Starting phenix.real_space_refine on Wed Mar 4 02:17:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uo9_20823/03_2026/6uo9_20823.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uo9_20823/03_2026/6uo9_20823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uo9_20823/03_2026/6uo9_20823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uo9_20823/03_2026/6uo9_20823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uo9_20823/03_2026/6uo9_20823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uo9_20823/03_2026/6uo9_20823.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 33 5.16 5 C 6262 2.51 5 N 1715 2.21 5 O 1904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9915 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 4822 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 646} Chain breaks: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 759 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'PHE:plan': 11, 'GLN:plan1': 7, 'ASN:plan1': 10, 'HIS:plan': 3, 'ARG:plan': 5, 'TYR:plan': 5, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 261 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 4906 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 28, 'TRANS': 661} Chain breaks: 1 Unresolved non-hydrogen bonds: 602 Unresolved non-hydrogen angles: 774 Unresolved non-hydrogen dihedrals: 495 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'ARG:plan': 7, 'TYR:plan': 5, 'PHE:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 239 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'QD7': 1} Classifications: {'undetermined': 1} Chain: "B" 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 Time building chain proxies: 2.54, per 1000 atoms: 0.26 Number of scatterers: 9915 At special positions: 0 Unit cell: (86.9142, 119.294, 167.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 1 15.00 O 1904 8.00 N 1715 7.00 C 6262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.05 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.05 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.05 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.04 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B1001 " - " ASN B 298 " " NAG B1002 " - " ASN B 453 " " NAG C 1 " - " ASN A 409 " " NAG D 1 " - " ASN A 514 " " NAG E 1 " - " ASN A 482 " " NAG F 1 " - " ASN A 440 " " NAG G 1 " - " ASN B 404 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 492.3 milliseconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2558 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 52.5% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 184 through 200 Proline residue: A 190 - end of helix removed outlier: 4.463A pdb=" N GLU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP A 198 " --> pdb=" O MET A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.758A pdb=" N ASN A 276 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 removed outlier: 3.921A pdb=" N LEU A 292 " --> pdb=" O SER A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.552A pdb=" N VAL A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 330 removed outlier: 3.779A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 367 through 380 removed outlier: 4.400A pdb=" N GLU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.950A pdb=" N PHE A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 485 removed outlier: 3.958A pdb=" N ALA A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.769A pdb=" N SER A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.937A pdb=" N GLY A 571 " --> pdb=" O TRP A 568 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 572' Processing helix chain 'A' and resid 589 through 616 removed outlier: 3.825A pdb=" N SER A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 642 removed outlier: 3.518A pdb=" N THR A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.512A pdb=" N LEU A 649 " --> pdb=" O PHE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 691 removed outlier: 3.549A pdb=" N PHE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 675 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 731 removed outlier: 3.841A pdb=" N ALA A 712 " --> pdb=" O TRP A 708 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 790 removed outlier: 3.552A pdb=" N LEU A 780 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 Proline