Starting phenix.real_space_refine on Wed Jun 18 08:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1f_40962/06_2025/8t1f_40962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1f_40962/06_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_40962/06_2025/8t1f_40962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1f_40962/06_2025/8t1f_40962.map" model { file = "/net/cci-nas-00/data/ceres_data/8t1f_40962/06_2025/8t1f_40962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1f_40962/06_2025/8t1f_40962.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.39, per 1000 atoms: 0.60 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: 4.68 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.97 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: 6.18 Time building geometry restraints manager: 5.51 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: 0.10 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: 2.040 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 44.900 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.420 ------------------------------------------------------------------------------- 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 : 4.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.002 TRP B 733 HIS 0.007 0.001 HIS B 265 PHE 0.033 0.002 PHE D 580 TYR 0.019 0.002 TYR A 508 ARG 0.015 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.31287 ( 845) hydrogen bonds : angle 10.34865 ( 2445) covalent geometry : bond 0.00616 (21270) covalent geometry : angle 1.32409 (28800) *********************** 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 : 2.511 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: 0.3568 time to fit residues: 359.4089 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 : 2.157 ------------------------------------------------------------------------------- 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 212 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 207 ASN A 228 ASN A 265 HIS ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 361 ASN A 474 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 541 ASN A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 784 ASN B 176 HIS B 201 ASN B 204 ASN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS B 338 ASN B 361 ASN B 492 GLN B 550 GLN B 588 ASN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN C 176 HIS C 228 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 474 ASN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 550 GLN C 637 ASN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 ASN D 204 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN D 326 HIS D 492 GLN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128527 restraints weight = 30091.479| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.17 r_work: 0.3231 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21270 Z= 0.192 Angle : 0.818 11.082 28800 Z= 0.417 Chirality : 0.046 0.303 3238 Planarity : 0.006 0.049 3584 Dihedral : 12.449 169.620 3078 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.61 % Favored : 88.92 % Rotamer: Outliers : 2.82 % Allowed : 13.27 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.15), residues: 2526 helix: -2.18 (0.11), residues: 1446 sheet: -3.02 (0.47), residues: 116 loop : -2.82 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 733 HIS 0.007 0.001 HIS B 176 PHE 0.025 0.002 PHE D 666 TYR 0.020 0.002 TYR D 574 ARG 0.007 0.001 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 845) hydrogen bonds : angle 5.41519 ( 2445) covalent geometry : bond 0.00440 (21270) covalent geometry : angle 0.81805 (28800) *********************** 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 523 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 460 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7755 (mtm-85) REVERT: A 215 ASP cc_start: 0.8137 (m-30) cc_final: 0.7927 (m-30) REVERT: A 222 ASN cc_start: 0.7847 (m110) cc_final: 0.7596 (m110) REVERT: A 477 SER cc_start: 0.8721 (m) cc_final: 0.8379 (t) REVERT: A 628 TYR cc_start: 0.8035 (m-80) cc_final: 0.7698 (m-80) REVERT: A 693 VAL cc_start: 0.7578 (t) cc_final: 0.7368 (p) REVERT: B 291 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9196 (tp) REVERT: B 345 MET cc_start: 0.8450 (mmm) cc_final: 0.8205 (mmm) REVERT: B 473 ILE cc_start: 0.9004 (mm) cc_final: 0.8742 (mt) REVERT: B 614 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8075 (tm) REVERT: B 705 LEU cc_start: 0.9172 (tp) cc_final: 0.8966 (tp) REVERT: B 791 ASN cc_start: 0.7999 (m110) cc_final: 0.6807 (p0) REVERT: C 156 ASP cc_start: 0.8015 (t0) cc_final: 0.7420 (t0) REVERT: C 179 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7772 (mtp85) REVERT: C 287 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 303 TYR cc_start: 0.8049 (t80) cc_final: 0.7736 (t80) REVERT: C 369 ASP cc_start: 