Starting phenix.real_space_refine on Fri Sep 11 15:37:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uo9_20823/09_2026/6uo9_20823.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uo9_20823/09_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_20823/09_2026/6uo9_20823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uo9_20823/09_2026/6uo9_20823.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uo9_20823/09_2026/6uo9_20823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uo9_20823/09_2026/6uo9_20823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uo9_20823/09_2026/6uo9_20823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uo9_20823/09_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-2.2.1-6174/lib/python3.11/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 chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Time building chain proxies: 2.34, per 1000 atoms: 0.24 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: 0.89 Conformation dependent library (CDL) restraints added in 326.9 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: 0.24 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: 1.62 Time building geometry restraints manager: 1.09 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 - 16.96: 5355 16.96 - 33.91: 422 33.91 - 50.87: 102 50.87 - 67.82: 17 67.82 - 84.78: 8 Dihedral angle restraints: 5904 sinusoidal: 1941 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 5901 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.540 Find NCS groups from input model: 0.060 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 13.559 84.775 3325 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/Z covalent geometry : bond 0.00628 / 0.33 (10123) covalent geometry : angle 1.37996 / 0.80 (13810) SS BOND : bond 0.01662 / 0.73 ( 7) SS BOND : angle 5.03992 / 3.40 ( 14) hydrogen bonds : bond 0.12441 / 8.12 ( 527) hydrogen bonds : angle 6.31651 / 4.34 ( 1554) link_BETA1-4 : bond 0.02277 / 1.08 ( 6) link_BETA1-4 : angle 8.55473 / 4.49 ( 18) link_NAG-ASN : bond 0.01044 / 0.51 ( 7) link_NAG-ASN : angle 6.86239 / 3.87 ( 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 : 0.385 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: 0.0848 time to fit residues: 15.0400 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 : 0.376 ------------------------------------------------------------------------------- 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... 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 = 0.062468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.054171 restraints weight = 95995.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055390 restraints weight = 54639.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.056113 restraints weight = 32900.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.056760 restraints weight = 23830.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056857 restraints weight = 19161.911| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10143 Z= 0.135 Angle : 0.779 12.411 13863 Z= 0.381 Chirality : 0.047 0.260 1598 Planarity : 0.005 0.053 1802 Dihedral : 5.087 42.450 1460 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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: -2.07 (0.22), residues: 1355 helix: -0.12 (0.19), residues: 699 sheet: -1.04 (0.37), residues: 190 loop : -3.47 (0.23), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 340 TYR 0.026 0.002 TYR B 285 PHE 0.033 0.002 PHE A 446 TRP 0.017 0.001 TRP A 390 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (10123) covalent geometry : angle 0.72268 / 0.37 (13810) SS BOND : bond 0.00740 / 0.33 ( 7) SS BOND : angle 3.76567 / 2.49 ( 14) hydrogen bonds : bond 0.04453 / 2.93 ( 527) hydrogen bonds : angle 4.75198 / 3.26 ( 1554) link_BETA1-4 : bond 0.01453 / 0.65 ( 6) link_BETA1-4 : angle 5.69845 / 3.02 ( 18) link_NAG-ASN : bond 0.00604 / 0.29 ( 7) link_NAG-ASN : angle 4.44695 / 2.48 ( 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 : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8936 (mmm) cc_final: 0.8471 (mmm) REVERT: A 668 TRP cc_start: 0.6300 (m-10) cc_final: 0.5626 (m-10) REVERT: B 240 VAL cc_start: 0.9247 (t) cc_final: 0.9012 (t) REVERT: B 259 MET cc_start: 0.9492 (mmp) cc_final: 0.8854 (mmm) REVERT: B 272 MET cc_start: 0.9224 (tpp) cc_final: 0.8880 (mmm) REVERT: B 311 MET cc_start: 0.9218 (ptt) cc_final: 0.8788 (ppp) REVERT: B 373 MET cc_start: 0.9617 (ttp) cc_final: 0.9235 (tmm) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.0743 time to fit residues: 11.4781 Evaluate side-chains 77 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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: 6.