Starting phenix.real_space_refine on Sat Jul 4 12:56:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t1f_40962/07_2026/8t1f_40962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1f_40962/07_2026/8t1f_40962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8t1f_40962/07_2026/8t1f_40962.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t1f_40962/07_2026/8t1f_40962.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t1f_40962/07_2026/8t1f_40962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1f_40962/07_2026/8t1f_40962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t1f_40962/07_2026/8t1f_40962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1f_40962/07_2026/8t1f_40962.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 104 5.16 5 C 13566 2.51 5 N 3414 2.21 5 O 3690 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20790 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5107 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 24, 'TRANS': 610} Chain breaks: 1 Chain: "B" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5116 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 24, 'TRANS': 611} Chain breaks: 1 Chain: "C" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5107 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 24, 'TRANS': 610} Chain breaks: 1 Chain: "D" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5116 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 24, 'TRANS': 611} Chain breaks: 1 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'POV': 1, 'X7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'POV': 1, 'X7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'POV': 1, 'X7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'POV': 1, 'X7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.38, per 1000 atoms: 0.21 Number of scatterers: 20790 At special positions: 0 Unit cell: (151.06, 147.74, 120.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 4 15.00 F 12 9.00 O 3690 8.00 N 3414 7.00 C 13566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 892.8 milliseconds 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4788 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 8 sheets defined 58.5% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.568A pdb=" N SER A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 removed outlier: 4.135A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.689A pdb=" N ALA A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.589A pdb=" N ALA A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.702A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.814A pdb=" N GLY A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 297 through 306 removed outlier: 3.817A pdb=" N VAL A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 3.804A pdb=" N LEU A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.528A pdb=" N THR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 removed outlier: 3.608A pdb=" N ALA A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.535A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.543A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 491 removed outlier: 4.265A pdb=" N VAL A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 533 removed outlier: 3.757A pdb=" N LEU A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 570 removed outlier: 4.054A pdb=" N PHE A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 557 " --> pdb=" O TYR A 553 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 560 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 removed outlier: 3.557A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.581A pdb=" N LEU A 590 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 591 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 removed outlier: 3.640A pdb=" N MET A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 626 removed outlier: 3.855A pdb=" N PHE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 633 removed outlier: 3.597A pdb=" N VAL A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.799A pdb=" N LEU A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 691 through 720 removed outlier: 3.647A pdb=" N ILE A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 710 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 748 removed outlier: 3.651A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 735 " --> pdb=" O HIS A 731 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.547A pdb=" N PHE B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.563A pdb=" N PHE B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.444A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.745A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 257 " --> pdb=" O TYR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.522A pdb=" N THR B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.548A pdb=" N VAL B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 337 through 357 removed outlier: 3.701A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 384 through 391 removed outlier: 3.700A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 removed outlier: 3.586A pdb=" N LEU B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.724A pdb=" N ILE B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 removed outlier: 4.146A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 removed outlier: 4.025A pdb=" N ASN B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 479 " --> pdb=" O VAL B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 491 Processing helix chain 'B' and resid 504 through 535 removed outlier: 3.646A pdb=" N LEU B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN B 528 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 529 " --> pdb=" O PHE B 525 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 removed outlier: 3.723A pdb=" N LEU B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 560 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 588 removed outlier: 3.717A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 removed outlier: 3.658A pdb=" N PHE B 592 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 593 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 612 removed outlier: 4.432A pdb=" N TYR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 3.516A pdb=" N VAL B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 622 " --> pdb=" O LEU B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 665 through 678 removed outlier: 3.603A pdb=" N PHE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 721 removed outlier: 3.777A pdb=" N PHE B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 708 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 748 removed outlier: 4.956A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.569A pdb=" N SER