Starting phenix.real_space_refine on Mon Jul 28 10:08:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w2x_21533/07_2025/6w2x_21533.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w2x_21533/07_2025/6w2x_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w2x_21533/07_2025/6w2x_21533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w2x_21533/07_2025/6w2x_21533.map" model { file = "/net/cci-nas-00/data/ceres_data/6w2x_21533/07_2025/6w2x_21533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w2x_21533/07_2025/6w2x_21533.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 13} 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: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 13} 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: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 13, 'ASP:plan': 20, 'PHE:plan': 1, 'GLU:plan': 27, 'ARG:plan': 12} 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 dihedrals: 6 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 dihedrals: 6 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: 11 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: 9.34, per 1000 atoms: 0.95 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: 2.94 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.08 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: 3.17 Time building geometry restraints manager: 3.33 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 - 24.18: 5635 24.18 - 48.37: 273 48.37 - 72.55: 14 72.55 - 96.73: 2 96.73 - 120.92: 6 Dihedral angle restraints: 5930 sinusoidal: 2023 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 5927 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: 6.110 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.410 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 13.836 120.917 3395 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (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 TRP 0.006 0.001 TRP A 143 HIS 0.003 0.001 HIS A 685 PHE 0.013 0.001 PHE A 624 TYR 0.014 0.001 TYR B 171 ARG 0.004 0.000 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 4) link_NAG-ASN : angle 4.35505 ( 12) link_BETA1-4 : bond 0.00988 ( 1) link_BETA1-4 : angle 17.09346 ( 3) hydrogen bonds : bond 0.18158 ( 510) hydrogen bonds : angle 6.09670 ( 1512) SS BOND : bond 0.12088 ( 5) SS BOND : angle 5.15632 ( 10) link_BETA1-3 : bond 0.00905 ( 1) link_BETA1-3 : angle 18.45321 ( 3) covalent geometry : bond 0.00502 (10097) covalent geometry : angle 0.75166 (13819) *********************** 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 : 1.053 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: 0.2152 time to fit residues: 44.0930 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 : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 63 optimal weight: 0.1980 chunk 77 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS B 126 ASN B 150 ASN B 180 ASN B 278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.162965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146020 restraints weight = 17671.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142733 restraints weight = 22143.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142088 restraints weight = 22958.879| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10108 Z= 0.150 Angle : 0.627 8.784 13847 Z= 0.312 Chirality : 0.045 0.359 1658 Planarity : 0.005 0.058 1716 Dihedral : 9.121 103.308 1641 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.69 % Allowed : 10.15 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.23), residues: 1330 helix: 0.27 (0.21), residues: 670 sheet: -1.19 (0.38), residues: 213 loop : -3.39 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 279 HIS 0.005 0.001 HIS A 176 PHE 0.020 0.001 PHE A 329 TYR 0.023 0.002 TYR B 273 ARG 0.008 0.001 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 4) link_NAG-ASN : angle 3.67499 ( 12) link_BETA1-4 : bond 0.00064 ( 1) link_BETA1-4 : angle 0.79313 ( 3) hydrogen bonds : bond 0.05768 ( 510) hydrogen bonds : angle 4.40256 ( 1512) SS BOND : bond 0.01042 ( 5) SS BOND : angle 0.88450 ( 10) link_BETA1-3 : bond 0.00360 ( 1) link_BETA1-3 : angle 4.90878 ( 3) covalent geometry : bond 0.00323 (10097) covalent geometry : angle 0.61354 (13819) *********************** 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 96 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 1.084 Fit side-chains REVERT: A 664 LEU cc_start: 0.8331 (tp) cc_final: 0.7226 (mp) REVERT: B 91 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7890 (tt0) outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.1724 time to fit residues: 25.8446 Evaluate side-chains 82 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 116 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140757 restraints weight = 15335.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.136185 restraints weight = 19079.