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 113 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.063112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054242 restraints weight = 95295.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.055383 restraints weight = 57037.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056159 restraints weight = 38258.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056727 restraints weight = 28132.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057040 restraints weight = 22023.003| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10143 Z= 0.125 Angle : 0.749 12.054 13863 Z= 0.360 Chirality : 0.047 0.278 1598 Planarity : 0.004 0.050 1802 Dihedral : 4.848 48.172 1460 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.61 % 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: -1.35 (0.22), residues: 1355 helix: 0.56 (0.20), residues: 702 sheet: -0.80 (0.37), residues: 191 loop : -3.28 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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/Z covalent geometry : bond 0.00259 / 0.12 (10123) covalent geometry : angle 0.68957 / 0.34 (13810) SS BOND : bond 0.00617 / 0.30 ( 7) SS BOND : angle 4.13762 / 2.79 ( 14) hydrogen bonds : bond 0.03948 / 2.60 ( 527) hydrogen bonds : angle 4.36114 / 3.00 ( 1554) link_BETA1-4 : bond 0.01574 / 0.72 ( 6) link_BETA1-4 : angle 5.53349 / 2.97 ( 18) link_NAG-ASN : bond 0.00631 / 0.32 ( 7) link_NAG-ASN : angle 4.44843 / 2.52 ( 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 97 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8896 (mmm) cc_final: 0.8604 (mmm) REVERT: A 390 TRP cc_start: 0.8613 (m100) cc_final: 0.8352 (m100) REVERT: A 668 TRP cc_start: 0.6377 (m-10) cc_final: 0.5720 (m-10) REVERT: B 272 MET cc_start: 0.9219 (tpp) cc_final: 0.8909 (mmm) REVERT: B 373 MET cc_start: 0.9588 (ttp) cc_final: 0.9219 (tmm) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.0719 time to fit residues: 11.0964 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 : 0.329 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 88 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 135 optimal weight: 30.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 GLN ** A 653 HIS ** 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 = 0.3214 r_free = 0.3214 target = 0.057018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048035 restraints weight = 100588.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049077 restraints weight = 60846.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049823 restraints weight = 41780.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050339 restraints weight = 31335.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.050708 restraints weight = 25090.113| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10143 Z= 0.236 Angle : 0.815 10.596 13863 Z= 0.409 Chirality : 0.047 0.238 1598 Planarity : 0.005 0.051 1802 Dihedral : 5.037 35.801 1460 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % 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: -0.72 (0.23), residues: 1355 helix: 1.18 (0.20), residues: 692 sheet: -0.98 (0.34), residues: 209 loop : -2.92 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 167 TYR 0.030 0.002 TYR B 193 PHE 0.029 0.002 PHE A 446 TRP 0.017 0.002 TRP A 304 HIS 0.009 0.002 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.24 (10123) covalent geometry : angle 0.77385 / 0.40 (13810) SS BOND : bond 0.00738 / 0.34 ( 7) SS BOND : angle 2.99421 / 2.44 ( 14) hydrogen bonds : bond 0.03944 / 2.65 ( 527) hydrogen