0.8681 (t0) cc_final: 0.8473 (t0) REVERT: C 379 LYS cc_start: 0.9132 (ttmt) cc_final: 0.8854 (ttmm) REVERT: C 477 SER cc_start: 0.8483 (m) cc_final: 0.8134 (t) REVERT: C 685 MET cc_start: 0.6715 (mmt) cc_final: 0.6298 (mmt) REVERT: D 156 ASP cc_start: 0.8385 (t70) cc_final: 0.8138 (t0) REVERT: D 253 TYR cc_start: 0.7925 (m-10) cc_final: 0.7720 (m-10) REVERT: D 263 ASP cc_start: 0.6974 (t0) cc_final: 0.6539 (t0) REVERT: D 473 ILE cc_start: 0.8999 (mm) cc_final: 0.8721 (mt) REVERT: D 612 LYS cc_start: 0.8527 (ttpm) cc_final: 0.8228 (mttt) REVERT: D 614 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8114 (tm) REVERT: D 728 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8259 (tm-30) REVERT: D 747 SER cc_start: 0.8939 (m) cc_final: 0.8706 (t) REVERT: D 791 ASN cc_start: 0.8036 (m110) cc_final: 0.7370 (p0) outliers start: 63 outliers final: 28 residues processed: 494 average time/residue: 0.3181 time to fit residues: 242.6657 Evaluate side-chains 412 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 380 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 557 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 704 ILE 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 575 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 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 264 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain 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 38 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 231 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 228 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.160062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125560 restraints weight = 29990.021| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.17 r_work: 0.3203 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21270 Z= 0.182 Angle : 0.762 11.465 28800 Z= 0.387 Chirality : 0.045 0.238 3238 Planarity : 0.005 0.045 3584 Dihedral : 11.295 167.300 3076 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.29 % Favored : 89.19 % Rotamer: Outliers : 3.84 % Allowed : 15.06 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.15), residues: 2526 helix: -1.31 (0.13), residues: 1436 sheet: -2.53 (0.55), residues: 88 loop : -2.74 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 733 HIS 0.005 0.001 HIS B 326 PHE 0.034 0.002 PHE C 751 TYR 0.025 0.002 TYR D 574 ARG 0.006 0.001 ARG D 446 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 845) hydrogen bonds : angle 4.93386 ( 2445) covalent geometry : bond 0.00421 (21270) covalent geometry : angle 0.76214 (28800) *********************** 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 509 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 423 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7965 (m110) cc_final: 0.7651 (m110) REVERT: A 531 ASP cc_start: 0.8141 (m-30) cc_final: 0.7864 (m-30) REVERT: A 534 MET cc_start: 0.7841 (mmp) cc_final: 0.7138 (ptt) REVERT: B 156 ASP cc_start: 0.8770 (t70) cc_final: 0.8470 (t0) REVERT: B 206 ARG cc_start: 0.7951 (mmp-170) cc_final: 0.7614 (mmp-170) REVERT: B 253 TYR cc_start: 0.7910 (m-10) cc_final: 0.7683 (m-10) REVERT: B 263 ASP cc_start: 0.6314 (t0) cc_final: 0.6067 (t0) REVERT: B 291 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9265 (tp) REVERT: B 614 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8103 (tm) REVERT: B 791 ASN cc_start: 0.8047 (m110) cc_final: 0.6967 (p0) REVERT: B 794 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7111 (pt) REVERT: C 156 ASP cc_start: 0.7917 (t0) cc_final: 0.7313 (t0) REVERT: C 185 PHE cc_start: 0.8510 (m-80) cc_final: 0.8224 (m-80) REVERT: C 287 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8731 (mp) REVERT: C 369 ASP cc_start: 0.8803 (t0) cc_final: 0.8597 (t0) REVERT: C 379 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8783 (ttmm) REVERT: C 477 SER cc_start: 0.8505 (m) cc_final: 0.8110 (t) REVERT: C 482 MET cc_start: 0.8056 (mmt) cc_final: 0.7505 (mpp) REVERT: C 523 LEU cc_start: 0.8460 (mp) cc_final: 0.7850 (tp) REVERT: C 531 ASP cc_start: 0.8211 (m-30) cc_final: 0.7736 (m-30) REVERT: C 607 GLN cc_start: 0.8130 (mp10) cc_final: 0.7714 (mm-40) REVERT: C 611 PHE cc_start: 0.8204 (m-10) cc_final: 0.7998 (m-10) REVERT: C 684 GLU cc_start: 0.6087 (tm-30) cc_final: 0.5872 (tm-30) REVERT: D 156 ASP cc_start: 0.8404 (t70) cc_final: 0.8152 (t0) REVERT: D 607 GLN cc_start: 0.7938 (mt0) cc_final: 0.7507 (mm110) REVERT: D 612 LYS cc_start: 0.8567 (ttpm) cc_final: 0.8195 (mttt) REVERT: D 614 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8093 (tm) REVERT: D 791 ASN cc_start: 0.7851 (m110) cc_final: 0.7151 (p0) outliers start: 86 outliers final: 39 residues processed: 473 average time/residue: 0.2937 time to fit residues: 220.3040 Evaluate side-chains 422 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 378 