Starting phenix.real_space_refine on Sun Oct 12 04:12:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1f_40962/10_2025/8t1f_40962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1f_40962/10_2025/8t1f_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t1f_40962/10_2025/8t1f_40962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1f_40962/10_2025/8t1f_40962.map" model { file = "/net/cci-nas-00/data/ceres_data/8t1f_40962/10_2025/8t1f_40962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1f_40962/10_2025/8t1f_40962.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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: 4.79, per 1000 atoms: 0.23 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: 2.08 Conformation dependent library (CDL) restraints added in 884.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.65 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: 3.18 Time building geometry restraints manager: 2.65 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: 12517 35.58 - 71.15: 181 71.15 - 106.73: 8 106.73 - 142.30: 4 142.30 - 177.88: 6 Dihedral angle restraints: 12716 sinusoidal: 5282 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 12713 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: 0.04 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.850 Find NCS groups from input model: 0.160 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 13.754 177.877 7928 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 aren 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 covalent geometry : bond 0.00616 (21270) covalent geometry : angle 1.32409 (28800) hydrogen bonds : bond 0.31287 ( 845) hydrogen bonds : angle 10.34865 ( 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 : 0.780 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: 0.7790 (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: 0.8572 (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: 0.1656 time to fit residues: 167.7261 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 : 0.678 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130334 restraints weight = 29899.765| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.26 r_work: 0.3282 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21270 Z= 0.157 Angle : 0.796 11.424 28800 Z= 0.406 Chirality : 0.045 0.300 3238 Planarity : 0.006 0.051 3584 Dihedral : 12.647 174.429 3078 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.82 % Favored : 89.71 % Rotamer: Outliers : 2.41 % Allowed : 13.63 % Favored : 83.96 % 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 aren not related in a simple way. whole: -3.84 (0.15), residues: 2526 helix: -2.26 (0.11), residues: 1442 sheet: -3.02 (0.47), residues: 116 loop : -2.73 (0.19), residues: 968 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 0.026 0.002 PHE D 666 TRP 0.025 0.002 TRP C 733 HIS 0.008 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00336 (21270) covalent geometry : angle 0.79586 (28800) hydrogen bonds : bond 0.05509 ( 845) hydrogen bonds : angle 5.49371 ( 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 520 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 466 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8120 (m-30) cc_final: 0.7879 (m-30) REVERT: A 222 ASN cc_start: 0.7861 (m110) cc_final: 0.7606 (m110) REVERT: A 477 SER cc_start: 0.8739 (m) cc_final: 0.8401 (t) REVERT: A 628 TYR cc_start: 0.8010 (m-80) cc_final: 0.7713 (m-80) REVERT: A 685 MET cc_start: 0.6768 (mmt) cc_final: 0.6557 (mmt) REVERT: A 696 ILE cc_start: 0.8463 (tp) cc_final: 0.8256 (pt) REVERT: B 289 LEU cc_start: 0.8736 (tp) cc_final: 0.7821 (tt) REVERT: B 291 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9076 (tp) REVERT: B 345 MET cc_start: 0.8370 (mmm) cc_final: 0.8067 (mmm) REVERT: B 614 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7973 (tm) REVERT: B 625 MET cc_start: 0.8005 (ttm) cc_final: 0.7107 (tmm) REVERT: B 791 ASN cc_start: 0.7884 (m110) cc_final: 0.6667 (p0) REVERT: C 156 ASP cc_start: 0.8038 (t0) cc_final: 0.7396 (t0) REVERT: C 179 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7739 (mtp85) REVERT: C 303 TYR cc_start: 0.7993 (t80) cc_final: 0.7613 (t80) REVERT: C 345 MET cc_start: 0.9142 (mmm) cc_final: 0.8849 (mmm) REVERT: C 543 LEU cc_start: 0.8568 (tt) cc_final: 0.8345 (mp) REVERT: C 553 TYR cc_start: 0.7934 (m-80) cc_final: 0.7724 (m-80) REVERT: C 607 GLN cc_start: 0.7805 (mp10) cc_final: 0.7564 (mp10) REVERT: D 156 ASP cc_start: 0.8368 (t70) cc_final: 0.8085 (t0) REVERT: D 395 THR cc_start: 0.8350 (p) cc_final: 0.8046 (m) REVERT: D 612 LYS cc_start: 0.8536 (ttpm) cc_final: 0.8216 (mttt) REVERT: D 614 