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133442 restraints weight = 19136.824| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10108 Z= 0.182 Angle : 0.644 9.360 13847 Z= 0.323 Chirality : 0.046 0.283 1658 Planarity : 0.005 0.053 1716 Dihedral : 8.017 75.971 1641 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.96 % Allowed : 14.53 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.24), residues: 1330 helix: 0.56 (0.21), residues: 678 sheet: -1.19 (0.36), residues: 227 loop : -3.16 (0.25), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 279 HIS 0.008 0.002 HIS A 176 PHE 0.022 0.002 PHE A 624 TYR 0.018 0.002 TYR B 268 ARG 0.012 0.001 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 4) link_NAG-ASN : angle 3.30601 ( 12) link_BETA1-4 : bond 0.00211 ( 1) link_BETA1-4 : angle 1.51012 ( 3) hydrogen bonds : bond 0.06161 ( 510) hydrogen bonds : angle 4.32455 ( 1512) SS BOND : bond 0.00301 ( 5) SS BOND : angle 1.24581 ( 10) link_BETA1-3 : bond 0.00630 ( 1) link_BETA1-3 : angle 3.88322 ( 3) covalent geometry : bond 0.00431 (10097) covalent geometry : angle 0.63306 (13819) *********************** 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 109 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.084 Fit side-chains REVERT: A 664 LEU cc_start: 0.8406 (tp) cc_final: 0.7271 (mp) outliers start: 17 outliers final: 10 residues processed: 104 average time/residue: 0.1824 time to fit residues: 29.3560 Evaluate side-chains 94 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU 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 333 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 669 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129353 restraints weight = 21488.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126903 restraints weight = 28089.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125360 restraints weight = 20804.849| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10108 Z= 0.192 Angle : 0.650 9.577 13847 Z= 0.326 Chirality : 0.045 0.246 1658 Planarity : 0.005 0.067 1716 Dihedral : 7.857 72.837 1641 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.77 % Allowed : 17.42 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.24), residues: 1330 helix: 0.64 (0.21), residues: 679 sheet: -1.08 (0.36), residues: 229 loop : -2.96 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 279 HIS 0.006 0.001 HIS A 176 PHE 0.027 0.002 PHE B 582 TYR 0.026 0.002 TYR B 273 ARG 0.010 0.001 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 4) link_NAG-ASN : angle 2.99264 ( 12) link_BETA1-4 : bond 0.00726 ( 1) link_BETA1-4 : angle 1.01482 ( 3) hydrogen bonds : bond 0.06074 ( 510) hydrogen bonds : angle 4.33417 ( 1512) SS BOND : bond 0.00346 ( 5) SS BOND : angle 1.18903 ( 10) link_BETA1-3 : bond 0.00670 ( 1) link_BETA1-3 : angle 3.91699 ( 3) covalent geometry : bond 0.00465 (10097) covalent geometry : angle 0.64085 (13819) *********************** 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 107 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 1.025 Fit side-chains REVERT: A 508 SER cc_start: 0.6681 (OUTLIER) cc_final: 0.6270 (p) REVERT: A 664 LEU cc_start: 0.8341 (tp) cc_final: 0.7300 (mp) REVERT: B 91 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7847 (tt0) outliers start: 24 outliers final: 19 residues processed: 101 average time/residue: 0.1599 time to fit residues: 25.9702 Evaluate side-chains 103 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 282 ASN Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 624 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 365 ILE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 692 ILE 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 62 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 0.0040 chunk 45 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 1 optimal weight: 0.0770 overall best weight: 0.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 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 = 0.3752 r_free = 0.3752 target = 0.154716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132384 restraints weight = 14397.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128523 restraints weight = 18344.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126232 restraints weight = 17952.194| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3681 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= 0.119 Angle : 0.550 7.567 13847 Z= 0.276 Chirality : 0.042 0.233 1658 Planarity : 0.004 0.046 1716 Dihedral : 7.313 69.270 1641 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.65 % Allowed : 18.22 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.24), residues: 1330 helix: 0.99 (0.21), residues: 679 sheet: -0.86 (0.36), residues: 228 loop : -2.74 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 279 HIS 0.004 0.001 HIS A 685 PHE 0.021 0.001 PHE B 582 TYR 0.024 0.001 TYR B 273 ARG 0.010 0.000 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 4) link_NAG-ASN : angle 2.66367 ( 12) link_BETA1-4 : bond 0.00432 ( 1) link_BETA1-4 : angle 1.00361 ( 3) hydrogen bonds : bond 0.04825 ( 510) hydrogen bonds : angle 4.03491 ( 1512) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.71033 ( 10) link_BETA1-3 : bond 0.00793 ( 1) link_BETA1-3 : angle 3.73935 ( 3) covalent geometry : bond 0.00259 (10097) covalent geometry : angle 0.54115 (13819) *********************** 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 107 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.998 Fit side-chains REVERT: A 508 SER cc_start: 0.6684 (OUTLIER) cc_final: 0.6272 (p) REVERT: B 91 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7697 (tt0) REVERT: B 449 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8216 (tt) outliers start: 23 outliers final: 15 residues processed: 102 average time/residue: 0.1913 time to fit residues: 30.8339 Evaluate side-chains 97 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130078 restraints weight = 14761.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126529 restraints weight = 20184.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124503 restraints weight = 21261.899| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10108 Z= 0.168 Angle : 0.604 8.712 13847 Z= 0.306 Chirality : 0.044 0.220 1658 Planarity : 0.004 0.046 1716 Dihedral : 7.377 69.481 1641 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.54 % Allowed : 19.