Starting phenix.real_space_refine on Mon Jul 28 06:33:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uo9_20823/07_2025/6uo9_20823.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uo9_20823/07_2025/6uo9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6uo9_20823/07_2025/6uo9_20823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uo9_20823/07_2025/6uo9_20823.map" model { file = "/net/cci-nas-00/data/ceres_data/6uo9_20823/07_2025/6uo9_20823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uo9_20823/07_2025/6uo9_20823.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 7, 'ARG:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 11, 'GLU:plan': 5, 'ASP:plan': 5} 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, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 8, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 239 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'QD7': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.37, per 1000 atoms: 0.64 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: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.35 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: 2.86 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3275 1.34 - 1.48: 2635 1.48 - 1.61: 4160 1.61 - 1.75: 0 1.75 - 1.88: 53 Bond restraints: 10123 Sorted by residual: bond pdb=" C PHE A 659 " pdb=" N PRO A 660 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.28e-02 6.10e+03 1.99e+01 bond pdb=" C ALA A 820 " pdb=" N PRO A 821 " ideal model delta sigma weight residual 1.337 1.367 -0.031 9.80e-03 1.04e+04 9.83e+00 bond pdb=" CAG QD7 A1001 " pdb=" PAE QD7 A1001 " ideal model delta sigma weight residual 1.830 1.777 0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.86e+00 ... (remaining 10118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 13535 3.96 - 7.93: 241 7.93 - 11.89: 22 11.89 - 15.85: 7 15.85 - 19.81: 5 Bond angle restraints: 13810 Sorted by residual: angle pdb=" N LYS A 709 " pdb=" CA LYS A 709 " pdb=" C LYS A 709 " ideal model delta sigma weight residual 110.97 122.99 -12.02 1.09e+00 8.42e-01 1.22e+02 angle pdb=" CA CYS B 108 " pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " ideal model delta sigma weight residual 114.40 130.97 -16.57 2.30e+00 1.89e-01 5.19e+01 angle pdb=" C PRO B 236 " pdb=" N CYS B 237 " pdb=" CA CYS B 237 " ideal model delta sigma weight residual 122.83 113.04 9.79 1.54e+00 4.22e-01 4.04e+01 angle pdb=" N PHE B 431 " pdb=" CA PHE B 431 " pdb=" C PHE B 431 " ideal model delta sigma weight residual 108.41 118.20 -9.79 1.61e+00 3.86e-01 3.70e+01 angle pdb=" CA CYS A 246 " pdb=" CB CYS A 246 " pdb=" SG CYS A 246 " ideal model delta sigma weight residual 114.40 128.36 -13.96 2.30e+00 1.89e-01 3.68e+01 ... (remaining 13805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 5725 20.80 - 41.60: 374 41.60 - 62.40: 57 62.40 - 83.20: 14 83.20 - 104.00: 5 Dihedral angle restraints: 6175 sinusoidal: 2212 harmonic: 3963 Sorted by residual: dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N ASN B 298 " pdb=" CA ASN B 298 " ideal model delta harmonic sigma weight residual 180.00 137.22 42.78 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual 93.00 17.94 75.06 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual 93.00 27.09 65.91 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 6172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1354 0.092 - 0.183: 206 0.183 - 0.275: 32 0.275 - 0.366: 5 0.366 - 0.458: 1 Chirality restraints: 1598 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.20e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 482 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.49e+00 ... (remaining 1595 not shown) Planarity restraints: 1809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 237 " 0.039 2.00e-02 2.50e+03 7.98e-02 6.37e+01 pdb=" C CYS B 237 " -0.138 2.00e-02 2.50e+03 pdb=" O CYS B 237 " 0.051 2.00e-02 2.50e+03 pdb=" N THR B 238 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 87 " 0.033 2.00e-02 2.50e+03 6.59e-02 4.35e+01 pdb=" C GLN B 87 " -0.114 2.00e-02 2.50e+03 pdb=" O GLN B 87 " 0.043 2.00e-02 2.50e+03 pdb=" N ILE B 88 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 382 " -0.032 2.00e-02 2.50e+03 6.40e-02 4.10e+01 pdb=" C HIS B 382 " 0.111 2.00e-02 2.50e+03 pdb=" O HIS B 382 " -0.042 2.00e-02 2.50e+03 pdb=" N GLN B 383 " -0.037 2.00e-02 2.50e+03 ... (remaining 1806 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1840 2.76 - 3.30: 9558 3.30 - 3.83: 16005 3.83 - 4.37: 16805 4.37 - 4.90: 28476 Nonbonded interactions: 72684 Sorted by model distance: nonbonded pdb=" OG1 THR A 291 " pdb=" OD2 ASP A 325 " model vdw 2.227 3.040 nonbonded pdb=" O HIS B 377 " pdb=" NE ARG B 381 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR B 468 " pdb=" O ASP B 638 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A 411 " pdb=" OE1 GLU A 414 " model vdw 2.251 3.040 nonbonded pdb=" NH1 ARG B 422 " pdb=" O MET B 423 " model vdw 2.262 3.120 ... (remaining 72679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.400 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10143 Z= 0.336 Angle : 1.445 19.815 13863 Z= 0.813 Chirality : 0.070 0.458 1598 Planarity : 0.009 0.080 1802 Dihedral : 14.281 104.005 3596 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.07 % Allowed : 9.50 % Favored : 89.43 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (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 TRP 0.038 0.003 TRP A 304 HIS 0.009 0.002 HIS B 127 PHE 0.025 0.003 PHE B 173 TYR 0.055 0.003 TYR B 697 ARG 0.005 0.001 ARG B 422 Details of bonding type rmsd link_NAG-ASN : bond 0.01044 ( 7) link_NAG-ASN : angle 6.86239 ( 21) link_BETA1-4 : bond 0.02277 ( 6) link_BETA1-4 : angle 8.55473 ( 18) hydrogen bonds : bond 0.12441 ( 527) hydrogen bonds : angle 6.31651 ( 1554) SS BOND : bond 0.01662 ( 7) SS BOND : angle 5.03992 ( 14) covalent geometry : bond 0.00628 (10123) covalent geometry : angle 1.37996 (13810) *********************** 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 : 1.196 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: 0.2032 time to fit residues: 35.3558 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 : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 0.0870 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 30.0000 overall best weight: 3.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 314 GLN A 457 HIS A 503 GLN A 653 HIS B 206 GLN B 278 GLN B 326 GLN B 393 HIS B 716 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.059390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050563 restraints weight = 97511.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.051668 restraints weight = 58295.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052429 restraints weight = 39645.632| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10143 Z= 0.207 Angle : 0.825 12.411 13863 Z= 0.411 Chirality : 0.047 0.218 1598 Planarity : 0.005 0.056 1802 Dihedral : 7.801 65.316 1731 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.36 % Allowed : 6.89 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.22), residues: 1355 helix: 0.08 (0.19), residues: 696 sheet: -1.12 (0.37), residues: 190 loop : -3.34 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 304 HIS 0.006 0.002 HIS A 457 PHE 0.035 0.002 PHE A 446 TYR 0.030 0.002 TYR B 193 ARG 0.005 0.001 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 7) link_NAG-ASN : angle 4.40879 ( 21) link_BETA1-4 : bond 0.01297 ( 6) link_BETA1-4 : angle 5.76697 ( 18) hydrogen bonds : bond 0.04447 ( 527) hydrogen bonds : angle 4.83255 ( 1554) SS BOND : bond 0.00851 ( 7) SS BOND : angle 3.63597 ( 14) covalent geometry : bond 0.00417 (10123) covalent geometry : angle 0.77219 (13810) *********************** 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 88 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9667 (pt) cc_final: 0.9457 (pp) REVERT: A 243 MET cc_start: 0.8973 (mmm) cc_final: 0.8611 (mmm) REVERT: A 390 TRP cc_start: 0.8773 (m100) cc_final: 0.8459 (m100) REVERT: B 59 MET cc_start: 0.9220 (mtm) cc_final: 0.8985 (mmm) REVERT: B 203 GLN cc_start: 0.8776 (tt0) cc_final: 0.7980 (mt0) REVERT: B 240 VAL cc_start: 0.9288 (t) cc_final: 0.9043 (t) REVERT: B 259 MET cc_start: 0.9521 (mmp) cc_final: 0.9009 (mmm) REVERT: B 272 MET cc_start: 0.9263 (tpp) cc_final: 0.9004 (mmm) REVERT: B 311 MET cc_start: 0.9232 (ptt) cc_final: 0.8793 (ppp) REVERT: B 373 MET cc_start: 0.9608 (ttp) cc_final: 0.9244 (tmm) outliers start: 3 outliers final: 2 residues processed: 88 average time/residue: 0.1621 time to fit residues: 23.0259 Evaluate side-chains 70 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 121 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 47 optimal weight: 0.0370 chunk 58 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 overall best weight: 4.