C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 removed outlier: 4.135A pdb=" N LEU C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.690A pdb=" N ALA C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.590A pdb=" N ALA C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.702A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.815A pdb=" N GLY C 279 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.816A pdb=" N VAL C 301 " --> pdb=" O GLN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 removed outlier: 3.805A pdb=" N LEU C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 356 removed outlier: 3.528A pdb=" N THR C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 removed outlier: 3.609A pdb=" N ALA C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.535A pdb=" N PHE C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 454 through 465 removed outlier: 3.542A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 491 removed outlier: 4.266A pdb=" N VAL C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS C 480 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 485 " --> pdb=" O ALA C 481 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 533 removed outlier: 3.757A pdb=" N LEU C 523 " --> pdb=" O PHE C 519 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 570 removed outlier: 4.054A pdb=" N PHE C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 557 " --> pdb=" O TYR C 553 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 586 removed outlier: 3.557A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 581 " --> pdb=" O VAL C 577 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 586 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 594 removed outlier: 3.582A pdb=" N LEU C 590 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 591 " --> pdb=" O ASN C 588 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR C 593 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 613 removed outlier: 3.640A pdb=" N MET C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 606 " --> pdb=" O TYR C 602 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 607 " --> pdb=" O SER C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 626 removed outlier: 3.855A pdb=" N PHE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 633 removed outlier: 3.597A pdb=" N VAL C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 679 removed outlier: 3.799A pdb=" N LEU C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 Processing helix chain 'C' and resid 691 through 720 removed outlier: 3.648A pdb=" N ILE C 704 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 710 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 720 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 748 removed outlier: 3.651A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 734 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 747 " --> pdb=" O ASP C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.548A pdb=" N PHE D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP D 156 " --> pdb=" O PRO D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 removed outlier: 3.565A pdb=" N PHE D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 176 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.445A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.746A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 3.522A pdb=" N THR D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 removed outlier: 3.548A pdb=" N VAL D 301 " --> pdb=" O GLN D 297 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 331 Processing helix chain 'D' and resid 337 through 357 removed outlier: 3.702A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 380 Processing helix chain 'D' and resid 384 through 391 removed outlier: 3.699A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 403 removed outlier: 3.586A pdb=" N LEU D 402 " --> pdb=" O THR D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 removed outlier: 3.723A pdb=" N ILE D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 4.146A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 465 " --> pdb=" O ASP D 461 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE D 466 " --> pdb=" O LYS D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 479 removed outlier: 4.024A pdb=" N ASN D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 479 " --> pdb=" O VAL D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 491 Processing helix chain 'D' and resid 504 through 535 removed outlier: 3.645A pdb=" N LEU D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 515 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN D 528 " --> pdb=" O PHE D 524 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 529 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 534 " --> pdb=" O LYS D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 568 removed outlier: 3.724A pdb=" N LEU D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 560 " --> pdb=" O TYR D 556 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 588 removed outlier: 3.717A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP D 586 " --> pdb=" O LEU D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 594 removed outlier: 3.658A pdb=" N PHE D 592 " --> pdb=" O ALA D 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 593 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 612 removed outlier: 4.432A pdb=" N TYR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 607 " --> pdb=" O SER D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 3.516A pdb=" N VAL D 620 " --> pdb=" O ARG D 616 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 622 " --> pdb=" O LEU D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 633 Processing helix chain 'D' and resid 665 through 678 removed outlier: 3.603A pdb=" N PHE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 721 removed outlier: 3.777A pdb=" N PHE D 695 " --> pdb=" O TYR D 691 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 708 " --> pdb=" O ILE D 704 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 714 " --> pdb=" O LEU D 710 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 717 " --> pdb=" O MET D 713 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 718 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 748 removed outlier: 4.955A pdb=" N LYS D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS D 731 " --> pdb=" O LYS D 727 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 747 " --> pdb=" O ASP D 743 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 754 Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 410 removed outlier: 6.562A pdb=" N SER A 416 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 763 through 766 removed outlier: 6.756A pdb=" N ASP A 773 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 