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.24), residues: 1330 helix: 0.90 (0.21), residues: 678 sheet: -0.88 (0.36), residues: 229 loop : -2.86 (0.25), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 279 HIS 0.007 0.001 HIS A 176 PHE 0.020 0.002 PHE B 582 TYR 0.027 0.002 TYR B 273 ARG 0.008 0.001 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 4) link_NAG-ASN : angle 2.63692 ( 12) link_BETA1-4 : bond 0.00385 ( 1) link_BETA1-4 : angle 0.80099 ( 3) hydrogen bonds : bond 0.05687 ( 510) hydrogen bonds : angle 4.14186 ( 1512) SS BOND : bond 0.00316 ( 5) SS BOND : angle 1.09707 ( 10) link_BETA1-3 : bond 0.00743 ( 1) link_BETA1-3 : angle 3.56437 ( 3) covalent geometry : bond 0.00399 (10097) covalent geometry : angle 0.59637 (13819) *********************** 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 104 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.001 Fit side-chains REVERT: A 508 SER cc_start: 0.6827 (OUTLIER) cc_final: 0.6433 (p) REVERT: B 163 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8373 (mp) REVERT: B 449 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8206 (tt) outliers start: 22 outliers final: 15 residues processed: 100 average time/residue: 0.1682 time to fit residues: 26.5692 Evaluate side-chains 98 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 243 ARG Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 624 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 229 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 669 LEU 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 47 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 33 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133821 restraints weight = 22715.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131176 restraints weight = 26353.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130192 restraints weight = 17667.824| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10108 Z= 0.112 Angle : 0.543 13.322 13847 Z= 0.267 Chirality : 0.041 0.214 1658 Planarity : 0.004 0.038 1716 Dihedral : 6.974 71.314 1641 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.31 % Allowed : 19.38 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1330 helix: 1.18 (0.21), residues: 677 sheet: -0.65 (0.36), residues: 229 loop : -2.56 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 279 HIS 0.004 0.001 HIS A 685 PHE 0.016 0.001 PHE B 582 TYR 0.026 0.001 TYR B 273 ARG 0.009 0.000 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 4) link_NAG-ASN : angle 2.32927 ( 12) link_BETA1-4 : bond 0.00468 ( 1) link_BETA1-4 : angle 0.91675 ( 3) hydrogen bonds : bond 0.04330 ( 510) hydrogen bonds : angle 3.91444 ( 1512) SS BOND : bond 0.00156 ( 5) SS BOND : angle 0.69376 ( 10) link_BETA1-3 : bond 0.00772 ( 1) link_BETA1-3 : angle 3.39018 ( 3) covalent geometry : bond 0.00242 (10097) covalent geometry : angle 0.53628 (13819) *********************** 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 106 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.100 Fit side-chains REVERT: A 508 SER cc_start: 0.6461 (t) cc_final: 0.6149 (p) REVERT: B 280 ILE cc_start: 0.8226 (mm) cc_final: 0.7963 (mt) REVERT: B 449 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8145 (tt) outliers start: 20 outliers final: 16 residues processed: 104 average time/residue: 0.1714 time to fit residues: 28.1045 Evaluate side-chains 100 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 243 ARG Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 669 LEU 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 99 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.150014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130021 restraints weight = 17163.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126577 restraints weight = 19751.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124535 restraints weight = 22107.744| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10108 Z= 0.205 Angle : 0.651 11.157 13847 Z= 0.327 Chirality : 0.046 0.206 1658 Planarity : 0.005 0.048 1716 Dihedral : 7.404 76.239 1641 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.65 % Allowed : 19.95 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1330 helix: 0.92 (0.21), residues: 676 sheet: -0.76 (0.36), residues: 228 loop : -2.80 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 279 HIS 0.007 0.002 HIS A 176 PHE 0.018 0.002 PHE A 258 TYR 0.025 0.002 TYR B 663 ARG 0.008 0.001 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 4) link_NAG-ASN : angle 2.57599 ( 12) link_BETA1-4 : bond 0.00297 ( 1) link_BETA1-4 : angle 0.75522 ( 3) hydrogen bonds : bond 0.06222 ( 510) hydrogen bonds : angle 4.22746 ( 1512) SS BOND : bond 0.00329 ( 5) SS BOND : angle 1.32560 ( 10) link_BETA1-3 : bond 0.00706 ( 1) link_BETA1-3 : angle 3.34004 ( 3) covalent geometry : bond 0.00503 (10097) covalent geometry : angle 0.64383 (13819) *********************** 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 107 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 508 SER cc_start: 0.6724 (OUTLIER) cc_final: 0.6401 (p) REVERT: B 449 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8137 (tt) REVERT: B 581 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6747 (mt) REVERT: B 608 ASP cc_start: 0.7846 (m-30) cc_final: 0.7600 (m-30) outliers start: 23 outliers final: 19 residues processed: 103 average time/residue: 0.1640 time to fit residues: 26.7657 Evaluate side-chains 106 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 243 ARG Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 669 LEU 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 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 121 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133187 restraints weight = 22962.