Starting phenix.real_space_refine on Fri Feb 14 10:41:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uo9_20823/02_2025/6uo9_20823.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uo9_20823/02_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_20823/02_2025/6uo9_20823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uo9_20823/02_2025/6uo9_20823.map" model { file = "/net/cci-nas-00/data/ceres_data/6uo9_20823/02_2025/6uo9_20823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uo9_20823/02_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-5592/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: 6.30, 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: 2.80 Conformation dependent library (CDL) restraints added in 1.3 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: 1.20 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: 3.22 Time building geometry restraints manager: 3.11 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: 2.520 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 25.500 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: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- 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 10123 Z= 0.417 Angle : 1.380 19.815 13810 Z= 0.799 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 *********************** 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 : 1.144 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: 0.1969 time to fit residues: 34.3328 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 : 1.138 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050542 restraints weight = 97510.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051657 restraints weight = 58421.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.052386 restraints weight = 39730.233| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 10123 Z= 0.272 Angle : 0.772 10.190 13810 Z= 0.398 Chirality : 0.047 0.218 1598 Planarity : 0.005 0.056 1802 Dihedral : 7.801 65.315 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 *********************** 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 : 1.211 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: 0.8976 (mmm) cc_final: 0.8612 (mmm) REVERT: A 390 TRP cc_start: 0.8770 (m100) cc_final: 0.8456 (m100) REVERT: B 59 MET cc_start: 0.9229 (mtm) cc_final: 0.8990 (mmm) REVERT: B 203 GLN cc_start: 0.8779 (tt0) cc_final: 0.7986 (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: 0.9012 (mmm) REVERT: B 272 MET cc_start: 0.9266 (tpp) cc_final: 0.9006 (mmm) REVERT: B 311 MET cc_start: 0.9230 (ptt) cc_final: 0.8793 (ppp) REVERT: B 373 MET cc_start: 0.9613 (ttp) cc_final: 0.9252 (tmm) outliers start: 3 outliers final: 2 residues processed: 88 average time/residue: 0.1615 time to fit residues: 22.9949 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 : 1.166 ------------------------------------------------------------------------------- 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: 9.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 503 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046539 restraints weight = 101291.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047564 restraints weight = 61528.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048253 restraints weight = 42495.505| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10123 Z= 0.378 Angle : 0.848 9.988 13810 Z= 0.443 Chirality : 0.049 0.315 1598 Planarity : 0.005 0.058 1802 Dihedral : 8.233 69.268 1731 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.12 % Allowed : 9.74 % Favored : 90.14 % 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: -1.12 (0.23), residues: 1355 helix: 0.81 (0.20), residues: 699 sheet: -1.16 (0.35), residues: 209 loop : -3.10 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 304 HIS 0.009 0.002 HIS A 524 PHE 0.031 0.003 PHE A 401 TYR 0.026 0.002 TYR B 193 ARG 0.006 0.001 ARG A 585 *********************** 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 76 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8954 (mmm) cc_final: 0.8583 (mmm) REVERT: A 390 TRP cc_start: 0.8904 (m100) cc_final: 0.8586 (m100) REVERT: B 171 TYR cc_start: 0.9158 (m-80) cc_final: 0.8745 (m-80) REVERT: B 172 PHE cc_start: 0.8667 (t80) cc_final: 0.8326 (t80) REVERT: B 259 MET cc_start: 0.9595 (mmp) cc_final: 0.9323 (mmm) REVERT: B 311 MET cc_start: 0.8862 (ptt) cc_final: 0.8618 (ppp) REVERT: B 373 MET cc_start: 0.9661 (ttp) cc_final: 0.9342 (tpp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1692 time to fit residues: 21.3197 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 : 1.173 ------------------------------------------------------------------------------- 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: 0.0370 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.058616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050265 restraints weight = 97391.