residue: A 821 - end of helix removed outlier: 3.906A pdb=" N MET A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 853 removed outlier: 3.553A pdb=" N ALA A 837 " --> pdb=" O ALA A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 860 Processing helix chain 'B' and resid 71 through 92 Proline residue: B 79 - end of helix removed outlier: 4.205A pdb=" N GLU B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.748A pdb=" N LEU B 163 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 191 removed outlier: 3.606A pdb=" N LEU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 219 removed outlier: 3.954A pdb=" N ARG B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 259 through 270 removed outlier: 3.573A pdb=" N GLU B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.534A pdb=" N VAL B 293 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 344 Processing helix chain 'B' and resid 354 through 374 removed outlier: 3.646A pdb=" N ALA B 358 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 385 Processing helix chain 'B' and resid 392 through 405 removed outlier: 3.541A pdb=" N GLY B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 506 Processing helix chain 'B' and resid 509 through 513 removed outlier: 3.552A pdb=" N LYS B 513 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 538 removed outlier: 3.782A pdb=" N ASN B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 582 removed outlier: 3.832A pdb=" N CYS B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 619 Processing helix chain 'B' and resid 654 through 678 Processing helix chain 'B' and resid 690 through 713 Processing helix chain 'B' and resid 719 through 750 Proline residue: B 742 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 217 removed outlier: 4.232A pdb=" N ILE A 241 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.490A pdb=" N ILE A 309 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 339 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N PHE A 343 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLN A 313 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.490A pdb=" N ILE A 309 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 339 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LYS A 308 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL A 363 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 310 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU A 365 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 312 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE A 393 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP A 390 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR A 425 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A 392 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N HIS A 422 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 542 " --> pdb=" O HIS A 422 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR A 537 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR A 552 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 583 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105 removed outlier: 5.952A pdb=" N LEU B 56 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ARG B 102 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE B 58 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TYR B 104 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY B 60 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N MET B 129 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N SER B 57 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N PHE B 131 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N MET B 59 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N LEU B 154 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 130 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN B 153 " --> pdb=" O PHE B 173 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 225 through 231 removed outlier: 7.829A pdb=" N VAL B 198 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR B 229 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR B 200 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER B 231 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR B 202 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE B 250 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 