bonds : angle 4.48493 / 3.09 ( 1554) link_BETA1-4 : bond 0.01401 / 0.62 ( 6) link_BETA1-4 : angle 5.17522 / 2.78 ( 18) link_NAG-ASN : bond 0.00461 / 0.22 ( 7) link_NAG-ASN : angle 3.94589 / 2.30 ( 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 78 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8849 (mmm) cc_final: 0.8455 (mmm) REVERT: A 390 TRP cc_start: 0.8909 (m100) cc_final: 0.8536 (m100) REVERT: A 509 ILE cc_start: 0.9721 (tp) cc_final: 0.9498 (pt) REVERT: B 129 MET cc_start: 0.9306 (tpp) cc_final: 0.9059 (tpp) REVERT: B 172 PHE cc_start: 0.8521 (t80) cc_final: 0.8302 (t80) REVERT: B 272 MET cc_start: 0.9246 (tpp) cc_final: 0.9007 (mmm) REVERT: B 311 MET cc_start: 0.9104 (ppp) cc_final: 0.8244 (ppp) REVERT: B 373 MET cc_start: 0.9651 (ttp) cc_final: 0.9339 (tpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0760 time to fit residues: 9.6036 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 : 0.406 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.059228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050213 restraints weight = 98214.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051296 restraints weight = 58827.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052051 restraints weight = 39955.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052588 restraints weight = 29637.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052972 restraints weight = 23455.643| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10143 Z= 0.129 Angle : 0.717 9.974 13863 Z= 0.348 Chirality : 0.046 0.243 1598 Planarity : 0.004 0.052 1802 Dihedral : 4.826 36.162 1460 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: -0.38 (0.23), residues: 1355 helix: 1.53 (0.20), residues: 694 sheet: -0.72 (0.34), residues: 209 loop : -2.99 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.022 0.001 TYR B 697 PHE 0.024 0.001 PHE A 446 TRP 0.011 0.001 TRP A 390 HIS 0.003 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (10123) covalent geometry : angle 0.67277 / 0.34 (13810) SS BOND : bond 0.00444 / 0.17 ( 7) SS BOND : angle 3.16863 / 2.42 ( 14) hydrogen bonds : bond 0.03572 / 2.37 ( 527) hydrogen bonds : angle 4.12628 / 2.84 ( 1554) link_BETA1-4 : bond 0.01407 / 0.63 ( 6) link_BETA1-4 : angle 5.01238 / 2.73 ( 18) link_NAG-ASN : bond 0.00477 / 0.24 ( 7) link_NAG-ASN : angle 3.68822 / 2.13 ( 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 86 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8905 (mmm) cc_final: 0.8527 (mmm) REVERT: A 390 TRP cc_start: 0.8869 (m100) cc_final: 0.8601 (m100) REVERT: A 509 ILE cc_start: 0.9702 (tp) cc_final: 0.9488 (pt) REVERT: B 129 MET cc_start: 0.9351 (tpp) cc_final: 0.9054 (tpp) REVERT: B 171 TYR cc_start: 0.9036 (m-80) cc_final: 0.8672 (m-80) REVERT: B 172 PHE cc_start: 0.8537 (t80) cc_final: 0.8255 (t80) REVERT: B 272 MET cc_start: 0.9243 (tpp) cc_final: 0.9026 (mmm) REVERT: B 311 MET cc_start: 0.9047 (ppp) cc_final: 0.8052 (ppp) REVERT: B 373 MET cc_start: 0.9653 (ttp) cc_final: 0.9331 (tmm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0759 time to fit residues: 10.1843 Evaluate side-chains 68 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 5.9990 chunk 111 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 overall best weight: 3.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048489 restraints weight = 100495.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049398 restraints weight = 55949.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049979 restraints weight = 36291.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050508 restraints weight = 28278.