405 through 410 removed outlier: 6.640A pdb=" N SER B 416 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 762 through 766 removed outlier: 6.607A pdb=" N THR B 763 " --> pdb=" O ARG B 775 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ARG B 775 " --> pdb=" O THR B 763 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 765 " --> pdb=" O ASP B 773 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.561A pdb=" N SER C 416 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 763 through 766 removed outlier: 6.756A pdb=" N ASP C 773 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 405 through 410 removed outlier: 6.639A pdb=" N SER D 416 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 762 through 766 removed outlier: 6.607A pdb=" N THR D 763 " --> pdb=" O ARG D 775 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ARG D 775 " --> pdb=" O THR D 763 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY D 765 " --> pdb=" O ASP D 773 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2445 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: 3.26 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3485 1.32 - 1.45: 5674 1.45 - 1.57: 11927 1.57 - 1.69: 12 1.69 - 1.82: 172 Bond restraints: 21270 Sorted by residual: bond pdb=" C ILE B 210 " pdb=" N PRO B 211 " ideal model delta sigma weight residual 1.336 1.389 -0.054 1.23e-02 6.61e+03 1.91e+01 bond pdb=" C ILE D 210 " pdb=" N PRO D 211 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.23e-02 6.61e+03 1.88e+01 bond pdb=" C ARG A 151 " pdb=" N PRO A 152 " ideal model delta sigma weight residual 1.337 1.384 -0.048 1.11e-02 8.12e+03 1.85e+01 bond pdb=" C ARG C 151 " pdb=" N PRO C 152 " ideal model delta sigma weight residual 1.337 1.384 -0.048 1.11e-02 8.12e+03 1.85e+01 bond pdb=" C ILE C 210 " pdb=" N PRO C 211 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.23e-02 6.61e+03 1.30e+01 ... (remaining 21265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 28275 4.06 - 8.12: 465 8.12 - 12.18: 54 12.18 - 16.24: 2 16.24 - 20.30: 4 Bond angle restraints: 28800 Sorted by residual: angle pdb=" C THR A 721 " pdb=" N VAL A 722 " pdb=" CA VAL A 722 " ideal model delta sigma weight residual 121.97 133.98 -12.01 1.80e+00 3.09e-01 4.45e+01 angle pdb=" C THR C 721 " pdb=" N VAL C 722 " pdb=" CA VAL C 722 " ideal model delta sigma weight residual 121.97 133.95 -11.98 1.80e+00 3.09e-01 4.43e+01 angle pdb=" N ALA B 364 " pdb=" CA ALA B 364 " pdb=" C ALA B 364 " ideal model delta sigma weight residual 114.75 106.74 8.01 1.26e+00 6.30e-01 4.04e+01 angle pdb=" N ALA D 364 " pdb=" CA ALA D 364 " pdb=" C ALA D 364 " ideal model delta sigma weight residual 114.75 106.74 8.01 1.26e+00 6.30e-01 4.04e+01 angle pdb=" C SER A 189 " pdb=" N THR A 190 " pdb=" CA THR A 190 " ideal model delta sigma weight residual 121.54 133.38 -11.84 1.91e+00 2.74e-01 3.84e+01 ... (remaining 28795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 12500 35.58 - 71.15: 174 71.15 - 106.73: 8 106.73 - 142.30: 4 142.30 - 177.88: 6 Dihedral angle restraints: 12692 sinusoidal: 5258 harmonic: 7434 Sorted by residual: dihedral pdb=" CA VAL C 722 " pdb=" C VAL C 722 " pdb=" N GLY C 723 " pdb=" CA GLY C 723 " ideal model delta harmonic sigma weight residual -180.00 -112.53 -67.47 0 5.00e+00 4.00e-02 1.82e+02 dihedral pdb=" CA VAL A 722 " pdb=" C VAL A 722 " pdb=" N GLY A 723 " pdb=" CA GLY A 723 " ideal model delta harmonic sigma weight residual -180.00 -112.54 -67.46 0 5.00e+00 4.00e-02 1.82e+02 dihedral pdb=" CA SER A 189 " pdb=" C SER A 189 " pdb=" N THR A 190 " pdb=" CA THR A 190 " ideal model delta harmonic sigma weight residual -180.00 -132.57 -47.43 0 5.00e+00 4.00e-02 9.00e+01 ... (remaining 12689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2703 0.072 - 0.145: 470 0.145 - 0.217: 47 0.217 - 0.290: 16 0.290 - 0.362: 2 Chirality restraints: 3238 Sorted by residual: chirality pdb=" CB VAL C 722 " pdb=" CA VAL C 722 " pdb=" CG1 VAL C 722 " pdb=" CG2 VAL C 722 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CB VAL A 722 " pdb=" CA VAL A 722 " pdb=" CG1 VAL A 722 " pdb=" CG2 VAL A 722 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CG LEU B 551 " pdb=" CB LEU B 551 " pdb=" CD1 LEU B 551 " pdb=" CD2 LEU B 551 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 3235 not shown) Planarity restraints: 3584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 X7N B1201 " -0.084 2.00e-02 2.50e+03 5.36e-02 6.47e+01 pdb=" C17 X7N B1201 " 0.002 2.00e-02 2.50e+03 pdb=" C18 X7N B1201 " -0.013 2.00e-02 2.50e+03 pdb=" C19 X7N B1201 " -0.046 2.00e-02 2.50e+03 pdb=" C2 X7N B1201 " -0.015 2.00e-02 2.50e+03 pdb=" C26 X7N B1201 " 0.111 2.00e-02 2.50e+03 pdb=" C3 X7N B1201 " 0.003 2.00e-02 2.50e+03 pdb=" C4 X7N B1201 " 0.060 2.00e-02 2.50e+03 pdb=" N25 X7N B1201 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 X7N C1201 " -0.056 2.00e-02 2.50e+03 5.35e-02 6.45e+01 pdb=" C17 X7N C1201 " 0.054 2.00e-02 2.50e+03 pdb=" C18 X7N C1201 " 0.043 2.00e-02 2.50e+03 pdb=" C19 X7N C1201 " -0.101 2.00e-02 2.50e+03 pdb=" C2 X7N C1201 " 0.030 2.00e-02 2.50e+03 pdb=" C26 X7N C1201 " 0.013 2.00e-02 2.50e+03 pdb=" C3 X7N C1201 " 0.045 2.00e-02 2.50e+03 pdb=" C4 X7N C1201 " -0.060 2.00e-02 2.50e+03 pdb=" N25 X7N C1201 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 X7N D1201 " 0.074 2.00e-02 2.50e+03 4.90e-02 5.41e+01 pdb=" C17 X7N D1201 " 0.003 2.00e-02 2.50e+03 pdb=" C18 X7N D1201 " 0.015 2.00e-02 2.50e+03 pdb=" C19 X7N D1201 " 0.036 2.00e-02 2.50e+03 pdb=" C2 X7N D1201 " 0.015 2.00e-02 2.50e+03 pdb=" C26 X7N D1201 " -0.102 2.00e-02 2.50e+03 pdb=" C3 X7N D1201 " 0.001 2.00e-02 2.50e+03 pdb=" C4 X7N D1201 " -0.061 2.00e-02 2.50e+03 pdb=" N25 X7N D1201 " 0.018 2.00e-02 2.50e+03 ... (remaining 3581 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1114 2.72 - 3.26: 20235 3.26 - 3.81: 33049 3.81 - 4.35: 42356 4.35 - 4.90: 70141 Nonbonded interactions: 166895 Sorted by model distance: nonbonded pdb=" OH TYR A 235 " pdb=" O GLY D 800 " model vdw 2.171 3.040 nonbonded pdb=" O LEU D 686 " pdb=" OG1 THR D 689 " model vdw 2.263 3.040 nonbonded pdb=" O LEU B 686 " pdb=" OG1 THR B 689 " model vdw 2.264 3.040 nonbonded pdb=" O ARG A 206 " pdb=" OH TYR A 253 " model vdw 2.289 3.040 nonbonded pdb=" O ARG C 206 " pdb=" OH TYR C 253 " model vdw 2.290 3.040 ... (remaining 166890 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.010 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.830 Find NCS groups from input model: 0.180 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 0.066 21270 Z= 0.309 Angle : 1.324 20.302 28800 Z= 0.755 Chirality : 0.058 0.362 3238 Planarity : 0.007 0.065 3584 Dihedral : 13.666 177.877 7904 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.63 % Allowed : 11.64 % Favored : 87.73 % Rotamer: Outliers : 0.85 % Allowed : 8.67 