426 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU B 441 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE B 428 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 416 through 418 removed outlier: 4.792A pdb=" N VAL B 416 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 470 through 473 removed outlier: 6.390A pdb=" N LEU B 471 " --> pdb=" O ARG B 642 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B 644 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN B 473 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N GLU B 646 " --> pdb=" O GLN B 473 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3275 1.34 - 1.48: 2635 1.48 - 1.61: 4160 1.61 - 1.75: 0 1.75 - 1.88: 53 Bond restraints: 10123 Sorted by residual: bond pdb=" C PHE A 659 " pdb=" N PRO A 660 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.28e-02 6.10e+03 1.99e+01 bond pdb=" C ALA A 820 " pdb=" N PRO A 821 " ideal model delta sigma weight residual 1.337 1.367 -0.031 9.80e-03 1.04e+04 9.83e+00 bond pdb=" CAG QD7 A1001 " pdb=" PAE QD7 A1001 " ideal model delta sigma weight residual 1.830 1.777 0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.86e+00 ... (remaining 10118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 13535 3.96 - 7.93: 241 7.93 - 11.89: 22 11.89 - 15.85: 7 15.85 - 19.81: 5 Bond angle restraints: 13810 Sorted by residual: angle pdb=" N LYS A 709 " pdb=" CA LYS A 709 " pdb=" C LYS A 709 " ideal model delta sigma weight residual 110.97 122.99 -12.02 1.09e+00 8.42e-01 1.22e+02 angle pdb=" CA CYS B 108 " pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " ideal model delta sigma weight residual 114.40 130.97 -16.57 2.30e+00 1.89e-01 5.19e+01 angle pdb=" C PRO B 236 " pdb=" N CYS B 237 " pdb=" CA CYS B 237 " ideal model delta sigma weight residual 122.83 113.04 9.79 1.54e+00 4.22e-01 4.04e+01 angle pdb=" N PHE B 431 " pdb=" CA PHE B 431 " pdb=" C PHE B 431 " ideal model delta sigma weight residual 108.41 118.20 -9.79 1.61e+00 3.86e-01 3.70e+01 angle pdb=" CA CYS A 246 " pdb=" CB CYS A 246 " pdb=" SG CYS A 246 " ideal model delta sigma weight residual 114.40 128.36 -13.96 2.30e+00 1.89e-01 3.68e+01 ... (remaining 13805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 5725 20.80 - 41.60: 374 41.60 - 62.40: 57 62.40 - 83.20: 14 83.20 - 104.00: 5 Dihedral angle restraints: 6175 sinusoidal: 2212 harmonic: 3963 Sorted by residual: dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N ASN B 298 " pdb=" CA ASN B 298 " ideal model delta harmonic sigma weight residual 180.00 137.22 42.78 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual 93.00 17.94 75.06 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual 93.00 27.09 65.91 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 6172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1354 0.092 - 0.183: 206 0.183 - 0.275: 32 0.275 - 0.366: 5 0.366 - 0.458: 1 Chirality restraints: 1598 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.20e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 482 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.49e+00 ... (remaining 1595 not shown) Planarity restraints: 1809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 237 " 0.039 2.00e-02 2.50e+03 7.98e-02 6.37e+01 pdb=" C CYS B 237 " -0.138 2.00e-02 2.50e+03 pdb=" O CYS B 237 " 0.051 2.00e-02 2.50e+03 pdb=" N THR B 238 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 87 " 0.033 2.00e-02 2.50e+03 6.59e-02 4.35e+01 pdb=" C GLN B 87 " -0.114 2.00e-02 2.50e+03 pdb=" O GLN B 87 " 0.043 2.00e-02 2.50e+03 pdb=" N ILE B 88 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 382 " -0.032 2.00e-02 2.50e+03 6.40e-02 4.10e+01 pdb=" C HIS B 382 " 0.111 2.00e-02 2.50e+03 pdb=" O HIS B 382 " -0.042 2.00e-02 2.50e+03 pdb=" N GLN B 383 " -0.037 2.00e-02 2.50e+03 ... (remaining 1806 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1840 2.76 - 3.30: 9558 3.30 - 3.83: 16005 3.83 - 4.37: 16805 4.37 - 4.90: 28476 Nonbonded interactions: 72684 Sorted by model distance: nonbonded pdb=" OG1 THR A 291 " pdb=" OD2 ASP A 325 " model vdw 2.227 3.040 nonbonded pdb=" O HIS B 377 " pdb=" NE ARG B 381 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR B 468 " pdb=" O ASP B 638 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A 411 " pdb=" OE1 GLU A 414 " model vdw 2.251 3.040 nonbonded