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129458 restraints weight = 26885.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128374 restraints weight = 22929.279| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4333 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= 0.122 Angle : 0.548 10.651 13847 Z= 0.272 Chirality : 0.042 0.204 1658 Planarity : 0.004 0.038 1716 Dihedral : 6.961 78.062 1641 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.19 % Allowed : 20.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1330 helix: 1.18 (0.21), residues: 676 sheet: -0.55 (0.37), residues: 228 loop : -2.52 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 279 HIS 0.004 0.001 HIS A 685 PHE 0.016 0.001 PHE B 582 TYR 0.026 0.001 TYR B 273 ARG 0.005 0.000 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 4) link_NAG-ASN : angle 2.29281 ( 12) link_BETA1-4 : bond 0.00382 ( 1) link_BETA1-4 : angle 0.84341 ( 3) hydrogen bonds : bond 0.04662 ( 510) hydrogen bonds : angle 3.97992 ( 1512) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.81431 ( 10) link_BETA1-3 : bond 0.00725 ( 1) link_BETA1-3 : angle 3.31903 ( 3) covalent geometry : bond 0.00275 (10097) covalent geometry : angle 0.54130 (13819) *********************** 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 105 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 1.000 Fit side-chains REVERT: A 508 SER cc_start: 0.6461 (OUTLIER) cc_final: 0.6216 (p) REVERT: B 280 ILE cc_start: 0.8213 (mm) cc_final: 0.7934 (mt) REVERT: B 449 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8123 (tt) outliers start: 19 outliers final: 17 residues processed: 102 average time/residue: 0.1885 time to fit residues: 30.0405 Evaluate side-chains 104 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 243 ARG Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 669 LEU 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 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.0040 chunk 9 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 0.0370 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.2870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.157930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140025 restraints weight = 21735.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137728 restraints weight = 28329.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135849 restraints weight = 25346.971| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10108 Z= 0.099 Angle : 0.522 10.187 13847 Z= 0.258 Chirality : 0.041 0.203 1658 Planarity : 0.004 0.037 1716 Dihedral : 6.574 80.035 1641 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.42 % Allowed : 20.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1330 helix: 1.39 (0.22), residues: 675 sheet: -0.29 (0.37), residues: 224 loop : -2.42 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 279 HIS 0.003 0.001 HIS A 685 PHE 0.016 0.001 PHE B 582 TYR 0.028 0.001 TYR B 663 ARG 0.005 0.000 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 4) link_NAG-ASN : angle 2.08452 ( 12) link_BETA1-4 : bond 0.00400 ( 1) link_BETA1-4 : angle 0.85781 ( 3) hydrogen bonds : bond 0.03894 ( 510) hydrogen bonds : angle 3.81449 ( 1512) SS BOND : bond 0.00121 ( 5) SS BOND : angle 0.67588 ( 10) link_BETA1-3 : bond 0.00654 ( 1) link_BETA1-3 : angle 3.11083 ( 3) covalent geometry : bond 0.00205 (10097) covalent geometry : angle 0.51607 (13819) ********************** 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 108 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.078 Fit side-chains REVERT: B 280 ILE cc_start: 0.8168 (mm) cc_final: 0.7882 (mt) outliers start: 21 outliers final: 19 residues processed: 105 average time/residue: 0.1780 time to fit residues: 29.4798 Evaluate side-chains 100 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 243 ARG Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 669 LEU 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 32 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134822 restraints weight = 17840.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132082 restraints weight = 24553.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130795 restraints weight = 23334.903| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4482 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= 0.136 Angle : 0.563 9.486 13847 Z= 0.280 Chirality : 0.043 0.197 1658 Planarity : 0.004 0.042 1716 Dihedral : 6.631 83.453 1641 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.08 % Allowed : 20.99 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1330 helix: 1.36 (0.21), residues: 673 sheet: -0.47 (0.37), residues: 230 loop : -2.43 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 279 HIS 0.005 0.001 HIS A 176 PHE 0.016 0.001 PHE B 582 TYR 0.026 0.001 TYR B 273 ARG 0.004 0.000 ARG A 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 4) link_NAG-ASN : angle 2.11678 ( 12) link_BETA1-4 : bond 0.00408 ( 1) link_BETA1-4 : angle 0.82299 ( 3) hydrogen bonds : bond 0.04733 ( 510) hydrogen bonds : angle 3.92267 ( 1512) SS BOND : bond 0.00228 ( 5) SS BOND : angle 0.96743 ( 10) link_BETA1-3 : bond 0.00665 ( 1) link_BETA1-3 : angle 3.01499 ( 3) covalent geometry : bond 0.00318 (10097) covalent geometry : angle 0.55782 (13819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4154.28 seconds wall clock time: 73 minutes 39.99 seconds (4419.99 seconds total)