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8063 (tm) REVERT: D 747 SER cc_start: 0.8935 (m) cc_final: 0.8699 (t) outliers start: 54 outliers final: 23 residues processed: 500 average time/residue: 0.1461 time to fit residues: 114.0814 Evaluate side-chains 403 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 377 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 LEU 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 173 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 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: 3.9990 chunk 211 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 201 optimal weight: 0.3980 chunk 171 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN 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 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 = 0.3902 r_free = 0.3902 target = 0.162977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128799 restraints weight = 30179.219| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.27 r_work: 0.3242 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3520 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= 0.157 Angle : 0.740 11.490 28800 Z= 0.376 Chirality : 0.044 0.246 3238 Planarity : 0.005 0.047 3584 Dihedral : 11.372 173.794 3076 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.13 % Favored : 89.39 % Rotamer: Outliers : 3.62 % Allowed : 15.19 % Favored : 81.19 % 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 aren not related in a simple way. whole: -2.90 (0.16), residues: 2526 helix: -1.31 (0.12), residues: 1442 sheet: -2.38 (0.58), residues: 88 loop : -2.71 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 151 TYR 0.019 0.001 TYR A 253 PHE 0.033 0.002 PHE C 751 TRP 0.020 0.002 TRP B 733 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00348 (21270) covalent geometry : angle 0.74005 (28800) hydrogen bonds : bond 0.04160 ( 845) hydrogen bonds : angle 4.88321 ( 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 507 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 426 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7953 (m110) cc_final: 0.7651 (m110) REVERT: A 295 THR cc_start: 0.8688 (p) cc_final: 0.8076 (t) REVERT: A 477 SER cc_start: 0.8675 (m) cc_final: 0.8331 (t) REVERT: A 531 ASP cc_start: 0.8113 (m-30) cc_final: 0.7861 (m-30) REVERT: A 534 MET cc_start: 0.7842 (mmp) cc_final: 0.7107 (ptt) REVERT: B 156 ASP cc_start: 0.8758 (t70) cc_final: 0.8454 (t0) REVERT: B 206 ARG cc_start: 0.7930 (mmp-170) cc_final: 0.7585 (mmp-170) REVERT: B 291 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9245 (tp) REVERT: B 730 LYS cc_start: 0.8393 (mttm) cc_final: 0.8163 (tttm) REVERT: B 791 ASN cc_start: 0.7893 (m110) cc_final: 0.6861 (p0) REVERT: B 794 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7034 (pt) REVERT: C 156 ASP cc_start: 0.7948 (t0) cc_final: 0.7344 (t0) REVERT: C 287 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8729 (mp) REVERT: C 318 ASP cc_start: 0.7933 (t0) cc_final: 0.7580 (m-30) REVERT: C 345 MET cc_start: 0.9137 (mmm) cc_final: 0.8792 (mmt) REVERT: C 477 SER cc_start: 0.8457 (m) cc_final: 0.8094 (t) REVERT: C 482 MET cc_start: 0.7942 (mmt) cc_final: 0.7287 (mpp) REVERT: C 523 LEU cc_start: 0.8401 (mp) cc_final: 0.7794 (tp) REVERT: C 531 ASP cc_start: 0.8199 (m-30) cc_final: 0.7703 (m-30) REVERT: C 553 TYR cc_start: 0.7922 (m-80) cc_final: 0.7700 (m-80) REVERT: C 607 GLN cc_start: 0.7993 (mp10) cc_final: 0.7657 (mm-40) REVERT: C 611 PHE cc_start: 0.8195 (m-10) cc_final: 0.7986 (m-10) REVERT: D 156 ASP cc_start: 0.8396 (t70) cc_final: 0.8133 (t0) REVERT: D 609 ILE cc_start: 0.9175 (mm) cc_final: 0.8972 (mt) REVERT: D 612 LYS cc_start: 0.8538 (ttpm) cc_final: 0.8192 (mttt) REVERT: D 614 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8065 (tm) outliers start: 81 outliers final: 33 residues processed: 480 average time/residue: 0.1264 time to fit residues: 98.5830 Evaluate side-chains 415 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 378 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 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 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 636 LEU 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 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 596 LEU 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 212 VAL 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 583 VAL 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: 2.9990 chunk 207 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 240 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 92 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131596 restraints weight = 