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.051349 restraints weight = 54485.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.052143 restraints weight = 33993.745| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10123 Z= 0.171 Angle : 0.684 10.107 13810 Z= 0.342 Chirality : 0.046 0.250 1598 Planarity : 0.004 0.054 1802 Dihedral : 6.976 57.332 1731 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (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: -0.57 (0.23), residues: 1355 helix: 1.28 (0.20), residues: 702 sheet: -0.77 (0.34), residues: 208 loop : -2.99 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 558 HIS 0.004 0.001 HIS A 287 PHE 0.031 0.002 PHE A 446 TYR 0.021 0.001 TYR B 697 ARG 0.005 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8902 (mmm) cc_final: 0.8535 (mmm) REVERT: A 390 TRP cc_start: 0.8874 (m100) cc_final: 0.8648 (m100) REVERT: B 59 MET cc_start: 0.9325 (mtm) cc_final: 0.9061 (mmm) REVERT: B 129 MET cc_start: 0.9243 (tpp) cc_final: 0.8833 (tpp) REVERT: B 172 PHE cc_start: 0.8588 (t80) cc_final: 0.8260 (t80) REVERT: B 259 MET cc_start: 0.9592 (mmp) cc_final: 0.9279 (mmm) REVERT: B 272 MET cc_start: 0.9211 (mmp) cc_final: 0.8927 (mmm) REVERT: B 311 MET cc_start: 0.8810 (ptt) cc_final: 0.8599 (ppp) REVERT: B 373 MET cc_start: 0.9677 (ttp) cc_final: 0.9358 (tpp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1872 time to fit residues: 24.0290 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 : 1.202 ------------------------------------------------------------------------------- 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: 7.9990 chunk 96 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 113 optimal weight: 0.0980 chunk 52 optimal weight: 9.9990 chunk 23 optimal weight: 0.0270 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.049329 restraints weight = 98203.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050403 restraints weight = 59229.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051162 restraints weight = 40319.963| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10123 Z= 0.173 Angle : 0.655 9.596 13810 Z= 0.329 Chirality : 0.045 0.234 1598 Planarity : 0.004 0.053 1802 Dihedral : 6.276 57.830 1731 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: -0.30 (0.24), residues: 1355 helix: 1.54 (0.20), residues: 696 sheet: -0.58 (0.34), residues: 206 loop : -2.90 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.004 0.001 HIS A 524 PHE 0.023 0.001 PHE A 446 TYR 0.017 0.001 TYR B 697 ARG 0.004 0.000 ARG A 167 *********************** 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 75 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8986 (mmm) cc_final: 0.8673 (mmm) REVERT: A 375 PHE cc_start: 0.9195 (m-10) cc_final: 0.8531 (m-80) REVERT: A 390 TRP cc_start: 0.8903 (m100) cc_final: 0.8699 (m100) REVERT: A 509 ILE cc_start: 0.9707 (tp) cc_final: 0.9484 (pt) REVERT: B 129 MET cc_start: 0.9303 (tpp) cc_final: 0.9079 (tpp) REVERT: B 172 PHE cc_start: 0.8630 (t80) cc_final: 0.8279 (t80) REVERT: B 259 MET cc_start: 0.9593 (mmp) cc_final: 0.9267 (mmm) REVERT: B 272 MET cc_start: 0.9282 (mmp) cc_final: 0.8970 (mmm) REVERT: B 311 MET cc_start: 0.8811 (ptt) cc_final: 0.8581 (ppp) REVERT: B 373 MET cc_start: 0.9646 (ttp) cc_final: 0.9355 (tpp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1618 time to fit residues: 19.9097 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 : 1.166 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046317 restraints weight = 100912.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047320 restraints weight = 61892.