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.59 (0.12), residues: 2526 helix: -3.95 (0.08), residues: 1402 sheet: -3.48 (0.42), residues: 116 loop : -3.12 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 594 TYR 0.019 0.002 TYR A 508 PHE 0.033 0.002 PHE D 580 TRP 0.029 0.002 TRP B 733 HIS 0.007 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.31 (21270) covalent geometry : angle 1.32409 / 0.76 (28800) hydrogen bonds : bond 0.31287 / 20.81 ( 845) hydrogen bonds : angle 10.34865 / 7.25 ( 2445) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 664 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8204 (m-30) cc_final: 0.7829 (m-30) REVERT: A 222 ASN cc_start: 0.8033 (m110) cc_final: 0.7791 (m-40) REVERT: A 287 LEU cc_start: 0.8266 (tt) cc_final: 0.8040 (mt) REVERT: A 411 TYR cc_start: 0.8794 (t80) cc_final: 0.8448 (t80) REVERT: A 530 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7833 (tttp) REVERT: A 534 MET cc_start: 0.8069 (mpm) cc_final: 0.7780 (mpm) REVERT: A 543 LEU cc_start: 0.8758 (mm) cc_final: 0.8530 (mp) REVERT: A 628 TYR cc_start: 0.8068 (m-80) cc_final: 0.7602 (m-80) REVERT: A 698 LEU cc_start: 0.7722 (mp) cc_final: 0.7490 (mp) REVERT: A 773 ASP cc_start: 0.8344 (t0) cc_final: 0.8134 (t0) REVERT: B 206 ARG cc_start: 0.8031 (mmp-170) cc_final: 0.7810 (mmp-170) REVERT: B 625 MET cc_start: 0.7985 (ttm) cc_final: 0.7776 (ttt) REVERT: B 691 TYR cc_start: 0.7073 (m-80) cc_final: 0.6688 (m-80) REVERT: B 712 ASN cc_start: 0.7053 (t0) cc_final: 0.6841 (t0) REVERT: C 156 ASP cc_start: 0.7983 (t0) cc_final: 0.7371 (t0) REVERT: C 179 ARG cc_start: 0.7944 (mmm-85) cc_final: 0.7498 (mtp85) REVERT: C 411 TYR cc_start: 0.8616 (t80) cc_final: 0.8304 (t80) REVERT: C 477 SER cc_start: 0.8341 (m) cc_final: 0.7766 (t) REVERT: C 530 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7766 (tttp) REVERT: C 572 GLU cc_start: 0.7791 (tp30) cc_final: 0.7582 (mt-10) REVERT: C 799 PRO cc_start: 0.8571 (Cg_endo) cc_final: 0.8362 (Cg_exo) REVERT: D 156 ASP cc_start: 0.8244 (t70) cc_final: 0.7839 (t0) REVERT: D 172 PHE cc_start: 0.8550 (t80) cc_final: 0.8233 (t80) REVERT: D 331 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8446 (pt) REVERT: D 395 THR cc_start: 0.8382 (p) cc_final: 0.8122 (m) REVERT: D 612 LYS cc_start: 0.8576 (ttpm) cc_final: 0.8097 (mmmt) REVERT: D 621 TYR cc_start: 0.8561 (t80) cc_final: 0.8056 (t80) REVERT: D 685 MET cc_start: 0.6947 (mpt) cc_final: 0.6513 (mmm) REVERT: D 730 LYS cc_start: 0.8697 (ptmm) cc_final: 0.8487 (pttm) REVERT: D 736 GLN cc_start: 0.8498 (mt0) cc_final: 0.8032 (mt0) outliers start: 19 outliers final: 1 residues processed: 672 average time/residue: 0.1641 time to fit residues: 166.7659 Evaluate side-chains 410 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 408 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain D residue 331 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 HIS A 207 ASN A 228 ASN A 265 HIS A 338 ASN A 361 ASN A 474 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 541 ASN A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 784 ASN B 176 HIS B 201 ASN B 204 ASN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS B 338 ASN B 361 ASN B 492 GLN B 550 GLN B 588 ASN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN C 176 HIS C 228 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 474 ASN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 550 GLN C 637 ASN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 ASN D 204 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN D 326 HIS D 492 GLN D 784 ASN D 789 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130505 restraints weight = 29962.808| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.26 r_work: 0.3278 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21270 Z= 0.160 Angle : 0.797 11.383 28800 Z= 0.406 Chirality : 0.045 0.313 3238 Planarity : 0.006 0.053 3584 Dihedral : 12.229 172.096 3054 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.78 % Favored : 89.75 % Rotamer: Outliers : 2.37 % Allowed : 13.76 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.14), residues: 2526 helix: -2.28 (0.11), residues: 1438 sheet: -3.04 (0.46), residues: 116 loop : -2.73 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 271 TYR 0.018 0.002 TYR D 574 PHE 0.025 0.002 PHE D 666 TRP 0.025 0.002 TRP C 733 HIS 0.007 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (21270) covalent geometry : angle 0.79700 / 0.41 (28800) hydrogen bonds : bond 0.05439 / 3.61 ( 845) hydrogen bonds : angle 5.46882 / 3.78 ( 2445) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 474 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8117 (m-30) cc_final: 0.7888 (m-30) REVERT: A 222 ASN cc_start: 0.7861 (m110) cc_final: 0.7587 (m110) REVERT: A 477 SER cc_start: 0.8733 (m) cc_final: 0.8403 (t) REVERT: A 628 TYR cc_start: 0.8001 (m-80) cc_final: 0.7687 (m-80) REVERT: A 685 MET cc_start: 0.6760 (mmt) cc_final: 0.6549 (mmt) REVERT: A 696 ILE cc_start: 0.8466 (tp) cc_final: 0.8259 (pt) REVERT: B 263 ASP cc_start: 0.6453 (t0) cc_final: 0.6184 (t0) REVERT: B 289 LEU cc_start: 0.8737 (tp) cc_final: 0.7809 (tt) REVERT: B 291 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9089 (tp) REVERT: B 345 MET cc_start: 0.8393 (mmm) cc_final: 0.8088 (mmm) REVERT: B 614 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8032 (tm) REVERT: B 791 ASN cc_start: 0.7876 (m110) cc_final: 0.6671 (p0) REVERT: C 156 ASP cc_start: 0.8029 (t0) cc_final: 0.7381 (t0) REVERT: C 179 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7737 (mtp85) REVERT: C 303 TYR cc_start: 0.7993 (t80) cc_final: 0.7607 (t80) REVERT: C 345 MET cc_start: 0.9135 (mmm) cc_final: 0.8841 (mmm) REVERT: C 369 ASP cc_start: 0.8628 (t0) cc_final: 0.8408 (t0) REVERT: C 530 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7923 (tttp) REVERT: C 553 TYR cc_start: 0.7920 (m-80) cc_final: 0.7702 (m-80) REVERT: C 607 GLN cc_start: 0.7771 (mp10) cc_final: 0.7511 (mp10) REVERT: D 156 ASP cc_start: 0.8371 (t70) cc_final: 0.8094 (t0) REVERT: D 253 TYR cc_start: 0.7852 (m-10) cc_final: 0.7634 (m-10) REVERT: D 263 ASP cc_start: 0.6641 (t0) cc_final: 0.6308 (t0) REVERT: D 395 THR cc_start: 0.8358 (p) cc_final: 0.8042 (m) REVERT: D 473 ILE cc_start: 0.8929 (mm) cc_final: 0.8656 (mt) REVERT: D 612 LYS cc_start: 0.8512 (ttpm) cc_final: 0.8223 (mttt) REVERT: D 614 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8059 (tm) REVERT: D 747 SER cc_start: 0.8938 (m) cc_final: 0.8722 (t) outliers start: 53 outliers final: 22 residues processed: 506 average time/residue: 0.1504 time to fit residues: 118.7302 Evaluate side-chains 398 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 373 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 717 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 132 optimal weight: 