pdb=" NH1 ARG B 422 " pdb=" O MET B 423 " model vdw 2.262 3.120 ... (remaining 72679 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' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.040 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 0.071 10143 Z= 0.336 Angle : 1.445 19.815 13863 Z= 0.813 Chirality : 0.070 0.458 1598 Planarity : 0.009 0.080 1802 Dihedral : 14.281 104.005 3596 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.07 % Allowed : 9.50 % Favored : 89.43 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.19), residues: 1355 helix: -1.79 (0.16), residues: 696 sheet: -1.53 (0.37), residues: 189 loop : -3.96 (0.20), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 422 TYR 0.055 0.003 TYR B 697 PHE 0.025 0.003 PHE B 173 TRP 0.038 0.003 TRP A 304 HIS 0.009 0.002 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00628 (10123) covalent geometry : angle 1.37996 (13810) SS BOND : bond 0.01662 ( 7) SS BOND : angle 5.03992 ( 14) hydrogen bonds : bond 0.12441 ( 527) hydrogen bonds : angle 6.31651 ( 1554) link_BETA1-4 : bond 0.02277 ( 6) link_BETA1-4 : angle 8.55473 ( 18) link_NAG-ASN : bond 0.01044 ( 7) link_NAG-ASN : angle 6.86239 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9547 (pt) cc_final: 0.9285 (pt) REVERT: A 243 MET cc_start: 0.8854 (mmm) cc_final: 0.8528 (mmm) REVERT: A 370 GLU cc_start: 0.9649 (mp0) cc_final: 0.9353 (mp0) REVERT: A 513 MET cc_start: 0.9412 (ptp) cc_final: 0.8880 (ptp) REVERT: A 668 TRP cc_start: 0.6383 (m-10) cc_final: 0.5744 (m-10) REVERT: B 59 MET cc_start: 0.8739 (mtm) cc_final: 0.8302 (mmm) REVERT: B 169 TYR cc_start: 0.8797 (m-80) cc_final: 0.8367 (m-10) REVERT: B 272 MET cc_start: 0.9114 (tpp) cc_final: 0.8733 (mmp) REVERT: B 311 MET cc_start: 0.9081 (ptt) cc_final: 0.8858 (ppp) REVERT: B 373 MET cc_start: 0.9515 (ttp) cc_final: 0.9195 (tmm) outliers start: 9 outliers final: 3 residues processed: 118 average time/residue: 0.0902 time to fit residues: 15.7224 Evaluate side-chains 83 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 314 GLN A 457 HIS B 206 GLN B 278 GLN B 326 GLN B 382 HIS B 393 HIS B 716 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.054160 restraints weight = 95986.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.055343 restraints weight = 54567.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056194 restraints weight = 33005.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056503 restraints weight = 23420.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056688 restraints weight = 20335.738| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10143 Z= 0.133 Angle : 0.771 12.627 13863 Z= 0.375 Chirality : 0.047 0.254 1598 Planarity : 0.005 0.052 1802 Dihedral : 7.582 63.542 1731 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.36 % Allowed : 5.46 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.22), residues: 1355 helix: -0.09 (0.19), residues: 701 sheet: -1.03 (0.38), residues: 190 loop : -3.45 (0.23), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.023 0.002 TYR B 285 PHE 0.034 0.001 PHE A 446 TRP 0.016 0.001 TRP A 304 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00267 (10123) covalent geometry : angle 0.71487 (13810) SS BOND : bond 0.00759 ( 7) SS BOND : angle 3.61958 ( 14) hydrogen bonds : bond 0.04260 ( 527) hydrogen bonds : angle 4.71214 ( 1554) link_BETA1-4 : bond 0.01432 ( 6) link_BETA1-4 : angle 5.76552 ( 18) link_NAG-ASN : bond 0.00573 ( 7) link_NAG-ASN : angle 4.42232 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8891 (mmm) cc_final: 0.8461 (mmm) REVERT: A 668 TRP cc_start: 0.6329 (m-10) cc_final: 0.5645 (m-10) REVERT: B 240 VAL cc_start: 0.9230 (t) cc_final: 0.8998 (t) REVERT: B 259 MET cc_start: 0.9468 (mmp) cc_final: 0.8841 (mmm) REVERT: B 272 MET cc_start: 0.9189 (tpp) cc_final: 0.8841 (mmm) REVERT: B 311 MET cc_start: 0.9195 (ptt) cc_final: 0.8787 (ppp) REVERT: B 373 MET cc_start: 0.9589 (ttp) cc_final: 0.9208 (tmm) outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 0.0721 time to fit residues: 11.2278 Evaluate side-chains 73 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 5.9990 chunk 54 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 132 optimal weight: 0.2980 chunk 46 optimal weight: 6.9990 chunk 113 optimal weight: 0.0470 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 overall best weight: 0.6294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.063471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054468 restraints weight = 94081.