle 0.80552 / 0.42 ( 3) link_NAG-ASN : bond 0.00268 / 0.13 ( 4) link_NAG-ASN : angle 2.02944 / 1.12 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1981.03 seconds wall clock time: 34 minutes 39.17 seconds (2079.17 seconds total)