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048005 restraints weight = 42985.293| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10123 Z= 0.289 Angle : 0.726 9.535 13810 Z= 0.372 Chirality : 0.047 0.223 1598 Planarity : 0.005 0.052 1802 Dihedral : 6.577 58.850 1731 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: -0.35 (0.23), residues: 1355 helix: 1.46 (0.20), residues: 699 sheet: -0.56 (0.34), residues: 204 loop : -2.90 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 149 HIS 0.009 0.002 HIS A 524 PHE 0.020 0.002 PHE A 446 TYR 0.018 0.002 TYR B 193 ARG 0.006 0.001 ARG A 167 *********************** 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 68 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8826 (mmm) cc_final: 0.8500 (mmm) REVERT: A 375 PHE cc_start: 0.9245 (m-10) cc_final: 0.9038 (m-80) REVERT: B 172 PHE cc_start: 0.8557 (t80) cc_final: 0.8136 (t80) REVERT: B 259 MET cc_start: 0.9546 (mmp) cc_final: 0.9136 (mmm) REVERT: B 272 MET cc_start: 0.9187 (mmp) cc_final: 0.8868 (mmm) REVERT: B 373 MET cc_start: 0.9578 (ttp) cc_final: 0.9314 (tpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1623 time to fit residues: 18.3140 Evaluate side-chains 59 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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: 8.9990 chunk 94 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 129 optimal weight: 0.0030 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.056742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047845 restraints weight = 100679.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048882 restraints weight = 61386.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049591 restraints weight = 42167.694| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10123 Z= 0.190 Angle : 0.663 9.560 13810 Z= 0.333 Chirality : 0.046 0.233 1598 Planarity : 0.004 0.053 1802 Dihedral : 6.107 57.266 1731 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % 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 (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: -0.07 (0.24), residues: 1355 helix: 1.67 (0.20), residues: 700 sheet: -0.31 (0.36), residues: 199 loop : -2.79 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 149 HIS 0.004 0.001 HIS A 524 PHE 0.019 0.001 PHE A 446 TYR 0.020 0.001 TYR A 678 ARG 0.004 0.000 ARG A 167 *********************** 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 73 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8835 (mmm) cc_final: 0.8552 (mmm) REVERT: B 129 MET cc_start: 0.9161 (tpp) cc_final: 0.8787 (tpp) REVERT: B 172 PHE cc_start: 0.8554 (t80) cc_final: 0.8144 (t80) REVERT: B 259 MET cc_start: 0.9588 (mmp) cc_final: 0.9146 (mmm) REVERT: B 272 MET cc_start: 0.9216 (mmp) cc_final: 0.8898 (mmm) REVERT: B 311 MET cc_start: 0.8768 (ppp) cc_final: 0.8222 (ppp) REVERT: B 373 MET cc_start: 0.9563 (ttp) cc_final: 0.9323 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1720 time to fit residues: 20.0211 Evaluate side-chains 60 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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: 20.0000 chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 113 optimal weight: 0.0670 chunk 15 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.053586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044848 restraints weight = 102089.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.045816 restraints weight = 62979.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046461 restraints weight = 44072.321| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10123 Z= 0.360 Angle : 0.781 9.574 13810 Z= 0.402 Chirality : 0.047 0.222 1598 Planarity : 0.005 0.054 1802 Dihedral : 6.761 58.440 1731 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1355 helix: 1.43 (0.20), residues: 693 sheet: -0.65 (0.35), residues: 210 loop : -2.87 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 149 HIS 0.005 0.002 HIS A 422 PHE 0.021 0.002 PHE A 773 TYR 0.020 0.002 TYR A 615 ARG 0.006 0.001 ARG A 666 *********************** 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 66 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8789 (mmm) cc_final: 0.8460 (mmm) REVERT: B 172 PHE cc_start: 0.8562 (t80) cc_final: 0.8134 (t80) REVERT: B 259 MET cc_start: 0.9614 (mmp) cc_final: 0.9266 (mmm) REVERT: B 272 MET cc_start: 0.9194 (mmp) cc_final: 0.8881 (mmm) REVERT: B 311 MET cc_start: 0.8869 (ppp) cc_final: 0.8026 (ppp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1774 time to fit residues: 18.7989 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 : 1.108 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3172 r_free = 0.3172 target = 0.055231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046484 restraints weight = 100717.