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.055600 restraints weight = 56218.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056387 restraints weight = 37831.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.056949 restraints weight = 27833.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.057277 restraints weight = 21816.976| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10143 Z= 0.120 Angle : 0.746 12.363 13863 Z= 0.355 Chirality : 0.047 0.299 1598 Planarity : 0.004 0.049 1802 Dihedral : 6.624 56.498 1731 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.23), residues: 1355 helix: 0.59 (0.20), residues: 702 sheet: -0.78 (0.37), residues: 191 loop : -3.27 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.018 0.001 TYR B 697 PHE 0.029 0.001 PHE A 446 TRP 0.024 0.001 TRP A 390 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00237 (10123) covalent geometry : angle 0.68406 (13810) SS BOND : bond 0.00628 ( 7) SS BOND : angle 3.94051 ( 14) hydrogen bonds : bond 0.03899 ( 527) hydrogen bonds : angle 4.32486 ( 1554) link_BETA1-4 : bond 0.01578 ( 6) link_BETA1-4 : angle 5.71880 ( 18) link_NAG-ASN : bond 0.00666 ( 7) link_NAG-ASN : angle 4.61397 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8999 (mmm) cc_final: 0.8655 (mmm) REVERT: A 390 TRP cc_start: 0.8685 (m100) cc_final: 0.8369 (m100) REVERT: A 668 TRP cc_start: 0.6333 (m-10) cc_final: 0.5694 (m-10) REVERT: B 146 LEU cc_start: 0.9192 (tp) cc_final: 0.8966 (tp) REVERT: B 272 MET cc_start: 0.9298 (tpp) cc_final: 0.8995 (mmm) REVERT: B 373 MET cc_start: 0.9649 (ttp) cc_final: 0.9290 (tmm) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.0709 time to fit residues: 10.5307 Evaluate side-chains 72 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 88 optimal weight: 0.1980 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 26 optimal weight: 0.0980 chunk 7 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN A 653 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050471 restraints weight = 98621.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051570 restraints weight = 59147.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052323 restraints weight = 40212.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052851 restraints weight = 29952.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.053216 restraints weight = 23841.328| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10143 Z= 0.168 Angle : 0.737 11.059 13863 Z= 0.362 Chirality : 0.045 0.255 1598 Planarity : 0.004 0.049 1802 Dihedral : 6.209 57.995 1731 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1355 helix: 1.22 (0.20), residues: 697 sheet: -0.83 (0.36), residues: 204 loop : -3.01 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 167 TYR 0.025 0.002 TYR B 193 PHE 0.028 0.002 PHE A 446 TRP 0.013 0.002 TRP A 395 HIS 0.006 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00345 (10123) covalent geometry : angle 0.68971 (13810) SS BOND : bond 0.00538 ( 7) SS BOND : angle 2.77197 ( 14) hydrogen bonds : bond 0.03602 ( 527) hydrogen bonds : angle 4.23115 ( 1554) link_BETA1-4 : bond 0.01343 ( 6) link_BETA1-4 : angle 5.40164 ( 18) link_NAG-ASN : bond 0.00454 ( 7) link_NAG-ASN : angle 3.89989 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9601 (pt) cc_final: 0.9388 (pp) REVERT: A 243 MET cc_start: 0.8934 (mmm) cc_final: 0.8570 (mmm) REVERT: A 390 TRP cc_start: 0.8808 (m100) cc_final: 0.8444 (m100) REVERT: A 509 ILE cc_start: 0.9720 (tp) cc_final: 0.9507 (pt) REVERT: B 172 PHE cc_start: 0.8599 (t80) cc_final: 0.8328 (t80) REVERT: B 272 MET cc_start: 0.9270 (tpp) cc_final: 0.9046 (mmm) REVERT: B 311 MET cc_start: 0.9104 (ppp) cc_final: 0.8239 (ppp) REVERT: B 373 MET cc_start: 0.9660 (ttp) cc_final: 0.9328 (tmm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0822 time to fit residues: 10.4972 Evaluate side-chains 66 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.061486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052489 restraints weight = 96727.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.053618 restraints weight = 57828.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.054391 restraints weight = 39061.