30033.177| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.21 r_work: 0.3244 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21270 Z= 0.129 Angle : 0.703 11.882 28800 Z= 0.354 Chirality : 0.042 0.263 3238 Planarity : 0.005 0.060 3584 Dihedral : 10.838 176.671 3076 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.78 % Favored : 89.79 % Rotamer: Outliers : 3.08 % Allowed : 16.13 % Favored : 80.79 % 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 aren not related in a simple way. whole: -2.39 (0.16), residues: 2526 helix: -0.74 (0.13), residues: 1436 sheet: -2.36 (0.57), residues: 88 loop : -2.74 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 179 TYR 0.022 0.001 TYR B 621 PHE 0.025 0.001 PHE D 666 TRP 0.017 0.001 TRP B 733 HIS 0.004 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00281 (21270) covalent geometry : angle 0.70253 (28800) hydrogen bonds : bond 0.03572 ( 845) hydrogen bonds : angle 4.58901 ( 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 474 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 405 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7891 (m110) cc_final: 0.7588 (m110) REVERT: A 296 ASN cc_start: 0.9232 (t0) cc_final: 0.8952 (t0) REVERT: A 442 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7413 (tttt) REVERT: A 477 SER cc_start: 0.8719 (m) cc_final: 0.8357 (t) REVERT: A 531 ASP cc_start: 0.8094 (m-30) cc_final: 0.7732 (m-30) REVERT: A 534 MET cc_start: 0.7728 (mmp) cc_final: 0.7262 (ptt) REVERT: B 156 ASP cc_start: 0.8794 (t70) cc_final: 0.8542 (t0) REVERT: B 206 ARG cc_start: 0.7992 (mmp-170) cc_final: 0.7704 (mmp-170) REVERT: B 213 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8290 (mm) REVERT: B 253 TYR cc_start: 0.7771 (m-10) cc_final: 0.7550 (m-10) REVERT: B 291 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9275 (tp) REVERT: B 345 MET cc_start: 0.8310 (mmm) cc_final: 0.7906 (mmm) REVERT: B 430 GLU cc_start: 0.7111 (tt0) cc_final: 0.6801 (tt0) REVERT: B 683 LEU cc_start: 0.5444 (OUTLIER) cc_final: 0.5123 (tp) REVERT: B 791 ASN cc_start: 0.7927 (m110) cc_final: 0.6934 (p0) REVERT: B 794 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7120 (pt) REVERT: C 156 ASP cc_start: 0.7921 (t0) cc_final: 0.7318 (t0) REVERT: C 287 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8639 (mp) REVERT: C 345 MET cc_start: 0.9114 (mmm) cc_final: 0.8766 (mmt) REVERT: C 477 SER cc_start: 0.8528 (m) cc_final: 0.8158 (t) REVERT: C 531 ASP cc_start: 0.8108 (m-30) cc_final: 0.7560 (m-30) REVERT: C 534 MET cc_start: 0.7708 (mpm) cc_final: 0.6760 (mmt) REVERT: C 553 TYR cc_start: 0.7893 (m-80) cc_final: 0.7657 (m-80) REVERT: C 567 TYR cc_start: 0.8053 (t80) cc_final: 0.7661 (t80) REVERT: D 156 ASP cc_start: 0.8449 (t70) cc_final: 0.8198 (t0) REVERT: D 607 GLN cc_start: 0.7929 (mt0) cc_final: 0.7615 (mm110) REVERT: D 612 LYS cc_start: 0.8464 (ttpm) cc_final: 0.7991 (mttt) REVERT: D 614 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8059 (tm) outliers start: 69 outliers final: 32 residues processed: 449 average time/residue: 0.1384 time to fit residues: 100.1299 Evaluate side-chains 405 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 367 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 213 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 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 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 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 596 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL 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 614 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 174 optimal weight: 0.0060 chunk 230 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 588 ASN ** 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 = 0.3902 r_free = 0.3902 target = 0.163266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129297 restraints weight = 30022.995| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.25 r_work: 0.3218 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4273 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 : 0.704 11.760 28800 Z= 0.355 Chirality : 0.043 0.261 3238 Planarity : 0.005 0.062 3584 Dihedral : 10.542 178.628 3076 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.21 % Favored : 89.35 % Rotamer: Outliers : 3.26 % Allowed : 17.38 % Favored : 79.36 % 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 aren not related in a simple way. whole: -2.08 (0.16), residues: 2526 helix: -0.46 (0.13), residues: 1450 sheet: -2.16 (0.56), residues: 88 loop : -2.68 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 269 TYR 0.016 0.002 TYR C 628 PHE 0.024 0.001 PHE D 666 TRP 0.015 0.001 