7.9990 chunk 211 optimal weight: 0.0370 chunk 233 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN B 784 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN D 176 HIS D 228 ASN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.163327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129130 restraints weight = 30160.550| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.18 r_work: 0.3252 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21270 Z= 0.151 Angle : 0.739 11.660 28800 Z= 0.374 Chirality : 0.044 0.264 3238 Planarity : 0.005 0.060 3584 Dihedral : 10.830 153.908 3052 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.94 % Favored : 89.59 % Rotamer: Outliers : 3.66 % Allowed : 14.97 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.16), residues: 2526 helix: -1.31 (0.12), residues: 1450 sheet: -2.54 (0.54), residues: 98 loop : -2.66 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 336 TYR 0.022 0.002 TYR A 253 PHE 0.031 0.002 PHE C 751 TRP 0.021 0.002 TRP B 733 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (21270) covalent geometry : angle 0.73860 / 0.37 (28800) hydrogen bonds : bond 0.04128 / 2.73 ( 845) hydrogen bonds : angle 4.83767 / 3.33 ( 2445) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 439 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7944 (m110) cc_final: 0.7627 (m110) REVERT: A 295 THR cc_start: 0.8643 (p) cc_final: 0.8036 (t) REVERT: A 477 SER cc_start: 0.8682 (m) cc_final: 0.8333 (t) REVERT: A 531 ASP cc_start: 0.8126 (m-30) cc_final: 0.7898 (m-30) REVERT: A 534 MET cc_start: 0.7765 (mmp) cc_final: 0.7087 (ptt) REVERT: B 156 ASP cc_start: 0.8762 (t70) cc_final: 0.8479 (t0) REVERT: B 206 ARG cc_start: 0.7926 (mmp-170) cc_final: 0.7591 (mmp-170) REVERT: B 263 ASP cc_start: 0.6545 (t0) cc_final: 0.6074 (t0) REVERT: B 291 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9269 (tp) REVERT: B 345 MET cc_start: 0.8457 (mmm) cc_final: 0.8197 (mmm) REVERT: B 625 MET cc_start: 0.7881 (ttt) cc_final: 0.7014 (tmm) REVERT: B 730 LYS cc_start: 0.8388 (mttm) cc_final: 0.8163 (tttm) REVERT: B 791 ASN cc_start: 0.7880 (m110) cc_final: 0.6869 (p0) REVERT: B 794 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7012 (pt) REVERT: C 156 ASP cc_start: 0.7930 (t0) cc_final: 0.7319 (t0) REVERT: C 287 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8676 (mp) REVERT: C 303 TYR cc_start: 0.7987 (t80) cc_final: 0.7627 (t80) REVERT: C 345 MET cc_start: 0.9139 (mmm) cc_final: 0.8803 (mmt) REVERT: C 369 ASP cc_start: 0.8683 (t0) cc_final: 0.8471 (t0) REVERT: C 477 SER cc_start: 0.8458 (m) cc_final: 0.8088 (t) REVERT: C 482 MET cc_start: 0.7939 (mmt) cc_final: 0.7330 (mpp) REVERT: C 523 LEU cc_start: 0.8394 (mp) cc_final: 0.7751 (tp) REVERT: C 531 ASP cc_start: 0.8208 (m-30) cc_final: 0.7692 (m-30) REVERT: C 553 TYR cc_start: 0.7898 (m-80) cc_final: 0.7675 (m-80) REVERT: C 607 GLN cc_start: 0.7976 (mp10) cc_final: 0.7692 (mm-40) REVERT: D 156 ASP cc_start: 0.8387 (t70) cc_final: 0.8134 (t0) REVERT: D 250 CYS cc_start: 0.7969 (t) cc_final: 0.7698 (t) REVERT: D 253 TYR cc_start: 0.7763 (m-10) cc_final: 0.7550 (m-10) REVERT: D 607 GLN cc_start: 0.7891 (mt0) cc_final: 0.7602 (mm110) REVERT: D 612 LYS cc_start: 0.8531 (ttpm) cc_final: 0.8177 (mttt) REVERT: D 614 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8082 (tm) outliers start: 82 outliers final: 34 residues processed: 490 average time/residue: 0.1373 time to fit residues: 108.4412 Evaluate side-chains 415 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 377 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 107 optimal weight: 1.9990 chunk 207 optimal weight: 0.2980 chunk 184 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 240 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 155 optimal weight: 0.0980 chunk 134 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 207 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN D 252 HIS D 297 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.165457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132909 restraints weight = 29793.078| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.14 r_work: 0.3268 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21270 Z= 0.126 Angle : 0.701 11.811 28800 Z= 0.354 Chirality : 0.042 0.263 3238 Planarity : 0.005 0.061 3584 Dihedral : 10.132 130.027 3052 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.74 % Favored : 89.87 % Rotamer: Outliers : 2.99 % Allowed : 16.26 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.16), residues: 2526 helix: -0.75 (0.13), residues: 1448 sheet: -2.36 (0.56), residues: 88 loop : -2.69 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 179 TYR 0.017 0.001 TYR C 702 PHE 0.024 0.001 PHE D 666 TRP 0.017 0.001 TRP D 733 HIS 0.003 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (21270) covalent geometry : angle 0.70106 / 0.35 (28800) hydrogen bonds : bond 0.03502 / 2.33 ( 845) hydrogen bonds : angle 4.55388 / 3.13 ( 2445) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 413 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7925 (mtm-85) REVERT: A 222 ASN cc_start: 0.7905 (m110) cc_final: 0.7595 (m110) REVERT: A 223 MET cc_start: 0.8684 (mmt) cc_final: 0.8215 (mmt) REVERT: A 296 ASN cc_start: 0.9197 (t0) cc_final: 0.8928 (t0) REVERT: A 442 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7358 (tttt) REVERT: A 531 ASP cc_start: 0.8059 (m-30) cc_final: 0.7768 (m-30) REVERT: B 156 ASP cc_start: 0.8770 (t70) cc_final: 0.8535 (t0) REVERT: B 291 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9324 (tp) REVERT: B 345 MET cc_start: 0.8452 (mmm) cc_final: 0.8184 (mmm) REVERT: B 683 LEU cc_start: 0.5435 (OUTLIER) cc_final: 0.5109 (tp) REVERT: B 791 ASN cc_start: 0.7865 (m110) cc_final: 0.6945 (p0) REVERT: B 794 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7084 (pt) REVERT: C 156 ASP cc_start: 0.7912 (t0) cc_final: 0.7307 (t0) REVERT: C 345 MET cc_start: 0.9088 (mmm) cc_final: 0.8753 (mmt) REVERT: C 369 ASP cc_start: 0.8625 (t0) cc_final: 0.8400 (t0) REVERT: C 477 SER cc_start: 0.8490 (m) cc_final: 0.8135 (t) REVERT: C 531 ASP cc_start: 0.8040 (m-30) cc_final: 0.7523 (m-30) REVERT: C 553 TYR cc_start: 0.7860 (m-80) cc_final: 0.7626 (m-80) REVERT: C 684 GLU cc_start: 0.6089 (tm-30) cc_final: 0.5779 (tm-30) REVERT: D 156 ASP cc_start: 0.8458 (t70) cc_final: 0.8228 (t0) REVERT: D 234 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8716 (mt) REVERT: D 607 GLN cc_start: 0.7885 (mt0) cc_final: 0.7622 (mm110) REVERT: D 612 LYS cc_start: 0.8435 (ttpm) cc_final: 0.7972 (mttt) REVERT: D 614 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8036 (tm) outliers start: 67 outliers final: 30 residues processed: 453 average time/residue: 0.1391 time to fit residues: 100.9804 Evaluate side-chains 401 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 