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.054940 restraints weight = 28775.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055301 restraints weight = 22633.333| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10143 Z= 0.109 Angle : 0.702 10.446 13863 Z= 0.333 Chirality : 0.045 0.252 1598 Planarity : 0.004 0.049 1802 Dihedral : 5.676 56.759 1731 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.23), residues: 1355 helix: 1.47 (0.20), residues: 701 sheet: -0.78 (0.35), residues: 211 loop : -2.96 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.023 0.001 TYR B 697 PHE 0.024 0.001 PHE A 446 TRP 0.013 0.001 TRP A 390 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00223 (10123) covalent geometry : angle 0.65318 (13810) SS BOND : bond 0.00704 ( 7) SS BOND : angle 3.31937 ( 14) hydrogen bonds : bond 0.03322 ( 527) hydrogen bonds : angle 3.95618 ( 1554) link_BETA1-4 : bond 0.01522 ( 6) link_BETA1-4 : angle 5.24538 ( 18) link_NAG-ASN : bond 0.00529 ( 7) link_NAG-ASN : angle 3.73574 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9601 (pt) cc_final: 0.9357 (pp) REVERT: A 243 MET cc_start: 0.8922 (mmm) cc_final: 0.8596 (mmm) REVERT: A 390 TRP cc_start: 0.8824 (m100) cc_final: 0.8526 (m100) REVERT: A 509 ILE cc_start: 0.9694 (tp) cc_final: 0.9486 (pt) REVERT: B 144 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8042 (tm-30) REVERT: B 272 MET cc_start: 0.9264 (tpp) cc_final: 0.8943 (mmm) REVERT: B 311 MET cc_start: 0.9116 (ppp) cc_final: 0.8123 (ppp) REVERT: B 373 MET cc_start: 0.9653 (ttp) cc_final: 0.9320 (tmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0724 time to fit residues: 10.3379 Evaluate side-chains 71 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.056435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047533 restraints weight = 101205.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048571 restraints weight = 61654.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049296 restraints weight = 42276.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049791 restraints weight = 31795.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050168 restraints weight = 25635.272| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10143 Z= 0.231 Angle : 0.784 10.032 13863 Z= 0.393 Chirality : 0.047 0.238 1598 Planarity : 0.004 0.047 1802 Dihedral : 6.197 58.919 1731 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.23), residues: 1355 helix: 1.52 (0.20), residues: 698 sheet: -0.74 (0.33), residues: 208 loop : -2.81 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 167 TYR 0.019 0.002 TYR B 697 PHE 0.026 0.002 PHE A 401 TRP 0.016 0.002 TRP A 395 HIS 0.009 0.002 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00471 (10123) covalent geometry : angle 0.74471 (13810) SS BOND : bond 0.00604 ( 7) SS BOND : angle 2.95914 ( 14) hydrogen bonds : bond 0.03782 ( 527) hydrogen bonds : angle 4.34292 ( 1554) link_BETA1-4 : bond 0.01271 ( 6) link_BETA1-4 : angle 5.07472 ( 18) link_NAG-ASN : bond 0.00362 ( 7) link_NAG-ASN : angle 3.66973 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8867 (mmm) cc_final: 0.8576 (mmm) REVERT: A 390 TRP cc_start: 0.8901 (m100) cc_final: 0.8612 (m100) REVERT: B 171 TYR cc_start: 0.9142 (m-10) cc_final: 0.8917 (m-80) REVERT: B 172 PHE cc_start: 0.8591 (t80) cc_final: 0.8264 (t80) REVERT: B 272 MET cc_start: 0.9221 (tpp) cc_final: 0.8445 (mmm) REVERT: B 311 MET cc_start: 0.9086 (ppp) cc_final: 0.7983 (ppp) REVERT: B 373 MET cc_start: 0.9629 (ttp) cc_final: 0.9386 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0739 time to fit residues: 8.6397 Evaluate side-chains 63 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048483 restraints weight = 99691.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049535 restraints weight = 60474.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050268 restraints weight = 41556.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.050773 restraints weight = 31149.