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050588 restraints weight = 23713.966| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10143 Z= 0.188 Angle : 0.745 9.467 13863 Z= 0.370 Chirality : 0.046 0.241 1598 Planarity : 0.004 0.049 1802 Dihedral : 4.997 36.628 1460 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: -0.31 (0.23), residues: 1355 helix: 1.52 (0.20), residues: 695 sheet: -0.66 (0.33), residues: 208 loop : -2.87 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 277 TYR 0.017 0.002 TYR B 193 PHE 0.022 0.002 PHE A 446 TRP 0.013 0.002 TRP A 304 HIS 0.007 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (10123) covalent geometry : angle 0.70479 / 0.36 (13810) SS BOND : bond 0.00946 / 0.47 ( 7) SS BOND : angle 3.35995 / 2.47 ( 14) hydrogen bonds : bond 0.03684 / 2.45 ( 527) hydrogen bonds : angle 4.32180 / 2.97 ( 1554) link_BETA1-4 : bond 0.01335 / 0.60 ( 6) link_BETA1-4 : angle 4.79010 / 2.61 ( 18) link_NAG-ASN : bond 0.00383 / 0.20 ( 7) link_NAG-ASN : angle 3.51443 / 2.07 ( 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 78 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8837 (mmm) cc_final: 0.8507 (mmm) REVERT: A 390 TRP cc_start: 0.8995 (m100) cc_final: 0.8724 (m100) REVERT: B 171 TYR cc_start: 0.9099 (m-80) cc_final: 0.8727 (m-80) REVERT: B 172 PHE cc_start: 0.8586 (t80) cc_final: 0.8225 (t80) REVERT: B 272 MET cc_start: 0.9234 (tpp) cc_final: 0.8459 (mmm) REVERT: B 311 MET cc_start: 0.8999 (ppp) cc_final: 0.8633 (ppp) REVERT: B 373 MET cc_start: 0.9662 (ttp) cc_final: 0.9407 (tpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0797 time to fit residues: 9.9373 Evaluate side-chains 62 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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: 5.9990 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.059783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050949 restraints weight = 97801.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052031 restraints weight = 58923.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052795 restraints weight = 39890.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053338 restraints weight = 29630.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.053730 restraints weight = 23481.114| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10143 Z= 0.108 Angle : 0.693 9.586 13863 Z= 0.329 Chirality : 0.045 0.255 1598 Planarity : 0.004 0.050 1802 Dihedral : 4.625 33.867 1460 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 0.02 (0.24), residues: 1355 helix: 1.81 (0.20), residues: 694 sheet: -0.30 (0.34), residues: 204 loop : -2.84 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 212 TYR 0.021 0.001 TYR B 697 PHE 0.019 0.001 PHE A 446 TRP 0.011 0.001 TRP B 558 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (10123) covalent geometry : angle 0.65436 / 0.32 (13810) SS BOND : bond 0.00399 / 0.17 ( 7) SS BOND : angle 3.06580 / 2.30 ( 14) hydrogen bonds : bond 0.03279 / 2.17 ( 527) hydrogen bonds : angle 3.95274 / 2.72 ( 1554) link_BETA1-4 : bond 0.01512 / 0.68 ( 6) link_BETA1-4 : angle 4.70054 / 2.57 ( 18) link_NAG-ASN : bond 0.00548 / 0.27 ( 7) link_NAG-ASN : angle 3.26309 / 1.87 ( 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 84 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8901 (mmm) cc_final: 0.8464 (mmm) REVERT: A 375 PHE cc_start: 0.9121 (m-10) cc_final: 0.8487 (m-80) REVERT: A 390 TRP cc_start: 0.8833 (m100) cc_final: 0.8552 (m100) REVERT: B 129 MET cc_start: 0.9402 (tpp) cc_final: 0.8802 (tpp) REVERT: B 171 TYR cc_start: 0.9120 (m-80) cc_final: 0.8800 (m-80) REVERT: B 272 MET cc_start: 0.9251 (tpp) cc_final: 0.9013 (mmm) REVERT: B 311 MET cc_start: 0.8703 (ppp) cc_final: 0.8259 (ppp) REVERT: B 373 MET cc_start: 0.9616 (ttp) cc_final: 0.9370 (tpp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0672 time to fit residues: 9.3067 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 : 0.283 ------------------------------------------------------------------------------- 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: 0.9980 chunk 132 optimal weight: 5.9990 chunk 96 optimal weight: 0.0870 chunk 43 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049346 restraints weight = 98218.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050394 restraints weight = 59743.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051138 restraints weight = 40890.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051666 restraints weight = 30622.