TRP D 733 HIS 0.006 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00327 (21270) covalent geometry : angle 0.70447 (28800) hydrogen bonds : bond 0.03496 ( 845) hydrogen bonds : angle 4.50812 ( 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 471 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 398 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: A 295 THR cc_start: 0.8798 (p) cc_final: 0.8194 (t) REVERT: A 587 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7720 (mmm) REVERT: B 156 ASP cc_start: 0.8807 (t70) cc_final: 0.8544 (t0) REVERT: B 219 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7798 (mmt-90) REVERT: B 683 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.5165 (tp) REVERT: B 791 ASN cc_start: 0.7904 (m110) cc_final: 0.6985 (p0) REVERT: B 794 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7123 (pt) REVERT: C 156 ASP cc_start: 0.7907 (t0) cc_final: 0.7298 (t0) REVERT: C 345 MET cc_start: 0.9104 (mmm) cc_final: 0.8776 (mmt) REVERT: C 477 SER cc_start: 0.8573 (m) cc_final: 0.8168 (t) REVERT: C 531 ASP cc_start: 0.8101 (m-30) cc_final: 0.7593 (m-30) REVERT: C 534 MET cc_start: 0.7761 (mpm) cc_final: 0.7555 (mpm) REVERT: C 553 TYR cc_start: 0.7931 (m-80) cc_final: 0.7730 (m-80) REVERT: C 567 TYR cc_start: 0.8036 (t80) cc_final: 0.7693 (t80) REVERT: C 607 GLN cc_start: 0.8147 (mp10) cc_final: 0.7785 (mm-40) REVERT: D 156 ASP cc_start: 0.8470 (t70) cc_final: 0.8243 (t0) REVERT: D 232 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8068 (ptt180) REVERT: D 234 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8651 (mt) REVERT: D 607 GLN cc_start: 0.7974 (mt0) cc_final: 0.7675 (mm110) REVERT: D 612 LYS cc_start: 0.8357 (ttpm) cc_final: 0.8002 (mttt) REVERT: D 614 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8109 (tm) REVERT: D 636 LEU cc_start: 0.7370 (mm) cc_final: 0.7163 (pp) outliers start: 73 outliers final: 42 residues processed: 439 average time/residue: 0.1454 time to fit residues: 101.4026 Evaluate side-chains 399 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 350 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 610 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 699 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 516 ILE 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 606 ILE 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 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 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 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 356 LEU Chi-restraints excluded: chain D residue 442 LYS 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 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: 2.9990 chunk 49 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 226 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN 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 = 0.3861 r_free = 0.3861 target = 0.159659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125344 restraints weight = 29941.218| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.24 r_work: 0.3184 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21270 Z= 0.198 Angle : 0.749 11.729 28800 Z= 0.377 Chirality : 0.045 0.314 3238 Planarity : 0.005 0.060 3584 Dihedral : 10.428 175.805 3076 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.77 % Favored : 88.80 % Rotamer: Outliers : 3.75 % Allowed : 17.47 % Favored : 78.78 % 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 aren not related in a simple way. whole: -1.99 (0.16), residues: 2526 helix: -0.39 (0.13), residues: 1444 sheet: -2.06 (0.56), residues: 88 loop : -2.65 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 179 TYR 0.016 0.002 TYR D 253 PHE 0.029 0.002 PHE D 617 TRP 0.013 0.001 TRP D 733 HIS 0.006 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00467 (21270) covalent geometry : angle 0.74934 (28800) hydrogen bonds : bond 0.03625 ( 845) hydrogen bonds : angle 4.59830 ( 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 463 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 379 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8166 (mmp) cc_final: 0.7923 (mmp) REVERT: A 260 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: A 531 ASP cc_start: 0.8133 (m-30) cc_final: 0.7604 (m-30) REVERT: A 534 MET cc_start: 0.7940 (mmp) cc_final: 0.7256 (ptt) REVERT: A 553 TYR cc_start: 0.7654 (m-80) cc_final: 0.7405 (m-80) REVERT: A 625 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7276 (tmm) REVERT: B 156 ASP cc_start: 0.8790 (t70) cc_final: 0.8545 (t0) REVERT: B 219 ARG cc_start: 0.8139 (mmt-90) cc_final: 0.7833 (mmt-90) REVERT: B 252 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7449 (p-80) REVERT: B 791 ASN cc_start: 0.7987 (m110) cc_final: 0.7049 (p0) REVERT: B 794 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7105 (pt) REVERT: C 156 ASP cc_start: 0.7887 (t0) cc_final: 0.7269 (t0) REVERT: C 210 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7588 (tp) REVERT: C 318 ASP cc_start: 0.8066 (t0) cc_final: 0.7640 (m-30) REVERT: C 477 SER cc_start: 0.8643 (m) cc_final: 0.8143 (t) REVERT: C 531 ASP cc_start: 0.8102 (m-30) cc_final: 0.7555 (m-30) REVERT: C 534 MET cc_start: 0.7778 (mpm) cc_final: 0.7560 (mpm) REVERT: C 567 TYR cc_start: 0.8069 (t80) cc_final: 0.7731 (t80) REVERT: C 685 MET cc_start: 0.6929 (mmt) cc_final: 0.6547 (pmm) REVERT: D 156 ASP cc_start: 0.8474 (t70) cc_final: 0.8248 (t0) REVERT: D 232 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8104 (ptt90) REVERT: D 607 GLN cc_start: 0.8024 (mt0) cc_final: 0.7573 (mm110) REVERT: D 612 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8176 (mmtt) REVERT: D 636 LEU cc_start: 0.7338 (mm) cc_final: 0.7133 (pp) REVERT: D 702 TYR cc_start: 0.7935 (t80) cc_final: 0.7603 (t80) outliers start: 84 outliers final: 49 residues processed: 422 average time/residue: 0.1488 time to fit residues: 100.0054 Evaluate side-chains 404 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 348 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 710 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 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 579 VAL Chi-restraints excluded: chain B residue 605 MET 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 725 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 516 ILE 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 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 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 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 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: 2.9990 chunk 134 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 241 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN B 252 HIS B 297 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129610 restraints weight = 29915.495| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.20 r_work: 0.3238 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4735 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= 0.132 Angle : 0.710 12.497 28800 Z= 0.356 Chirality : 0.042 0.236 3238 Planarity : 0.005 0.055 3584 Dihedral : 10.169 169.326 3076 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.25 % Favored : 89.39 % Rotamer: Outliers : 2.77 % Allowed : 18.95 % Favored : 78.28 % 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 aren not related in a simple way. whole: -1.74 (0.17), residues: 2526 helix: -0.17 (0.14), residues: 1438 sheet: -2.08 (0.56), residues: 88 loop : -2.54 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 179 TYR 0.020 0.001 TYR D 253 PHE 0.024 0.001 PHE B 617 TRP 0.016 0.001 TRP D 733 HIS 0.016 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00295 (21270) covalent geometry : angle 0.70996 (28800) hydrogen bonds : bond 0.03330 ( 845) hydrogen bonds : angle 4.46893 ( 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 439 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 377 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: A 477 SER cc_start: 0.8726 (m) cc_final: 0.8312 (t) REVERT: A 531 ASP cc_start: 0.8141 (m-30) cc_final: 0.7528 (m-30) REVERT: A 534 MET cc_start: 0.7666 (mmp) cc_final: 0.7227 (ptt) REVERT: B 156 ASP cc_start: 0.8770 (t70) cc_final: 0.8488 (t0) REVERT: B 219 ARG cc_start: 0.8132 (mmt-90) cc_final: 0.7849 (mmt-90) REVERT: B 541 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6226 (m-40) REVERT: B 791 ASN cc_start: 0.7896 (m110) cc_final: 0.7013 (p0) REVERT: B 794 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7064 (pt) REVERT: C 156 ASP cc_start: 0.7870 (t0) cc_final: 0.7257 (t0) REVERT: C 179 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7425 (mtp85) REVERT: C 222 ASN cc_start: 0.7858 (m110) cc_final: 0.6902 (m110) REVERT: C 318 ASP cc_start: 0.8147 (t0) cc_final: 0.7663 (m-30) REVERT: C 345 MET cc_start: 0.9052 (mmm) cc_final: 0.8727 (mmt) REVERT: C 477 SER cc_start: 0.8649 (m) cc_final: 0.8177 (t) REVERT: C 531 ASP cc_start: 0.7953 (m-30) cc_final: 0.7381 (m-30) REVERT: C 534 MET cc_start: 0.7729 (mpm) cc_final: 0.7420 (mpm) REVERT: C 567 TYR cc_start: 0.7900 (t80) cc_final: 0.7629 (t80) REVERT: D 156 ASP cc_start: 0.8412 (t70) cc_final: 0.8207 (t0) REVERT: D 232 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8034 (ptt90) REVERT: D 234 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 252 HIS cc_start: 