686 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 128 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 174 optimal weight: 0.6980 chunk 230 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 252 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129771 restraints weight = 29812.910| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.09 r_work: 0.3233 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21270 Z= 0.144 Angle : 0.703 11.771 28800 Z= 0.355 Chirality : 0.043 0.285 3238 Planarity : 0.005 0.059 3584 Dihedral : 9.715 122.747 3052 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.06 % Favored : 89.55 % Rotamer: Outliers : 3.17 % Allowed : 17.25 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.16), residues: 2526 helix: -0.51 (0.13), residues: 1448 sheet: -2.17 (0.57), residues: 88 loop : -2.65 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 269 TYR 0.022 0.002 TYR B 621 PHE 0.023 0.001 PHE D 666 TRP 0.016 0.001 TRP D 733 HIS 0.003 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (21270) covalent geometry : angle 0.70298 / 0.35 (28800) hydrogen bonds : bond 0.03453 / 2.29 ( 845) hydrogen bonds : angle 4.51017 / 3.11 ( 2445) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 395 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7987 (m110) cc_final: 0.7474 (m110) REVERT: A 295 THR cc_start: 0.8761 (p) cc_final: 0.8170 (t) REVERT: A 531 ASP cc_start: 0.8121 (m-30) cc_final: 0.7552 (m-30) REVERT: A 534 MET cc_start: 0.7568 (mmp) cc_final: 0.7179 (ptt) REVERT: B 156 ASP cc_start: 0.8786 (t70) cc_final: 0.8541 (t0) REVERT: B 263 ASP cc_start: 0.6716 (t0) cc_final: 0.6265 (t70) REVERT: B 683 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.5153 (tp) REVERT: B 791 ASN cc_start: 0.7870 (m110) cc_final: 0.7003 (p0) REVERT: B 794 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7075 (pt) REVERT: C 156 ASP cc_start: 0.7915 (t0) cc_final: 0.7303 (t0) REVERT: C 260 GLN cc_start: 0.8763 (mp-120) cc_final: 0.8475 (mp10) REVERT: C 345 MET cc_start: 0.9123 (mmm) cc_final: 0.8801 (mmt) REVERT: C 369 ASP cc_start: 0.8640 (t0) cc_final: 0.8381 (t0) REVERT: C 477 SER cc_start: 0.8560 (m) cc_final: 0.8150 (t) REVERT: C 531 ASP cc_start: 0.7832 (m-30) cc_final: 0.7278 (m-30) REVERT: C 553 TYR cc_start: 0.7935 (m-80) cc_final: 0.7711 (m-80) REVERT: C 607 GLN cc_start: 0.8116 (mp10) cc_final: 0.7775 (mm-40) REVERT: D 156 ASP cc_start: 0.8463 (t70) cc_final: 0.8242 (t0) REVERT: D 232 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7935 (ptt90) REVERT: D 252 HIS cc_start: 0.8084 (p90) cc_final: 0.7706 (p90) REVERT: D 607 GLN cc_start: 0.7966 (mt0) cc_final: 0.7565 (mm110) REVERT: D 612 LYS cc_start: 0.8360 (ttpm) cc_final: 0.7974 (mttt) REVERT: D 761 MET cc_start: 0.8369 (tpp) cc_final: 0.8159 (mmt) outliers start: 71 outliers final: 44 residues processed: 436 average time/residue: 0.1413 time to fit residues: 98.5858 Evaluate side-chains 402 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 355 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 717 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 146 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 226 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.162362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128490 restraints weight = 29863.253| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.22 r_work: 0.3207 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21270 Z= 0.149 Angle : 0.707 11.836 28800 Z= 0.355 Chirality : 0.043 0.241 3238 Planarity : 0.005 0.056 3584 Dihedral : 9.460 120.630 3052 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.17 % Favored : 89.43 % Rotamer: Outliers : 3.40 % Allowed : 17.52 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2526 helix: -0.25 (0.14), residues: 1438 sheet: -2.03 (0.56), residues: 88 loop : -2.59 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 179 TYR 0.016 0.001 TYR B 628 PHE 0.026 0.001 PHE B 617 TRP 0.014 0.001 TRP D 733 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (21270) covalent geometry : angle 0.70728 / 0.36 (28800) hydrogen bonds : bond 0.03382 / 2.25 ( 845) hydrogen bonds : angle 4.48575 / 3.10 ( 2445) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 381 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7831 (m110) cc_final: 0.7565 (m-40) REVERT: A 223 MET cc_start: 0.8740 (mmt) cc_final: 0.8473 (mmt) REVERT: A 260 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: A 295 THR cc_start: 0.8859 (p) cc_final: 0.8222 (t) REVERT: A 531 ASP cc_start: 0.8060 (m-30) cc_final: 0.7471 (m-30) REVERT: A 534 MET cc_start: 0.7395 (mmp) cc_final: 0.7176 (ptt) REVERT: A 587 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7692 (mmm) REVERT: B 156 ASP cc_start: 0.8762 (t70) cc_final: 0.8486 (t0) REVERT: B 219 ARG cc_start: 0.8035 (mmt-90) cc_final: 0.7700 (mmt-90) REVERT: B 252 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7493 (p-80) REVERT: B 263 ASP cc_start: 0.6756 (t0) cc_final: 0.6229 (t70) REVERT: B 541 ASN cc_start: 0.7055 (OUTLIER) cc_final: 0.6250 (m-40) REVERT: B 683 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.5191 (tp) REVERT: B 791 ASN cc_start: 0.7931 (m110) cc_final: 0.6984 (p0) REVERT: B 794 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7136 (pt) REVERT: C 156 ASP cc_start: 0.7890 (t0) cc_final: 0.7270 (t0) REVERT: C 195 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8592 (tt) REVERT: C 210 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7871 (tt) REVERT: C 222 ASN cc_start: 0.7753 (m110) cc_final: 0.7279 (m110) REVERT: C 260 GLN cc_start: 0.8757 (mp-120) cc_final: 0.8514 (mp10) REVERT: C 318 ASP cc_start: 0.8120 (t0) cc_final: 0.7704 (m-30) REVERT: C 345 MET cc_start: 0.9071 (mmm) cc_final: 0.8764 (mmt) REVERT: C 477 SER cc_start: 0.8627 (m) cc_final: 0.8183 (t) REVERT: C 523 LEU cc_start: 0.8433 (mp) cc_final: 0.7789 (tp) REVERT: C 531 ASP cc_start: 0.7719 (m-30) cc_final: 0.7159 (m-30) REVERT: C 567 TYR cc_start: 0.8259 (t80) cc_final: 0.7863 (t80) REVERT: C 685 MET cc_start: 0.7056 (mmt) cc_final: 0.6518 (ptp) REVERT: D 232 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7927 (ptt90) REVERT: D 252 HIS cc_start: 0.8077 (p90) cc_final: 0.7873 (p90) REVERT: D 396 ASP cc_start: 0.7897 (t70) cc_final: 0.7319 (p0) REVERT: D 607 GLN cc_start: 0.8059 (mt0) cc_final: 0.7612 (mm110) REVERT: D 612 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8185 (mmtt) REVERT: D 702 TYR cc_start: 0.7910 (t80) cc_final: 0.7682 (t80) outliers start: 76 outliers final: 46 residues processed: 421 average time/residue: 0.1398 time to fit residues: 94.3090 Evaluate side-chains 414 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 358 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 717 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 217 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 147 optimal weight: 0.0870 chunk 237 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 108 optimal weight: 0.0870 chunk 121 optimal weight: 0.7980 chunk 241 optimal weight: 9.