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.052054 restraints weight = 24424.086| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3372 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= 0.130 Angle : 0.678 9.433 13863 Z= 0.329 Chirality : 0.045 0.228 1598 Planarity : 0.004 0.049 1802 Dihedral : 4.625 33.739 1460 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 0.13 (0.24), residues: 1355 helix: 1.89 (0.20), residues: 698 sheet: -0.30 (0.35), residues: 204 loop : -2.76 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 418 TYR 0.017 0.001 TYR A 615 PHE 0.017 0.001 PHE A 446 TRP 0.009 0.001 TRP A 400 HIS 0.004 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (10123) covalent geometry : angle 0.64085 / 0.32 (13810) SS BOND : bond 0.00522 / 0.24 ( 7) SS BOND : angle 2.91071 / 2.24 ( 14) hydrogen bonds : bond 0.03264 / 2.17 ( 527) hydrogen bonds : angle 3.97508 / 2.73 ( 1554) link_BETA1-4 : bond 0.01369 / 0.61 ( 6) link_BETA1-4 : angle 4.57266 / 2.49 ( 18) link_NAG-ASN : bond 0.00417 / 0.21 ( 7) link_NAG-ASN : angle 3.13026 / 1.83 ( 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 81 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8874 (mmm) cc_final: 0.8560 (mmp) REVERT: A 375 PHE cc_start: 0.9142 (m-10) cc_final: 0.8548 (m-80) REVERT: A 390 TRP cc_start: 0.8872 (m100) cc_final: 0.8571 (m100) REVERT: B 129 MET cc_start: 0.9458 (tpp) cc_final: 0.9113 (tpp) REVERT: B 171 TYR cc_start: 0.9138 (m-80) cc_final: 0.8798 (m-80) REVERT: B 272 MET cc_start: 0.9254 (tpp) cc_final: 0.9001 (mmm) REVERT: B 311 MET cc_start: 0.8862 (ppp) cc_final: 0.8486 (ppp) REVERT: B 373 MET cc_start: 0.9608 (ttp) cc_final: 0.9400 (tpp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0618 time to fit residues: 8.3095 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 : 0.235 ------------------------------------------------------------------------------- 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: 0.6980 chunk 120 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 HIS ** 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 = 0.3218 r_free = 0.3218 target = 0.057181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048374 restraints weight = 99016.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049417 restraints weight = 60625.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050139 restraints weight = 41851.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050643 restraints weight = 31443.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.051014 restraints weight = 25292.528| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3602 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= 0.157 Angle : 0.708 10.100 13863 Z= 0.345 Chirality : 0.046 0.253 1598 Planarity : 0.004 0.050 1802 Dihedral : 4.795 43.529 1460 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 0.18 (0.24), residues: 1355 helix: 1.91 (0.20), residues: 698 sheet: -0.38 (0.35), residues: 206 loop : -2.65 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 167 TYR 0.018 0.001 TYR A 615 PHE 0.018 0.002 PHE B 711 TRP 0.011 0.001 TRP A 400 HIS 0.005 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (10123) covalent geometry : angle 0.67646 / 0.34 (13810) SS BOND : bond 0.00539 / 0.25 ( 7) SS BOND : angle 2.82010 / 2.18 ( 14) hydrogen bonds : bond 0.03343 / 2.23 ( 527) hydrogen bonds : angle 4.11325 / 2.81 ( 1554) link_BETA1-4 : bond 0.01321 / 0.59 ( 6) link_BETA1-4 : angle 4.45785 / 2.44 ( 18) link_NAG-ASN : bond 0.00671 / 0.47 ( 7) link_NAG-ASN : angle 2.84805 / 1.69 ( 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 : 0.372 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8699 (mmm) cc_final: 0.8328 (mmm) REVERT: A 375 PHE cc_start: 0.9146 (m-10) cc_final: 0.8549 (m-80) REVERT: A 390 TRP cc_start: 0.8781 (m100) cc_final: 0.8568 (m100) REVERT: B 129 MET cc_start: 0.9412 (tpp) cc_final: 0.9079 (tpp) REVERT: B 171 TYR cc_start: 0.9148 (m-80) cc_final: 0.8800 (m-80) REVERT: B 272 MET cc_start: 0.9150 (tpp) cc_final: 0.8357 (mmm) REVERT: B 311 MET cc_start: 0.8734 (ppp) cc_final: 0.8389 (ppp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0603 time to fit residues: 7.5511 Evaluate side-chains 65 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 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 54 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 113 optimal weight: 0.0370 chunk 131 optimal weight: 7.9990 chunk 120 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN B 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.048479 restraints weight = 98164.