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047501 restraints weight = 61543.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048185 restraints weight = 42560.113| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10123 Z= 0.234 Angle : 0.723 10.701 13810 Z= 0.363 Chirality : 0.047 0.237 1598 Planarity : 0.004 0.054 1802 Dihedral : 7.096 57.810 1731 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -0.22 (0.24), residues: 1355 helix: 1.54 (0.20), residues: 698 sheet: -0.38 (0.37), residues: 197 loop : -2.82 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 149 HIS 0.004 0.001 HIS B 127 PHE 0.018 0.002 PHE A 446 TYR 0.019 0.002 TYR B 193 ARG 0.004 0.001 ARG B 212 *********************** 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 71 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8811 (mmm) cc_final: 0.8446 (mmm) REVERT: B 59 MET cc_start: 0.8861 (mtm) cc_final: 0.8496 (ptp) REVERT: B 129 MET cc_start: 0.9127 (tpp) cc_final: 0.8789 (tpp) REVERT: B 172 PHE cc_start: 0.8525 (t80) cc_final: 0.8108 (t80) REVERT: B 259 MET cc_start: 0.9615 (mmp) cc_final: 0.9274 (mmm) REVERT: B 272 MET cc_start: 0.9214 (mmp) cc_final: 0.8903 (mmm) REVERT: B 311 MET cc_start: 0.8861 (ppp) cc_final: 0.7958 (ppp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1796 time to fit residues: 20.5083 Evaluate side-chains 60 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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: 0.0030 chunk 103 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 83 optimal weight: 0.0570 chunk 86 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 overall best weight: 0.7910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049444 restraints weight = 97895.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050508 restraints weight = 59346.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.051244 restraints weight = 40608.760| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10123 Z= 0.154 Angle : 0.682 9.779 13810 Z= 0.333 Chirality : 0.046 0.251 1598 Planarity : 0.004 0.052 1802 Dihedral : 6.088 56.344 1731 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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: 0.13 (0.24), residues: 1355 helix: 1.87 (0.21), residues: 694 sheet: -0.17 (0.37), residues: 198 loop : -2.74 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 558 HIS 0.005 0.001 HIS B 127 PHE 0.017 0.001 PHE A 446 TYR 0.018 0.001 TYR A 615 ARG 0.005 0.000 ARG B 212 ********************** 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 74 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8973 (mmm) cc_final: 0.8531 (mmm) REVERT: B 59 MET cc_start: 0.9099 (mtm) cc_final: 0.8823 (ptp) REVERT: B 129 MET cc_start: 0.9252 (tpp) cc_final: 0.8899 (tpp) REVERT: B 172 PHE cc_start: 0.8576 (t80) cc_final: 0.8351 (t80) REVERT: B 259 MET cc_start: 0.9651 (mmp) cc_final: 0.9370 (mmm) REVERT: B 272 MET cc_start: 0.9253 (mmp) cc_final: 0.8965 (mmm) REVERT: B 311 MET cc_start: 0.8785 (ppp) cc_final: 0.7871 (ppp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1560 time to fit residues: 19.0168 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 : 1.197 ------------------------------------------------------------------------------- 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: 0.3980 chunk 62 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 = 0.3184 r_free = 0.3184 target = 0.055843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.047086 restraints weight = 100855.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048100 restraints weight = 61203.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048800 restraints weight = 42319.515| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10123 Z= 0.220 Angle : 0.682 9.466 13810 Z= 0.342 Chirality : 0.045 0.224 1598 Planarity : 0.004 0.051 1802 Dihedral : 6.165 57.827 1731 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % 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: 695 sheet: -0.28 (0.37), residues: 198 loop : -2.79 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 149 HIS 0.005 0.001 HIS A 524 PHE 0.016 0.002 PHE A 446 TYR 0.020 0.002 TYR B 193 ARG 0.004 0.001 ARG A 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.96 seconds wall clock time: 47 minutes 29.51 seconds (2849.51 seconds total)