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051158 restraints weight = 24991.690| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10143 Z= 0.157 Angle : 0.716 9.544 13863 Z= 0.349 Chirality : 0.046 0.233 1598 Planarity : 0.004 0.051 1802 Dihedral : 5.947 57.484 1731 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1355 helix: 1.77 (0.20), residues: 694 sheet: -0.61 (0.34), residues: 206 loop : -2.78 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.017 0.001 TYR B 193 PHE 0.020 0.001 PHE A 446 TRP 0.010 0.001 TRP B 290 HIS 0.004 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00326 (10123) covalent geometry : angle 0.67376 (13810) SS BOND : bond 0.00640 ( 7) SS BOND : angle 2.98225 ( 14) hydrogen bonds : bond 0.03494 ( 527) hydrogen bonds : angle 4.12870 ( 1554) link_BETA1-4 : bond 0.01382 ( 6) link_BETA1-4 : angle 4.90826 ( 18) link_NAG-ASN : bond 0.00424 ( 7) link_NAG-ASN : angle 3.60184 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8848 (mmm) cc_final: 0.8449 (mmm) REVERT: A 390 TRP cc_start: 0.8965 (m100) cc_final: 0.8666 (m100) REVERT: B 172 PHE cc_start: 0.8579 (t80) cc_final: 0.8231 (t80) REVERT: B 272 MET cc_start: 0.9219 (tpp) cc_final: 0.8462 (mmm) REVERT: B 311 MET cc_start: 0.8989 (ppp) cc_final: 0.8669 (ppp) REVERT: B 373 MET cc_start: 0.9635 (ttp) cc_final: 0.9402 (tpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0726 time to fit residues: 8.9669 Evaluate side-chains 64 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 77 optimal weight: 0.0670 chunk 49 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 overall best weight: 1.7722 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.058345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.049982 restraints weight = 97403.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051000 restraints weight = 56006.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051538 restraints weight = 35551.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052081 restraints weight = 28044.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052269 restraints weight = 22663.403| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10143 Z= 0.122 Angle : 0.684 9.546 13863 Z= 0.330 Chirality : 0.045 0.230 1598 Planarity : 0.004 0.049 1802 Dihedral : 5.664 57.263 1731 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1355 helix: 1.88 (0.20), residues: 697 sheet: -0.45 (0.34), residues: 205 loop : -2.67 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 372 TYR 0.016 0.001 TYR A 615 PHE 0.018 0.001 PHE A 446 TRP 0.009 0.001 TRP B 558 HIS 0.003 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00254 (10123) covalent geometry : angle 0.64266 (13810) SS BOND : bond 0.00518 ( 7) SS BOND : angle 2.93541 ( 14) hydrogen bonds : bond 0.03369 ( 527) hydrogen bonds : angle 4.00526 ( 1554) link_BETA1-4 : bond 0.01394 ( 6) link_BETA1-4 : angle 4.85529 ( 18) link_NAG-ASN : bond 0.00454 ( 7) link_NAG-ASN : angle 3.36120 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8848 (mmm) cc_final: 0.8525 (mmm) REVERT: A 375 PHE cc_start: 0.9029 (m-10) cc_final: 0.8465 (m-80) REVERT: A 390 TRP cc_start: 0.8963 (m100) cc_final: 0.8669 (m100) REVERT: B 129 MET cc_start: 0.9597 (tpp) cc_final: 0.9309 (tpp) REVERT: B 171 TYR cc_start: 0.9059 (m-80) cc_final: 0.8702 (m-80) REVERT: B 272 MET cc_start: 0.9238 (tpp) cc_final: 0.8931 (mmt) REVERT: B 311 MET cc_start: 0.8848 (ppp) cc_final: 0.8501 (ppp) REVERT: B 373 MET cc_start: 0.9646 (ttp) cc_final: 0.9418 (tpp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0721 time to fit residues: 9.1331 Evaluate side-chains 67 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 0.9980 chunk 120 optimal weight: 30.0000 chunk 109 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 HIS B 127 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.057108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.048952 restraints weight = 99290.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049745 restraints weight = 57662.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050366 restraints weight = 38060.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050936 restraints weight = 29550.