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049509 restraints weight = 60244.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.050221 restraints weight = 41488.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.050729 restraints weight = 31303.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.051078 restraints weight = 25173.067| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3749 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= 0.142 Angle : 0.690 9.478 13863 Z= 0.335 Chirality : 0.045 0.252 1598 Planarity : 0.004 0.050 1802 Dihedral : 4.756 39.886 1460 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.24 (0.24), residues: 1355 helix: 1.96 (0.21), residues: 696 sheet: -0.33 (0.35), residues: 204 loop : -2.61 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 371 TYR 0.026 0.001 TYR A 678 PHE 0.016 0.001 PHE A 446 TRP 0.011 0.001 TRP A 260 HIS 0.004 0.001 HIS B 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (10123) covalent geometry : angle 0.65811 / 0.33 (13810) SS BOND : bond 0.00551 / 0.25 ( 7) SS BOND : angle 2.77478 / 2.14 ( 14) hydrogen bonds : bond 0.03292 / 2.18 ( 527) hydrogen bonds : angle 4.08388 / 2.80 ( 1554) link_BETA1-4 : bond 0.01336 / 0.59 ( 6) link_BETA1-4 : angle 4.40087 / 2.41 ( 18) link_NAG-ASN : bond 0.00756 / 0.53 ( 7) link_NAG-ASN : angle 2.81271 / 1.65 ( 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 77 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8708 (mmm) cc_final: 0.8354 (mmm) REVERT: A 375 PHE cc_start: 0.9131 (m-10) cc_final: 0.8523 (m-80) REVERT: A 390 TRP cc_start: 0.8789 (m100) cc_final: 0.8566 (m100) REVERT: B 129 MET cc_start: 0.9431 (tpp) cc_final: 0.9101 (tpp) REVERT: B 171 TYR cc_start: 0.9160 (m-80) cc_final: 0.8797 (m-80) REVERT: B 272 MET cc_start: 0.9140 (tpp) cc_final: 0.8813 (mmt) REVERT: B 311 MET cc_start: 0.8662 (ppp) cc_final: 0.8423 (ppp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0690 time to fit residues: 8.8380 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 : 0.405 ------------------------------------------------------------------------------- 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: 3.9990 chunk 109 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 124 optimal weight: 0.0470 chunk 135 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.048567 restraints weight = 99351.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049596 restraints weight = 60854.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050288 restraints weight = 42034.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.050823 restraints weight = 31885.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.051209 restraints weight = 25498.839| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3884 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= 0.134 Angle : 0.680 9.471 13863 Z= 0.330 Chirality : 0.045 0.242 1598 Planarity : 0.004 0.049 1802 Dihedral : 4.693 39.611 1460 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % 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: 0.25 (0.24), residues: 1355 helix: 1.98 (0.20), residues: 695 sheet: -0.23 (0.36), residues: 197 loop : -2.65 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 212 TYR 0.020 0.001 TYR A 678 PHE 0.015 0.001 PHE A 446 TRP 0.010 0.001 TRP A 400 HIS 0.002 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10123) covalent geometry : angle 0.64782 / 0.32 (13810) SS BOND : bond 0.00503 / 0.23 ( 7) SS BOND : angle 2.77238 / 2.14 ( 14) hydrogen bonds : bond 0.03243 / 2.15 ( 527) hydrogen bonds : angle 4.05497 / 2.78 ( 1554) link_BETA1-4 : bond 0.01336 / 0.59 ( 6) link_BETA1-4 : angle 4.33155 / 2.37 ( 18) link_NAG-ASN : bond 0.00730 / 0.51 ( 7) link_NAG-ASN : angle 2.79909 / 1.65 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.27 seconds wall clock time: 24 minutes 54.98 seconds (1494.98 seconds total)