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047919 restraints weight = 99946.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048978 restraints weight = 60711.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049709 restraints weight = 41491.690| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10143 Z= 0.242 Angle : 0.837 12.048 13863 Z= 0.419 Chirality : 0.049 0.297 1598 Planarity : 0.005 0.056 1802 Dihedral : 7.749 63.213 1731 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.24 % Allowed : 8.19 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1355 helix: 0.90 (0.20), residues: 699 sheet: -1.13 (0.35), residues: 208 loop : -3.07 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 304 HIS 0.007 0.001 HIS A 524 PHE 0.030 0.002 PHE A 446 TYR 0.025 0.002 TYR B 193 ARG 0.005 0.001 ARG A 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00811 ( 7) link_NAG-ASN : angle 4.53582 ( 21) link_BETA1-4 : bond 0.01422 ( 6) link_BETA1-4 : angle 5.65048 ( 18) hydrogen bonds : bond 0.04443 ( 527) hydrogen bonds : angle 4.68152 ( 1554) SS BOND : bond 0.00850 ( 7) SS BOND : angle 3.73672 ( 14) covalent geometry : bond 0.00488 (10123) covalent geometry : angle 0.78525 (13810) *********************** 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 77 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8977 (mmm) cc_final: 0.8577 (mmm) REVERT: A 390 TRP cc_start: 0.8841 (m100) cc_final: 0.8533 (m100) REVERT: B 59 MET cc_start: 0.9292 (mtm) cc_final: 0.9087 (mmt) REVERT: B 171 TYR cc_start: 0.9120 (m-80) cc_final: 0.8815 (m-80) REVERT: B 172 PHE cc_start: 0.8662 (t80) cc_final: 0.8335 (t80) REVERT: B 258 ASN cc_start: 0.8686 (p0) cc_final: 0.7775 (p0) REVERT: B 259 MET cc_start: 0.9570 (mmp) cc_final: 0.9175 (mmm) REVERT: B 272 MET cc_start: 0.9248 (tpp) cc_final: 0.8998 (mmm) REVERT: B 311 MET cc_start: 0.8873 (ptt) cc_final: 0.8597 (ppp) REVERT: B 373 MET cc_start: 0.9659 (ttp) cc_final: 0.9333 (tpp) outliers start: 2 outliers final: 1 residues processed: 77 average time/residue: 0.1838 time to fit residues: 23.0022 Evaluate side-chains 63 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 103 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 0.0770 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN B 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047489 restraints weight = 99249.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048528 restraints weight = 60304.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049241 restraints weight = 41486.446| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10143 Z= 0.202 Angle : 0.781 10.517 13863 Z= 0.388 Chirality : 0.046 0.251 1598 Planarity : 0.005 0.056 1802 Dihedral : 7.313 58.516 1731 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.12 % Allowed : 6.41 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.23), residues: 1355 helix: 1.21 (0.20), residues: 702 sheet: -0.81 (0.34), residues: 208 loop : -3.01 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 304 HIS 0.007 0.001 HIS A 524 PHE 0.028 0.002 PHE A 446 TYR 0.020 0.002 TYR B 697 ARG 0.004 0.001 ARG A 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 7) link_NAG-ASN : angle 3.96381 ( 21) link_BETA1-4 : bond 0.01300 ( 6) link_BETA1-4 : angle 5.30948 ( 18) hydrogen bonds : bond 0.03998 ( 527) hydrogen bonds : angle 4.51992 ( 1554) SS BOND : bond 0.00847 ( 7) SS BOND : angle 2.99783 ( 14) covalent geometry : bond 0.00412 (10123) covalent geometry : angle 0.73649 (13810) *********************** 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 75 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9716 (pp) cc_final: 0.9509 (pp) REVERT: A 243 MET cc_start: 0.8847 (mmm) cc_final: 0.8622 (mmm) REVERT: A 509 ILE cc_start: 0.9696 (tp) cc_final: 0.9470 (pt) REVERT: B 171 TYR cc_start: 0.9021 (m-80) cc_final: 0.8771 (m-80) REVERT: B 172 PHE cc_start: 0.8569 (t80) cc_final: 0.8193 (t80) REVERT: B 259 MET cc_start: 0.9515 (mmp) cc_final: 0.9136 (mmm) REVERT: B 311 MET cc_start: 0.8850 (ptt) cc_final: 0.8642 (ppp) REVERT: B 373 MET cc_start: 0.9602 (ttp) cc_final: 0.9285 (tpp) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2332 time to fit residues: 26.8652 Evaluate side-chains 63 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 30.0000 chunk 96 optimal weight: 0.0030 chunk 129 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 90 optimal weight: 0.0570 chunk 74 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 overall best weight: 0.3908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3289 r_free = 0.3289 target = 0.060263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.051364 restraints weight = 96068.