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051117 restraints weight = 23721.300| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10143 Z= 0.151 Angle : 0.720 11.377 13863 Z= 0.348 Chirality : 0.046 0.235 1598 Planarity : 0.004 0.049 1802 Dihedral : 6.537 59.681 1731 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1355 helix: 1.90 (0.20), residues: 698 sheet: -0.45 (0.35), residues: 204 loop : -2.68 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.024 0.001 TYR B 697 PHE 0.017 0.001 PHE A 446 TRP 0.011 0.001 TRP A 400 HIS 0.006 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00314 (10123) covalent geometry : angle 0.67885 (13810) SS BOND : bond 0.00773 ( 7) SS BOND : angle 2.96134 ( 14) hydrogen bonds : bond 0.03413 ( 527) hydrogen bonds : angle 4.14410 ( 1554) link_BETA1-4 : bond 0.01338 ( 6) link_BETA1-4 : angle 4.77443 ( 18) link_NAG-ASN : bond 0.00460 ( 7) link_NAG-ASN : angle 3.75640 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8773 (mmm) cc_final: 0.8372 (mmm) REVERT: A 375 PHE cc_start: 0.9059 (m-10) cc_final: 0.8543 (m-80) REVERT: A 390 TRP cc_start: 0.8958 (m100) cc_final: 0.8660 (m100) REVERT: B 171 TYR cc_start: 0.9137 (m-80) cc_final: 0.8795 (m-80) REVERT: B 272 MET cc_start: 0.9236 (tpp) cc_final: 0.8467 (mmm) REVERT: B 311 MET cc_start: 0.8817 (ppp) cc_final: 0.8488 (ppp) REVERT: B 373 MET cc_start: 0.9613 (ttp) cc_final: 0.9402 (tpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0674 time to fit residues: 8.3022 Evaluate side-chains 64 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 120 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.037510 restraints weight = 87695.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.038531 restraints weight = 58760.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.039250 restraints weight = 43608.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.039768 restraints weight = 35007.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.040128 restraints weight = 29623.057| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10143 Z= 0.201 Angle : 0.773 9.681 13863 Z= 0.382 Chirality : 0.046 0.237 1598 Planarity : 0.004 0.050 1802 Dihedral : 6.403 58.431 1731 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.24), residues: 1355 helix: 1.79 (0.20), residues: 695 sheet: -0.48 (0.36), residues: 201 loop : -2.73 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 167 TYR 0.019 0.002 TYR A 615 PHE 0.021 0.002 PHE A 366 TRP 0.016 0.002 TRP B 149 HIS 0.006 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00418 (10123) covalent geometry : angle 0.73047 (13810) SS BOND : bond 0.00658 ( 7) SS BOND : angle 3.21403 ( 14) hydrogen bonds : bond 0.03714 ( 527) hydrogen bonds : angle 4.37050 ( 1554) link_BETA1-4 : bond 0.01272 ( 6) link_BETA1-4 : angle 4.75845 ( 18) link_NAG-ASN : bond 0.00455 ( 7) link_NAG-ASN : angle 4.19726 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8834 (mmm) cc_final: 0.8466 (mmm) REVERT: B 129 MET cc_start: 0.9514 (tpp) cc_final: 0.9227 (tpp) REVERT: B 172 PHE cc_start: 0.8455 (t80) cc_final: 0.8110 (t80) REVERT: B 272 MET cc_start: 0.9155 (tpp) cc_final: 0.8438 (mmm) REVERT: B 311 MET cc_start: 0.8703 (ppp) cc_final: 0.8348 (ppp) REVERT: B 373 MET cc_start: 0.9622 (ttp) cc_final: 0.9413 (tpp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0691 time to fit residues: 8.1311 Evaluate side-chains 61 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047178 restraints weight = 100930.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048191 restraints weight = 62005.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048898 restraints weight = 42817.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.049404 restraints weight = 32268.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049773 restraints weight = 25983.704| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10143 Z= 0.167 Angle : 0.731 9.544 13863 Z= 0.358 Chirality : 0.046 0.222 1598 Planarity : 0.004 0.050 1802 Dihedral : 6.299 57.726 1731 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.24), residues: 1355 helix: 1.82 (0.20), residues: 697 sheet: -0.57 (0.35), residues: 209 loop : -2.69 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 167 TYR 0.025 0.002 TYR A 678 PHE 0.017 0.002 PHE A 446 TRP 0.013 0.001 TRP A 668 HIS 0.004 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00345 (10123) covalent geometry : angle 0.68890 (13810) SS BOND : bond 0.00626 ( 7) SS BOND : angle 3.01473 ( 14) hydrogen bonds : bond 0.03577 ( 527) hydrogen bonds : angle 4.30046 ( 1554) link_BETA1-4 : bond 0.01357 ( 6) link_BETA1-4 : angle 4.71998 ( 18) link_NAG-ASN : bond 0.00579 ( 7) link_NAG-ASN : angle 3.94855 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1357.54 seconds wall clock time: 24 minutes 16.79 seconds (1456.79 seconds total)