0.8057 (p90) cc_final: 0.7740 (p90) REVERT: D 269 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8148 (ptp-110) REVERT: D 607 GLN cc_start: 0.7969 (mt0) cc_final: 0.7520 (mm110) REVERT: D 612 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8184 (mmtt) outliers start: 62 outliers final: 37 residues processed: 406 average time/residue: 0.1396 time to fit residues: 91.1520 Evaluate side-chains 396 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 353 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 540 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 610 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 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 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 181 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 240 optimal weight: 0.0270 chunk 72 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN B 243 HIS B 252 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129595 restraints weight = 29667.690| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.19 r_work: 0.3209 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4900 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= 0.134 Angle : 0.710 12.581 28800 Z= 0.356 Chirality : 0.043 0.258 3238 Planarity : 0.005 0.051 3584 Dihedral : 9.898 159.205 3076 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.49 % Favored : 89.15 % Rotamer: Outliers : 2.73 % Allowed : 19.08 % Favored : 78.19 % 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 aren not related in a simple way. whole: -1.63 (0.17), residues: 2526 helix: -0.04 (0.14), residues: 1428 sheet: -2.53 (0.52), residues: 106 loop : -2.45 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 336 TYR 0.022 0.001 TYR D 628 PHE 0.022 0.001 PHE C 674 TRP 0.014 0.001 TRP C 733 HIS 0.004 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00306 (21270) covalent geometry : angle 0.71014 (28800) hydrogen bonds : bond 0.03251 ( 845) hydrogen bonds : angle 4.42155 ( 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 433 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 372 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 SER cc_start: 0.8745 (m) cc_final: 0.8350 (t) REVERT: A 531 ASP cc_start: 0.8024 (m-30) cc_final: 0.7396 (m-30) REVERT: A 534 MET cc_start: 0.7617 (mmp) cc_final: 0.7290 (ptt) REVERT: A 553 TYR cc_start: 0.7731 (m-80) cc_final: 0.7432 (m-80) REVERT: B 155 PHE cc_start: 0.8199 (m-10) cc_final: 0.7975 (m-10) REVERT: B 156 ASP cc_start: 0.8815 (t70) cc_final: 0.8543 (t0) REVERT: B 219 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7840 (mmt-90) REVERT: B 541 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6130 (m-40) REVERT: B 761 MET cc_start: 0.8638 (mmt) cc_final: 0.8437 (mmm) REVERT: B 791 ASN cc_start: 0.7862 (m110) cc_final: 0.6947 (p0) REVERT: B 794 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7119 (pt) REVERT: C 156 ASP cc_start: 0.7970 (t0) cc_final: 0.7328 (t0) REVERT: C 318 ASP cc_start: 0.8238 (t0) cc_final: 0.7795 (m-30) REVERT: C 345 MET cc_start: 0.9009 (mmm) cc_final: 0.8696 (mmt) REVERT: C 477 SER cc_start: 0.8702 (m) cc_final: 0.8222 (t) REVERT: C 531 ASP cc_start: 0.7944 (m-30) cc_final: 0.7374 (m-30) REVERT: C 534 MET cc_start: 0.7833 (mpm) cc_final: 0.7346 (mpm) REVERT: C 567 TYR cc_start: 0.7886 (t80) cc_final: 0.7607 (t80) REVERT: C 685 MET cc_start: 0.8638 (pmm) cc_final: 0.7803 (ptp) REVERT: D 156 ASP cc_start: 0.8486 (t70) cc_final: 0.8276 (t0) REVERT: D 232 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8109 (ptt180) REVERT: D 396 ASP cc_start: 0.7872 (t70) cc_final: 0.7389 (p0) REVERT: D 607 GLN cc_start: 0.7986 (mt0) cc_final: 0.7653 (mm110) REVERT: D 612 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8208 (mmtt) REVERT: D 625 MET cc_start: 0.7171 (mmp) cc_final: 0.5692 (tmm) outliers start: 61 outliers final: 39 residues processed: 407 average time/residue: 0.1424 time to fit residues: 93.1378 Evaluate side-chains 395 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 352 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 582 LEU Chi-restraints excluded: chain A residue 588 ASN 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 709 LEU Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 383 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 622 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 369 ASP 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 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 181 THR 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 182 optimal weight: 0.0270 chunk 101 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 247 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 