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052452 restraints weight = 57816.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.053227 restraints weight = 39201.083| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10143 Z= 0.116 Angle : 0.718 10.096 13863 Z= 0.342 Chirality : 0.046 0.260 1598 Planarity : 0.004 0.054 1802 Dihedral : 6.109 56.263 1731 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1355 helix: 1.47 (0.20), residues: 699 sheet: -0.55 (0.34), residues: 208 loop : -2.87 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 390 HIS 0.005 0.001 HIS A 287 PHE 0.025 0.001 PHE A 446 TYR 0.014 0.001 TYR B 697 ARG 0.003 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 7) link_NAG-ASN : angle 3.64517 ( 21) link_BETA1-4 : bond 0.01568 ( 6) link_BETA1-4 : angle 5.21311 ( 18) hydrogen bonds : bond 0.03510 ( 527) hydrogen bonds : angle 4.14308 ( 1554) SS BOND : bond 0.00743 ( 7) SS BOND : angle 3.28712 ( 14) covalent geometry : bond 0.00229 (10123) covalent geometry : angle 0.67109 (13810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.9019 (mmm) cc_final: 0.8592 (mmm) REVERT: A 375 PHE cc_start: 0.9207 (m-10) cc_final: 0.8529 (m-80) REVERT: B 129 MET cc_start: 0.9159 (tpp) cc_final: 0.8737 (tpp) REVERT: B 172 PHE cc_start: 0.8654 (t80) cc_final: 0.8385 (t80) REVERT: B 259 MET cc_start: 0.9590 (mmp) cc_final: 0.9206 (mmm) REVERT: B 272 MET cc_start: 0.9224 (mmp) cc_final: 0.8958 (mmm) REVERT: B 311 MET cc_start: 0.8819 (ptt) cc_final: 0.8582 (ppp) REVERT: B 373 MET cc_start: 0.9667 (ttp) cc_final: 0.9364 (tpp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2149 time to fit residues: 28.9586 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 : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 29 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.039376 restraints weight = 86154.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.040420 restraints weight = 58073.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.041170 restraints weight = 43417.393| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10143 Z= 0.122 Angle : 0.683 9.944 13863 Z= 0.330 Chirality : 0.045 0.235 1598 Planarity : 0.004 0.052 1802 Dihedral : 5.850 57.233 1731 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1355 helix: 1.71 (0.20), residues: 696 sheet: -0.45 (0.35), residues: 208 loop : -2.88 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 289 HIS 0.003 0.001 HIS A 524 PHE 0.020 0.001 PHE A 446 TYR 0.014 0.001 TYR B 193 ARG 0.005 0.000 ARG A 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 7) link_NAG-ASN : angle 3.44870 ( 21) link_BETA1-4 : bond 0.01452 ( 6) link_BETA1-4 : angle 5.04678 ( 18) hydrogen bonds : bond 0.03391 ( 527) hydrogen bonds : angle 4.06325 ( 1554) SS BOND : bond 0.00705 ( 7) SS BOND : angle 3.20368 ( 14) covalent geometry : bond 0.00256 (10123) covalent geometry : angle 0.63713 (13810) *********************** 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 : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.9048 (mmm) cc_final: 0.8663 (mmm) REVERT: A 375 PHE cc_start: 0.9189 (m-10) cc_final: 0.8573 (m-80) REVERT: B 172 PHE cc_start: 0.8716 (t80) cc_final: 0.8419 (t80) REVERT: B 259 MET cc_start: 0.9596 (mmp) cc_final: 0.9203 (mmm) REVERT: B 272 MET cc_start: 0.9289 (mmp) cc_final: 0.8982 (mmm) REVERT: B 373 MET cc_start: 0.9691 (ttp) cc_final: 0.9420 (tpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2071 time to fit residues: 24.2149 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 : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 124 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 0.0770 chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046471 restraints weight = 102323.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047479 restraints weight = 62925.