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 588 ASN B 252 HIS B 297 GLN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN C 550 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.164809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131035 restraints weight = 29852.926| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.19 r_work: 0.3250 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21270 Z= 0.121 Angle : 0.689 12.471 28800 Z= 0.345 Chirality : 0.042 0.240 3238 Planarity : 0.005 0.059 3584 Dihedral : 9.280 118.561 3052 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.86 % Favored : 89.79 % Rotamer: Outliers : 3.40 % Allowed : 18.19 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.17), residues: 2526 helix: -0.07 (0.14), residues: 1444 sheet: -2.16 (0.54), residues: 92 loop : -2.51 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 336 TYR 0.017 0.001 TYR C 253 PHE 0.023 0.001 PHE B 617 TRP 0.014 0.001 TRP C 733 HIS 0.017 0.001 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21270) covalent geometry : angle 0.68873 / 0.34 (28800) hydrogen bonds : bond 0.03157 / 2.10 ( 845) hydrogen bonds : angle 4.37709 / 3.02 ( 2445) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 384 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7921 (m110) cc_final: 0.7648 (m-40) REVERT: A 223 MET cc_start: 0.8690 (mmt) cc_final: 0.8259 (mmt) REVERT: A 260 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: A 295 THR cc_start: 0.8774 (p) cc_final: 0.8204 (t) REVERT: A 477 SER cc_start: 0.8718 (m) cc_final: 0.8322 (t) REVERT: A 531 ASP cc_start: 0.8086 (m-30) cc_final: 0.7486 (m-30) REVERT: A 587 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7617 (mmm) REVERT: B 156 ASP cc_start: 0.8770 (t70) cc_final: 0.8506 (t0) REVERT: B 219 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7744 (mmt-90) REVERT: B 541 ASN cc_start: 0.7126 (OUTLIER) cc_final: 0.6370 (m-40) REVERT: B 791 ASN cc_start: 0.7795 (m110) cc_final: 0.6971 (p0) REVERT: B 794 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7046 (pt) REVERT: C 156 ASP cc_start: 0.7989 (t0) cc_final: 0.7374 (t0) REVERT: C 195 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8633 (tt) REVERT: C 260 GLN cc_start: 0.8724 (mp-120) cc_final: 0.8483 (mp10) REVERT: C 345 MET cc_start: 0.9052 (mmm) cc_final: 0.8749 (mmt) REVERT: C 477 SER cc_start: 0.8626 (m) cc_final: 0.8211 (t) REVERT: C 531 ASP cc_start: 0.7689 (m-30) cc_final: 0.7291 (m-30) REVERT: C 567 TYR cc_start: 0.8198 (t80) cc_final: 0.7829 (t80) REVERT: C 685 MET cc_start: 0.7029 (mmt) cc_final: 0.6675 (ptp) REVERT: D 232 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8090 (ptt180) REVERT: D 234 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8662 (mt) REVERT: D 252 HIS cc_start: 0.8026 (p90) cc_final: 0.7646 (p90) REVERT: D 269 ARG cc_start: 0.8284 (ttm110) cc_final: 0.8068 (ptp-110) REVERT: D 396 ASP cc_start: 0.7945 (t70) cc_final: 0.7398 (p0) REVERT: D 607 GLN cc_start: 0.7957 (mt0) cc_final: 0.7509 (mm110) REVERT: D 612 LYS cc_start: 0.8410 (ttpm) cc_final: 0.8178 (mmtt) outliers start: 76 outliers final: 43 residues processed: 419 average time/residue: 0.1355 time to fit residues: 91.6100 Evaluate side-chains 410 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 717 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 588 ASN B 252 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131063 restraints weight = 29564.714| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.07 r_work: 0.3249 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21270 Z= 0.141 Angle : 0.701 12.479 28800 Z= 0.353 Chirality : 0.042 0.239 3238 Planarity : 0.005 0.059 3584 Dihedral : 9.172 117.075 3052 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.49 % Favored : 89.15 % Rotamer: Outliers : 3.13 % Allowed : 19.12 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.17), residues: 2526 helix: 0.01 (0.14), residues: 1440 sheet: -2.00 (0.57), residues: 88 loop : -2.43 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 179 TYR 0.024 0.001 TYR D 628 PHE 0.021 0.001 PHE B 617 TRP 0.013 0.001 TRP B 733 HIS 0.002 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21270) covalent geometry : angle 0.70144 / 0.35 (28800) hydrogen bonds : bond 0.03223 / 2.16 ( 845) hydrogen bonds : angle 4.38568 / 3.03 ( 2445) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 364 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7936 (m110) cc_final: 0.7693 (m-40) REVERT: A 260 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: A 531 ASP cc_start: 0.7844 (m-30) cc_final: 0.7456 (m-30) REVERT: B 156 ASP cc_start: 0.8764 (t70) cc_final: 0.8498 (t0) REVERT: B 219 ARG cc_start: 0.8081 (mmt-90) cc_final: 0.7760 (mmt-90) REVERT: B 345 MET cc_start: 0.8328 (mtp) cc_final: 0.7935 (mmm) REVERT: B 541 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6137 (m-40) REVERT: B 791 ASN cc_start: 0.7766 (m110) cc_final: 0.6996 (p0) REVERT: B 794 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.6995 (pt) REVERT: C 156 ASP cc_start: 0.7959 (t0) cc_final: 0.7332 (t0) REVERT: C 260 GLN cc_start: 0.8691 (mp-120) cc_final: 0.8465 (mp10) REVERT: C 345 MET cc_start: 0.9018 (mmm) cc_final: 0.8731 (mmt) REVERT: C 477 SER cc_start: 0.8591 (m) cc_final: 0.8201 (t) REVERT: C 531 ASP cc_start: 0.7655 (m-30) cc_final: 0.7275 (m-30) REVERT: C 567 TYR cc_start: 0.8180 (t80) cc_final: 0.7867 (t80) REVERT: C 587 MET cc_start: 0.8187 (ttp) cc_final: 0.7981 (ttm) REVERT: D 232 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8067 (ptt180) REVERT: D 252 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7736 (p90) REVERT: D 396 ASP cc_start: 0.7896 (t70) cc_final: 0.7350 (p0) REVERT: D 612 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8223 (mmtt) REVERT: D 625 MET cc_start: 0.7199 (mmp) cc_final: 0.5582 (tmm) outliers start: 70 outliers final: 45 residues processed: 401 average time/residue: 0.1363 time to fit residues: 88.8267 Evaluate side-chains 403 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 352 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 3.9990 chunk 69 optimal weight: 0.0370 chunk 102 optimal weight: 0.0670 chunk 182 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 588 ASN A 712 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.163492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129462 restraints weight = 29850.981| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.31 r_work: 0.3222 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21270 Z= 0.136 Angle : 0.702 12.533 28800 Z= 0.352 Chirality : 0.042 