550 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.165045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131351 restraints weight = 29782.293| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.09 r_work: 0.3262 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21270 Z= 0.124 Angle : 0.708 12.898 28800 Z= 0.352 Chirality : 0.042 0.228 3238 Planarity : 0.005 0.051 3584 Dihedral : 9.598 146.900 3076 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.94 % Favored : 89.75 % Rotamer: Outliers : 2.46 % Allowed : 19.53 % Favored : 78.02 % 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 aren not related in a simple way. whole: -1.48 (0.17), residues: 2526 helix: 0.07 (0.14), residues: 1436 sheet: -2.47 (0.53), residues: 106 loop : -2.39 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 179 TYR 0.023 0.001 TYR D 253 PHE 0.025 0.001 PHE B 617 TRP 0.015 0.001 TRP C 733 HIS 0.003 0.000 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00270 (21270) covalent geometry : angle 0.70772 (28800) hydrogen bonds : bond 0.03127 ( 845) hydrogen bonds : angle 4.37260 ( 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 438 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 383 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7831 (mmm-85) REVERT: A 295 THR cc_start: 0.8876 (p) cc_final: 0.8316 (t) REVERT: A 477 SER cc_start: 0.8707 (m) cc_final: 0.8356 (t) REVERT: A 531 ASP cc_start: 0.7982 (m-30) cc_final: 0.7424 (m-30) REVERT: A 534 MET cc_start: 0.7493 (mmp) cc_final: 0.7281 (ptt) REVERT: A 553 TYR cc_start: 0.7694 (m-80) cc_final: 0.7353 (m-80) REVERT: A 685 MET cc_start: 0.6089 (mmt) cc_final: 0.5698 (ptp) REVERT: B 155 PHE cc_start: 0.8206 (m-10) cc_final: 0.8004 (m-10) REVERT: B 156 ASP cc_start: 0.8771 (t70) cc_final: 0.8512 (t0) REVERT: B 219 ARG cc_start: 0.8096 (mmt-90) cc_final: 0.7871 (mmt-90) REVERT: B 541 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6227 (m-40) REVERT: B 578 MET cc_start: 0.7154 (mmt) cc_final: 0.6855 (tpt) REVERT: B 761 MET cc_start: 0.8460 (mmt) cc_final: 0.8244 (mmm) REVERT: B 791 ASN cc_start: 0.7823 (m110) cc_final: 0.6921 (p0) REVERT: B 794 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7061 (pt) REVERT: C 156 ASP cc_start: 0.7922 (t0) cc_final: 0.7269 (t0) REVERT: C 215 ASP cc_start: 0.8308 (m-30) cc_final: 0.7988 (m-30) REVERT: C 318 ASP cc_start: 0.8232 (t0) cc_final: 0.7831 (m-30) REVERT: C 345 MET cc_start: 0.8978 (mmm) cc_final: 0.8678 (mmt) REVERT: C 477 SER cc_start: 0.8681 (m) cc_final: 0.8217 (t) REVERT: C 531 ASP cc_start: 0.7863 (m-30) cc_final: 0.7330 (m-30) REVERT: C 534 MET cc_start: 0.7748 (mpm) cc_final: 0.7298 (mpm) REVERT: C 567 TYR cc_start: 0.7778 (t80) cc_final: 0.7545 (t80) REVERT: C 685 MET cc_start: 0.8472 (pmm) cc_final: 0.7435 (mmt) REVERT: C 745 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: D 156 ASP cc_start: 0.8451 (t70) cc_final: 0.8245 (t0) REVERT: D 232 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8151 (ptt180) REVERT: D 396 ASP cc_start: 0.7839 (t70) cc_final: 0.7369 (p0) REVERT: D 625 MET cc_start: 0.7104 (mmp) cc_final: 0.5636 (tmm) REVERT: D 674 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7388 (t80) outliers start: 55 outliers final: 35 residues processed: 414 average time/residue: 0.1442 time to fit residues: 95.7687 Evaluate side-chains 400 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 360 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 582 LEU Chi-restraints excluded: chain A residue 588 ASN 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 748 PHE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 383 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 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 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 533 PHE 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 622 LEU Chi-restraints excluded: chain D residue 674 PHE 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: 0.6980 chunk 61 optimal weight: 4.9990 chunk 173 optimal weight: 0.0670 chunk 62 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 242 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN ** B 787 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127865 restraints weight = 29972.121| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.25 r_work: 0.3219 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21270 Z= 0.165 Angle : 0.730 12.909 28800 Z= 0.365 Chirality : 0.043 0.242 3238 Planarity : 0.005 0.065 3584 Dihedral : 9.525 140.466 3076 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.57 % Favored : 89.07 % Rotamer: Outliers : 2.14 % Allowed : 20.24 