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.048182 restraints weight = 43710.054| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10143 Z= 0.214 Angle : 0.771 9.463 13863 Z= 0.384 Chirality : 0.047 0.229 1598 Planarity : 0.005 0.052 1802 Dihedral : 6.309 59.087 1731 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.23), residues: 1355 helix: 1.66 (0.20), residues: 696 sheet: -0.48 (0.36), residues: 200 loop : -2.83 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 149 HIS 0.009 0.002 HIS A 524 PHE 0.021 0.002 PHE A 366 TYR 0.018 0.002 TYR A 615 ARG 0.014 0.001 ARG A 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 7) link_NAG-ASN : angle 3.50150 ( 21) link_BETA1-4 : bond 0.01209 ( 6) link_BETA1-4 : angle 4.94924 ( 18) hydrogen bonds : bond 0.03710 ( 527) hydrogen bonds : angle 4.42960 ( 1554) SS BOND : bond 0.00705 ( 7) SS BOND : angle 3.07888 ( 14) covalent geometry : bond 0.00440 (10123) covalent geometry : angle 0.73211 (13810) *********************** 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 71 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8898 (mmm) cc_final: 0.8585 (mmm) REVERT: B 172 PHE cc_start: 0.8583 (t80) cc_final: 0.8217 (t80) REVERT: B 259 MET cc_start: 0.9610 (mmp) cc_final: 0.9174 (mmm) REVERT: B 272 MET cc_start: 0.9270 (mmp) cc_final: 0.8953 (mmm) REVERT: B 311 MET cc_start: 0.9051 (ppp) cc_final: 0.8716 (ppp) REVERT: B 373 MET cc_start: 0.9623 (ttp) cc_final: 0.9379 (tpp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1843 time to fit residues: 20.4683 Evaluate side-chains 58 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046955 restraints weight = 100059.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047975 restraints weight = 61713.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048675 restraints weight = 42810.764| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10143 Z= 0.182 Angle : 0.747 10.485 13863 Z= 0.365 Chirality : 0.046 0.227 1598 Planarity : 0.004 0.053 1802 Dihedral : 6.647 58.139 1731 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1355 helix: 1.72 (0.20), residues: 700 sheet: -0.42 (0.36), residues: 201 loop : -2.85 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 149 HIS 0.007 0.001 HIS A 524 PHE 0.018 0.002 PHE A 446 TYR 0.019 0.002 TYR A 678 ARG 0.008 0.001 ARG B 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 7) link_NAG-ASN : angle 3.97717 ( 21) link_BETA1-4 : bond 0.01327 ( 6) link_BETA1-4 : angle 4.88818 ( 18) hydrogen bonds : bond 0.03652 ( 527) hydrogen bonds : angle 4.33606 ( 1554) SS BOND : bond 0.00613 ( 7) SS BOND : angle 2.87301 ( 14) covalent geometry : bond 0.00374 (10123) covalent geometry : angle 0.70485 (13810) *********************** 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 72 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8911 (mmm) cc_final: 0.8519 (mmm) REVERT: B 129 MET cc_start: 0.9222 (tpp) cc_final: 0.8947 (tpp) REVERT: B 172 PHE cc_start: 0.8606 (t80) cc_final: 0.8181 (t80) REVERT: B 259 MET cc_start: 0.9602 (mmp) cc_final: 0.9202 (mmm) REVERT: B 272 MET cc_start: 0.9257 (mmp) cc_final: 0.8944 (mmm) REVERT: B 311 MET cc_start: 0.8749 (ppp) cc_final: 0.7888 (ppp) REVERT: B 373 MET cc_start: 0.9613 (ttp) cc_final: 0.9369 (tpp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1672 time to fit residues: 19.9642 Evaluate side-chains 58 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047518 restraints weight = 99923.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048545 restraints weight = 61254.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049237 restraints weight = 42417.801| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3867 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= 0.150 Angle : 0.723 9.553 13863 Z= 0.350 Chirality : 0.045 0.235 1598 Planarity : 0.004 0.052 1802 Dihedral : 6.293 57.730 1731 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1355 helix: 1.83 (0.20), residues: 698 sheet: -0.40 (0.36), residues: 201 loop : -2.78 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 149 HIS 0.008 0.001 HIS B 127 PHE 0.017 0.001 PHE A 446 TYR 0.017 0.001 TYR A 678 ARG 0.004 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 7) link_NAG-ASN : angle 4.10208 ( 21) link_BETA1-4 : bond 0.01367 ( 6) link_BETA1-4 : angle 4.84682 ( 18) hydrogen bonds : bond 0.03536 ( 527) hydrogen bonds : angle 4.29050 ( 1554) SS BOND : bond 0.00597 ( 7) SS BOND : angle 2.93763 ( 14) covalent geometry : bond 0.00312 (10123) covalent geometry : angle 0.67762 (13810) *********************** 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 74 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8920 (mmm) cc_final: 0.8519 (mmm) REVERT: B 129 MET cc_start: 0.9313 (tpp) cc_final: 0.8972 (tpp) REVERT: B 172 PHE cc_start: 0.8587 (t80) cc_final: 0.8185 (t80) REVERT: B 259 MET cc_start: 0.9620 (mmp) cc_final: 0.9288 (mmm) REVERT: B 272 MET cc_start: 0.9286 (mmp) cc_final: 0.8975 (mmm) REVERT: B 311 MET cc_start: 0.8756 (ppp) cc_final: 0.7751 (ppp) REVERT: B 373 MET cc_start: 0.9621 (ttp) cc_final: 0.9411 (tpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1620 time to fit residues: 20.1649 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 : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 93 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 91 optimal weight: 0.0470 chunk 12 optimal weight: 0.4980 chunk 128 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049876 restraints weight = 97528.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050943 restraints weight = 59315.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051675 restraints weight = 40754.611| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10143 Z= 0.109 Angle : 0.693 9.560 13863 Z= 0.329 Chirality : 0.045 0.243 1598 Planarity : 0.004 0.051 1802 Dihedral : 5.774 56.630 1731 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.24), residues: 1355 helix: 2.01 (0.21), residues: 699 sheet: -0.34 (0.36), residues: 204 loop : -2.81 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 558 HIS 0.010 0.001 HIS B 127 PHE 0.017 0.001 PHE A 446 TYR 0.017 0.001 TYR A 678 ARG 0.004 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 7) link_NAG-ASN : angle 3.92723 ( 21) link_BETA1-4 : bond 0.01488 ( 6) link_BETA1-4 : angle 4.76697 ( 18) hydrogen bonds : bond 0.03266 ( 527) hydrogen bonds : angle 4.03436 ( 1554) SS BOND : bond 0.00500 ( 7) SS BOND : angle 2.93092 ( 14) covalent geometry : bond 0.00222 (10123) covalent geometry : angle 0.64883 (13810) ********************** 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 : 1.177 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8981 (mmm) cc_final: 0.8596 (mmm) REVERT: A 375 PHE cc_start: 0.9133 (m-10) cc_final: 0.8545 (m-80) REVERT: B 129 MET cc_start: 0.9337 (tpp) cc_final: 0.8948 (tpp) REVERT: B 171 TYR cc_start: 0.9136 (m-80) cc_final: 0.8713 (m-80) REVERT: B 172 PHE cc_start: 0.8599 (t80) cc_final: 0.8387 (t80) REVERT: B 259 MET cc_start: 0.9592 (mmp) cc_final: 0.9290 (mmm) REVERT: B 272 MET cc_start: 0.9276 (mmp) cc_final: 0.8977 (mmm) REVERT: B 311 MET cc_start: 0.8736 (ppp) cc_final: 0.7719 (ppp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1561 time to fit residues: 19.7066 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 : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 88 optimal weight: 0.0060 chunk 62 optimal weight: 30.0000 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.056316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047505 restraints weight = 100262.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048532 restraints weight = 61576.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049243 restraints weight = 42627.555| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4044 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= 0.163 Angle : 0.709 9.442 13863 Z= 0.346 Chirality : 0.045 0.227 1598 Planarity : 0.004 0.050 1802 Dihedral : 5.922 57.565 1731 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1355 helix: 1.97 (0.21), residues: 697 sheet: -0.38 (0.36), residues: 204 loop : -2.73 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 149 HIS 0.006 0.001 HIS A 524 PHE 0.015 0.001 PHE A 366 TYR 0.018 0.001 TYR A 615 ARG 0.004 0.001 ARG A 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 7) link_NAG-ASN : angle 3.89186 ( 21) link_BETA1-4 : bond 0.01300 ( 6) link_BETA1-4 : angle 4.70805 ( 18) hydrogen bonds : bond 0.03394 ( 527) hydrogen bonds : angle 4.19993 ( 1554) SS BOND : bond 0.00581 ( 7) SS BOND : angle 2.89474 ( 14) covalent geometry : bond 0.00339 (10123) covalent geometry : angle 0.66663 (13810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.23 seconds wall clock time: 54 minutes 10.68 seconds (3250.68 seconds total)