0.226 3238 Planarity : 0.005 0.060 3584 Dihedral : 9.064 115.895 3052 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.17 % Favored : 89.51 % Rotamer: Outliers : 2.90 % Allowed : 19.66 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 2526 helix: 0.02 (0.14), residues: 1444 sheet: -1.96 (0.57), residues: 88 loop : -2.38 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 336 TYR 0.018 0.001 TYR D 602 PHE 0.020 0.001 PHE D 666 TRP 0.013 0.001 TRP A 737 HIS 0.002 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21270) covalent geometry : angle 0.70184 / 0.35 (28800) hydrogen bonds : bond 0.03239 / 2.18 ( 845) hydrogen bonds : angle 4.39485 / 3.04 ( 2445) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 362 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7955 (m110) cc_final: 0.7670 (m-40) REVERT: A 531 ASP cc_start: 0.7961 (m-30) cc_final: 0.7500 (m-30) REVERT: A 604 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8985 (mm) REVERT: B 156 ASP cc_start: 0.8785 (t70) cc_final: 0.8516 (t0) REVERT: B 219 ARG cc_start: 0.8125 (mmt-90) cc_final: 0.7809 (mmt-90) REVERT: B 345 MET cc_start: 0.8375 (mtp) cc_final: 0.8161 (mmm) REVERT: B 541 ASN cc_start: 0.7044 (OUTLIER) cc_final: 0.6169 (m-40) REVERT: B 578 MET cc_start: 0.7072 (mmt) cc_final: 0.6740 (tpt) REVERT: B 625 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.5759 (tmm) REVERT: B 791 ASN cc_start: 0.7791 (m110) cc_final: 0.6921 (p0) REVERT: B 794 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7006 (pt) REVERT: C 156 ASP cc_start: 0.8024 (t0) cc_final: 0.7367 (t0) REVERT: C 215 ASP cc_start: 0.8396 (m-30) cc_final: 0.8088 (m-30) REVERT: C 260 GLN cc_start: 0.8748 (mp-120) cc_final: 0.8513 (mp10) REVERT: C 477 SER cc_start: 0.8708 (m) cc_final: 0.8242 (t) REVERT: C 531 ASP cc_start: 0.7613 (m-30) cc_final: 0.7230 (m-30) REVERT: C 684 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6924 (mm-30) REVERT: C 685 MET cc_start: 0.8534 (pmm) cc_final: 0.7925 (ptp) REVERT: D 232 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8143 (ptt180) REVERT: D 252 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7804 (p90) REVERT: D 612 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8218 (mmtt) REVERT: D 625 MET cc_start: 0.7081 (mmp) cc_final: 0.5540 (tmm) REVERT: D 674 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7514 (t80) outliers start: 65 outliers final: 44 residues processed: 397 average time/residue: 0.1364 time to fit residues: 87.5532 Evaluate side-chains 391 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 69 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 173 optimal weight: 0.4980 chunk 62 optimal weight: 0.4980 chunk 201 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 588 ASN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.164417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130777 restraints weight = 29892.077| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.24 r_work: 0.3239 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21270 Z= 0.127 Angle : 0.698 12.571 28800 Z= 0.350 Chirality : 0.042 0.219 3238 Planarity : 0.005 0.061 3584 Dihedral : 8.935 114.567 3052 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.25 % Favored : 89.43 % Rotamer: Outliers : 2.73 % Allowed : 20.06 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.17), residues: 2526 helix: 0.10 (0.14), residues: 1442 sheet: -2.42 (0.53), residues: 106 loop : -2.34 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 336 TYR 0.018 0.001 TYR D 602 PHE 0.023 0.001 PHE C 674 TRP 0.015 0.001 TRP B 733 HIS 0.007 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (21270) covalent geometry : angle 0.69785 / 0.35 (28800) hydrogen bonds : bond 0.03203 / 2.17 ( 845) hydrogen bonds : angle 4.36137 / 3.01 ( 2445) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 352 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7920 (m110) cc_final: 0.7655 (m-40) REVERT: A 531 ASP cc_start: 0.8053 (m-30) cc_final: 0.7531 (m-30) REVERT: A 685 MET cc_start: 0.6018 (mmt) cc_final: 0.5545 (ptp) REVERT: B 156 ASP cc_start: 0.8763 (t70) cc_final: 0.8507 (t0) REVERT: B 219 ARG cc_start: 0.8133 (mmt-90) cc_final: 0.7824 (mmt-90) REVERT: B 541 ASN cc_start: 0.7151 (OUTLIER) cc_final: 0.6276 (m-40) REVERT: B 578 MET cc_start: 0.7035 (mmt) cc_final: 0.6726 (tpt) REVERT: B 625 MET cc_start: 0.7230 (mmp) cc_final: 0.5793 (tmm) REVERT: B 791 ASN cc_start: 0.7752 (m110) cc_final: 0.6864 (p0) REVERT: B 794 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7005 (pt) REVERT: C 156 ASP cc_start: 0.8018 (t0) cc_final: 0.7324 (t0) REVERT: C 215 ASP cc_start: 0.8476 (m-30) cc_final: 0.8140 (m-30) REVERT: C 260 GLN cc_start: 0.8755 (mp-120) cc_final: 0.8522 (mp10) REVERT: C 345 MET cc_start: 0.9013 (mmm) cc_final: 0.8704 (mmt) REVERT: C 477 SER cc_start: 0.8712 (m) cc_final: 0.8270 (t) REVERT: C 531 ASP cc_start: 0.7454 (m-30) cc_final: 0.6923 (m-30) REVERT: C 588 ASN cc_start: 0.8488 (t0) cc_final: 0.8007 (t0) REVERT: C 685 MET cc_start: 0.8506 (pmm) cc_final: 0.7298 (mmt) REVERT: D 232 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8190 (ptt180) REVERT: D 534 MET cc_start: 0.6926 (mmt) cc_final: 0.6582 (mtt) REVERT: D 612 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8230 (mmtt) REVERT: D 625 MET cc_start: 0.7046 (mmp) cc_final: 0.5453 (tmm) REVERT: D 674 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7482 (t80) outliers start: 61 outliers final: 43 residues processed: 387 average time/residue: 0.1324 time to fit residues: 81.7958 Evaluate side-chains 390 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 342 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 6 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.163814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131150 restraints weight = 29626.646| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.21 r_work: 0.3227 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21270 Z= 0.132 Angle : 0.697 13.878 28800 Z= 0.350 Chirality : 0.042 0.220 3238 Planarity : 0.005 0.059 3584 Dihedral : 8.860 113.762 3052 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.02 % Favored : 89.67 % Rotamer: Outliers : 2.68 % Allowed : 20.24 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 2526 helix: 0.17 (0.14), residues: 1438 sheet: -2.08 (0.58), residues: 96 loop : -2.37 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 391 TYR 0.026 0.001 TYR C 303 PHE 0.019 0.001 PHE D 666 TRP 0.016 0.001 TRP B 733 HIS 0.007 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21270) covalent geometry : angle 0.69657 / 0.35 (28800) hydrogen bonds : bond 0.03198 / 2.16 ( 845) hydrogen bonds : angle 4.37112 / 3.03 ( 2445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4558.85 seconds wall clock time: 79 minutes 18.27 seconds (4758.27 seconds total)