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -1.50 (0.17), residues: 2526 helix: 0.04 (0.14), residues: 1444 sheet: -2.46 (0.52), residues: 106 loop : -2.40 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 336 TYR 0.031 0.002 TYR D 253 PHE 0.022 0.001 PHE A 751 TRP 0.015 0.001 TRP B 733 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00386 (21270) covalent geometry : angle 0.73025 (28800) hydrogen bonds : bond 0.03305 ( 845) hydrogen bonds : angle 4.41928 ( 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 414 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 366 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.8028 (m-30) cc_final: 0.7494 (m-30) REVERT: A 534 MET cc_start: 0.7508 (mmp) cc_final: 0.7276 (ptt) REVERT: A 553 TYR cc_start: 0.7757 (m-80) cc_final: 0.7438 (m-80) REVERT: B 156 ASP cc_start: 0.8778 (t70) cc_final: 0.8520 (t0) REVERT: B 219 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7895 (mmt-90) REVERT: B 263 ASP cc_start: 0.6272 (t0) cc_final: 0.5924 (t70) REVERT: B 541 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.6097 (m-40) REVERT: B 578 MET cc_start: 0.7057 (mmt) cc_final: 0.6736 (tpt) REVERT: B 625 MET cc_start: 0.7321 (mmp) cc_final: 0.5733 (tmm) REVERT: B 791 ASN cc_start: 0.7781 (m110) cc_final: 0.6895 (p0) REVERT: B 794 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7024 (pt) REVERT: C 156 ASP cc_start: 0.7910 (t0) cc_final: 0.7263 (t0) REVERT: C 215 ASP cc_start: 0.8444 (m-30) cc_final: 0.8108 (m-30) REVERT: C 318 ASP cc_start: 0.8242 (t0) cc_final: 0.7796 (m-30) REVERT: C 345 MET cc_start: 0.9051 (mmm) cc_final: 0.8762 (mmt) REVERT: C 442 LYS cc_start: 0.7770 (ptmt) cc_final: 0.7245 (tttt) REVERT: C 444 GLU cc_start: 0.7659 (mp0) cc_final: 0.7147 (mp0) REVERT: C 477 SER cc_start: 0.8707 (m) cc_final: 0.8193 (t) REVERT: C 531 ASP cc_start: 0.7952 (m-30) cc_final: 0.7379 (m-30) REVERT: C 567 TYR cc_start: 0.7839 (t80) cc_final: 0.7615 (t80) REVERT: C 745 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: D 156 ASP cc_start: 0.8452 (t70) cc_final: 0.8248 (t0) REVERT: D 232 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8129 (ptt90) REVERT: D 625 MET cc_start: 0.7248 (mmp) cc_final: 0.5546 (tmm) REVERT: D 674 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7564 (t80) outliers start: 48 outliers final: 32 residues processed: 396 average time/residue: 0.1416 time to fit residues: 90.0395 Evaluate side-chains 382 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 345 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 582 LEU Chi-restraints excluded: chain A residue 588 ASN 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 B residue 173 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 383 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 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 222 ASN 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 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 518 LEU 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 622 LEU Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 717 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 6 optimal weight: 0.4980 chunk 232 optimal weight: 0.0770 chunk 244 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 181 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 550 GLN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 588 ASN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3926 r_free = 0.3926 target = 0.165044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131540 restraints weight = 29703.233| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.23 r_work: 0.3248 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5313 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= 0.123 Angle : 0.712 14.283 28800 Z= 0.354 Chirality : 0.042 0.279 3238 Planarity : 0.005 0.063 3584 Dihedral : 9.345 131.871 3076 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.58 % Favored : 90.10 % Rotamer: Outliers : 2.19 % Allowed : 20.42 % Favored : 77.39 % 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 aren not related in a simple way. whole: -1.41 (0.17), residues: 2526 helix: 0.11 (0.14), residues: 1446 sheet: -2.40 (0.53), residues: 106 loop : -2.36 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 179 TYR 0.037 0.001 TYR D 253 PHE 0.020 0.001 PHE C 751 TRP 0.021 0.001 TRP B 733 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00269 (21270) covalent geometry : angle 0.71159 (28800) hydrogen bonds : bond 0.03184 ( 845) hydrogen bonds : angle 4.36561 ( 2445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4725.81 seconds wall clock time: 81 minutes 57.95 seconds (4917.95 seconds total)