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 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 614 LEU Chi-restraints excluded: chain B residue 622 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 209 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 704 ILE 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 213 LEU Chi-restraints excluded: chain D residue 335 THR 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 575 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 28 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 171 optimal weight: 0.4980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 297 GLN ** 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 = 0.3864 r_free = 0.3864 target = 0.159792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125858 restraints weight = 30062.986| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.27 r_work: 0.3196 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21270 Z= 0.173 Angle : 0.732 11.774 28800 Z= 0.371 Chirality : 0.043 0.269 3238 Planarity : 0.005 0.059 3584 Dihedral : 10.773 160.267 3076 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.61 % Favored : 88.95 % Rotamer: Outliers : 3.53 % Allowed : 16.13 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.16), residues: 2526 helix: -0.93 (0.13), residues: 1466 sheet: -2.41 (0.54), residues: 88 loop : -2.77 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 733 HIS 0.006 0.001 HIS D 252 PHE 0.023 0.001 PHE D 666 TYR 0.027 0.002 TYR D 574 ARG 0.010 0.001 ARG D 269 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 845) hydrogen bonds : angle 4.68504 ( 2445) covalent geometry : bond 0.00393 (21270) covalent geometry : angle 0.73196 (28800) *********************** 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: 79 poor density : 395 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7873 (m110) cc_final: 0.7564 (m110) REVERT: A 223 MET cc_start: 0.8744 (mmt) cc_final: 0.8446 (mmt) REVERT: A 369 ASP cc_start: 0.8877 (t0) cc_final: 0.8640 (t0) REVERT: A 442 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7549 (tttt) REVERT: A 531 ASP cc_start: 0.8126 (m-30) cc_final: 0.7839 (m-30) REVERT: A 575 LEU cc_start: 0.9162 (mt) cc_final: 0.8361 (pt) REVERT: B 156 ASP cc_start: 0.8800 (t70) cc_final: 0.8564 (t0) REVERT: B 206 ARG cc_start: 0.7995 (mmp-170) cc_final: 0.7755 (mmp-170) REVERT: B 291 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9281 (tp) REVERT: B 614 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8082 (tm) REVERT: B 791 ASN cc_start: 0.8053 (m110) cc_final: 0.7059 (p0) REVERT: B 794 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7117 (pt) REVERT: C 156 ASP cc_start: 0.7997 (t0) cc_final: 0.7377 (t0) REVERT: C 185 PHE cc_start: 0.8511 (m-80) cc_final: 0.8222 (m-80) REVERT: C 318 ASP cc_start: 0.8126 (t0) cc_final: 0.7734 (m-30) REVERT: C 477 SER cc_start: 0.8656 (m) cc_final: 0.8195 (t) REVERT: C 531 ASP cc_start: 0.8055 (m-30) cc_final: 0.7506 (m-30) REVERT: C 567 TYR cc_start: 0.8043 (t80) cc_final: 0.7658 (t80) REVERT: D 156 ASP cc_start: 0.8441 (t70) cc_final: 0.8184 (t0) REVERT: D 607 GLN cc_start: 0.7935 (mt0) cc_final: 0.7634 (mm110) REVERT: D 612 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8136 (mttt) REVERT: D 614 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8059 (tm) REVERT: D 791 ASN cc_start: 0.7909 (m110) cc_final: 0.7176 (p0) outliers start: 79 outliers final: 40 residues processed: 438 average time/residue: 0.2862 time to fit residues: 197.9940 Evaluate side-chains 405 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 360 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 LEU 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 209 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 421 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 616 ARG 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 442 LYS Chi-restraints excluded: chain D residue 453 GLU 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 612 LYS Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 69 optimal weight: 0.9980 chunk 251 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 161 optimal weight: 0.0270 chunk 40 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- 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 252 HIS B 297 GLN B 784 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.162127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129011 restraints weight = 30017.663| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.09 r_work: 0.3247 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4419 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= 0.139 Angle : 0.704 11.863 28800 Z= 0.356 Chirality : 0.042 0.238 3238 Planarity : 0.005 0.060 3584 Dihedral : 10.347 145.762 3076 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.94 % Favored : 89.63 % Rotamer: Outliers : 3.40 % Allowed : 16.98 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.16), residues: 2526 helix: -0.54 (0.13), residues: 1452 sheet: -2.22 (0.56), residues: 88 loop : -2.64 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 733 HIS 0.008 0.001 HIS D 252 PHE 0.038 0.001 PHE D 617 TYR 0.023 0.002 TYR D 574 ARG 0.006 0.000 ARG B 757 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 845) hydrogen bonds : angle 4.54018 ( 2445) covalent geometry : bond 0.00310 (21270) covalent geometry : angle 0.70393 (28800) *********************** 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 480 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 404 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7874 (m110) cc_final: 0.7422 (m110) REVERT: A 260 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: A 369 ASP cc_start: 0.8861 (t0) cc_final: 0.8549 (t0) REVERT: A 531 ASP cc_start: 0.8144 (m-30) cc_final: 0.7559 (m-30) REVERT: A 534 MET cc_start: 0.7565 (mmp) cc_final: 0.7202 (ptt) REVERT: A 587 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7893 (mmm) REVERT: B 156 ASP cc_start: 0.8749 (t70) cc_final: 0.8502 (t0) REVERT: B 206 ARG cc_start: 0.8046 (mmp-170) cc_final: 0.7372 (mmp-170) REVERT: B 219 ARG cc_start: 0.8140 (mmt-90) cc_final: 0.7854 (mmt-90) REVERT: B 252 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7220 (p-80) REVERT: B 614 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8033 (tm) REVERT: B 683 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.5118 (tp) REVERT: B 791 ASN cc_start: 0.7976 (m110) cc_final: 0.7093 (p0) REVERT: B 794 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7070 (pt) REVERT: C 156 ASP cc_start: 0.7943 (t0) cc_final: 0.7322 (t0) REVERT: C 287 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8630 (mp) REVERT: C 477 SER cc_start: 0.8659 (m) cc_final: 0.8205 (t) REVERT: C 531 ASP cc_start: 0.7823 (m-30) cc_final: 0.7247 (m-30) REVERT: C 567 TYR cc_start: 0.7931 (t80) cc_final: 0.7524 (t80) REVERT: C 598 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8278 (tm) REVERT: D 156 ASP cc_start: 0.8405 (t70) cc_final: 0.8195 (t0) REVERT: D 232 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8213 (ptt180) REVERT: D 607 GLN cc_start: 0.7936 (mt0) cc_final: 0.7570 (mm110) REVERT: D 612 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8253 (mmtt) REVERT: D 614 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8036 (tm) REVERT: D 791 ASN cc_start: 0.7869 (m110) cc_final: 0.7137 (p0) outliers start: 76 outliers final: 41 residues processed: 449 average time/residue: 0.3086 time to fit residues: 217.3092 Evaluate side-chains 413 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 361 time to evaluate : 2.157 ------------------------------------------------------------------------------- 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 610 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain 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 209 THR Chi-restraints excluded: chain B residue 252 HIS 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 614 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 520 THR 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 598 LEU Chi-restraints excluded: chain C residue 616 ARG Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 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 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 614 LEU Chi-restraints excluded: chain D residue 622 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 101 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 243 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 252 HIS ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127850 restraints weight = 29890.481| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.16 r_work: 0.3218 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4637 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= 0.149 Angle : 0.711 12.211 28800 Z= 0.358 Chirality : 0.043 0.249 3238 Planarity : 0.005 0.054 3584 Dihedral : 10.106 124.257 3076 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.25 % Favored : 89.31 % Rotamer: Outliers : 3.66 % Allowed : 17.29 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2526 helix: -0.36 (0.14), residues: 1446 sheet: -2.06 (0.56), residues: 88 loop : -2.61 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 733 HIS 0.025 0.001 HIS B 252 PHE 0.031 0.001 PHE D 617 TYR 0.023 0.002 TYR B 621 ARG 0.007 0.001 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 845) hydrogen bonds : angle 4.48115 ( 2445) covalent geometry : bond 0.00345 (21270) covalent geometry : angle 0.71062 (28800) *********************** 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 468 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 386 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7863 (mtp85) REVERT: A 223 MET cc_start: 0.8849 (mmt) cc_final: 0.8465 (mmt) REVERT: A 260 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: A 369 ASP cc_start: 0.8902 (t0) cc_final: 0.8680 (t0) REVERT: A 531 ASP cc_start: 0.8111 (m-30) cc_final: 0.7476 (m-30) REVERT: A 534 MET cc_start: 0.7397 (mmp) cc_final: 0.7162 (ptt) REVERT: B 156 ASP cc_start: 0.8756 (t70) cc_final: 0.8459 (t0) REVERT: B 219 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7850 (mmt-90) REVERT: B 232 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8306 (ptt90) REVERT: B 345 MET cc_start: 0.8355 (mmm) cc_final: 0.8073 (mmm) REVERT: B 541 ASN cc_start: 0.7040 (OUTLIER) cc_final: 0.6112 (m-40) REVERT: B 614 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8028 (tm) REVERT: B 683 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5306 (tp) REVERT: B 791 ASN cc_start: 0.7974 (m110) cc_final: 0.7048 (p0) REVERT: B 794 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7057 (pt) REVERT: C 156 ASP cc_start: 0.7945 (t0) cc_final: 0.7302 (t0) REVERT: C 287 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8740 (mp) REVERT: C 477 SER cc_start: 0.8655 (m) cc_final: 0.8203 (t) REVERT: C 531 ASP cc_start: 0.7768 (m-30) cc_final: 0.7188 (m-30) REVERT: C 567 TYR cc_start: 0.7898 (t80) cc_final: 0.7516 (t80) REVERT: C 604 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8823 (mm) REVERT: D 156 ASP cc_start: 0.8434 (t70) cc_final: 0.8229 (t0) REVERT: D 232 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8177 (ptt180) REVERT: D 252 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7882 (p90) REVERT: D 607 GLN cc_start: 0.7952 (mt0) cc_final: 0.7642 (mm110) REVERT: D 612 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8227 (mmtt) REVERT: D 791 ASN cc_start: 0.7882 (m110) cc_final: 0.7062 (p0) outliers start: 82 outliers final: 52 residues processed: 429 average time/residue: 0.2953 time to fit residues: 200.8849 Evaluate side-chains 428 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 365 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET 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 173 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 383 ILE 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 614 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 683 LEU 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 158 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 407 LYS 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 551 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 616 ARG Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 453 GLU 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 583 VAL Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 705 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 34 optimal weight: 5.9990 chunk 203 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 260 GLN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.163027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130887 restraints weight = 29791.752| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.17 r_work: 0.3252 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21270 Z= 0.127 Angle : 0.699 12.404 28800 Z= 0.350 Chirality : 0.042 0.236 3238 Planarity : 0.005 0.051 3584 Dihedral : 9.839 121.773 3076 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.90 % Favored : 89.75 % Rotamer: Outliers : 3.53 % Allowed : 17.96 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2526 helix: -0.14 (0.14), residues: 1430 sheet: -2.17 (0.57), residues: 96 loop : -2.52 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 733 HIS 0.006 0.001 HIS D 252 PHE 0.035 0.001 PHE C 485 TYR 0.019 0.001 TYR D 574 ARG 0.008 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 845) hydrogen bonds : angle 4.39700 ( 2445) covalent geometry : bond 0.00284 (21270) covalent geometry : angle 0.69927 (28800) *********************** 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 470 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 391 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8309 (mmt90) REVERT: A 222 ASN cc_start: 0.7892 (m110) cc_final: 0.7312 (m110) REVERT: A 260 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: A 296 ASN cc_start: 0.9226 (t0) cc_final: 0.8982 (t0) REVERT: A 369 ASP cc_start: 0.8900 (t0) cc_final: 0.8558 (t0) REVERT: A 477 SER cc_start: 0.8753 (m) cc_final: 0.8330 (t) REVERT: A 531 ASP cc_start: 0.8096 (m-30) cc_final: 0.7485 (m-30) REVERT: A 587 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7793 (mtp) REVERT: B 156 ASP cc_start: 0.8751 (t70) cc_final: 0.8452 (t0) REVERT: B 219 ARG cc_start: 0.8151 (mmt-90) cc_final: 0.7878 (mmt-90) REVERT: B 345 MET cc_start: 0.8268 (mmm) cc_final: 0.8036 (mmm) REVERT: B 541 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6248 (m-40) REVERT: B 614 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7997 (tm) REVERT: B 791 ASN cc_start: 0.7907 (m110) cc_final: 0.6992 (p0) REVERT: B 794 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7054 (pt) REVERT: C 156 ASP cc_start: 0.7889 (t0) cc_final: 0.7253 (t0) REVERT: C 210 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7774 (tt) REVERT: C 287 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8711 (mp) REVERT: C 477 SER cc_start: 0.8640 (m) cc_final: 0.8169 (t) REVERT: C 531 ASP cc_start: 0.7685 (m-30) cc_final: 0.7286 (m-30) REVERT: C 567 TYR cc_start: 0.7754 (t80) cc_final: 0.7484 (t80) REVERT: C 604 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8848 (mm) REVERT: D 232 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8125 (ptt180) REVERT: D 234 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8582 (mt) REVERT: D 252 HIS cc_start: 0.8050 (OUTLIER) cc_final: 0.7735 (p90) REVERT: D 253 TYR cc_start: 0.7284 (m-10) cc_final: 0.7061 (m-10) REVERT: D 607 GLN cc_start: 0.7967 (mt0) cc_final: 0.7610 (mm110) REVERT: D 612 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8224 (mmtt) REVERT: D 713 MET cc_start: 0.7789 (tpp) cc_final: 0.7587 (mmt) REVERT: D 791 ASN cc_start: 0.7883 (m110) cc_final: 0.7063 (p0) outliers start: 79 outliers final: 37 residues processed: 433 average time/residue: 0.2892 time to fit residues: 198.9188 Evaluate side-chains 420 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 371 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 366 LEU 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 610 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 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 614 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 551 LEU 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 705 LEU Chi-restraints excluded: chain D residue 714 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 142 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 238 optimal weight: 20.0000 chunk 114 optimal weight: 0.0470 chunk 170 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- 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 252 HIS C 207 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 HIS D 550 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.160549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126867 restraints weight = 29895.790| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.32 r_work: 0.3174 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21270 Z= 0.164 Angle : 0.731 13.504 28800 Z= 0.364 Chirality : 0.043 0.241 3238 Planarity : 0.005 0.048 3584 Dihedral : 9.702 120.610 3076 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.49 % Favored : 89.15 % Rotamer: Outliers : 3.40 % Allowed : 18.45 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2526 helix: -0.13 (0.14), residues: 1442 sheet: -2.47 (0.52), residues: 106 loop : -2.61 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 733 HIS 0.006 0.001 HIS D 252 PHE 0.033 0.001 PHE C 485 TYR 0.019 0.001 TYR D 574 ARG 0.009 0.001 ARG D 336 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 845) hydrogen bonds : angle 4.44972 ( 2445) covalent geometry : bond 0.00387 (21270) covalent geometry : angle 0.73079 (28800) *********************** 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 442 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 366 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7791 (m110) cc_final: 0.7502 (m110) REVERT: A 260 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8100 (mp10) REVERT: A 369 ASP cc_start: 0.8965 (t0) cc_final: 0.8627 (t0) REVERT: A 531 ASP cc_start: 0.7827 (m-30) cc_final: 0.7420 (m-30) REVERT: B 155 PHE cc_start: 0.8164 (m-10) cc_final: 0.7944 (m-10) REVERT: B 156 ASP cc_start: 0.8777 (t70) cc_final: 0.8494 (t0) REVERT: B 219 ARG cc_start: 0.8151 (mmt-90) cc_final: 0.7876 (mmt-90) REVERT: B 257 LEU cc_start: 0.8869 (mt) cc_final: 0.8637 (mp) REVERT: B 345 MET cc_start: 0.8462 (mmm) cc_final: 0.8251 (mmm) REVERT: B 541 ASN cc_start: 0.7065 (OUTLIER) cc_final: 0.6174 (m-40) REVERT: B 614 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8017 (tm) REVERT: B 625 MET cc_start: 0.7553 (mmp) cc_final: 0.5976 (tmm) REVERT: B 791 ASN cc_start: 0.7937 (m110) cc_final: 0.7045 (p0) REVERT: B 794 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7165 (pt) REVERT: C 156 ASP cc_start: 0.8012 (t0) cc_final: 0.7354 (t0) REVERT: C 215 ASP cc_start: 0.8394 (m-30) cc_final: 0.8132 (m-30) REVERT: C 366 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8808 (mp) REVERT: C 477 SER cc_start: 0.8691 (m) cc_final: 0.8216 (t) REVERT: C 531 ASP cc_start: 0.7681 (m-30) cc_final: 0.7291 (m-30) REVERT: C 567 TYR cc_start: 0.7832 (t80) cc_final: 0.7501 (t80) REVERT: C 604 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8928 (mm) REVERT: C 685 MET cc_start: 0.8438 (ptp) cc_final: 0.7774 (mmt) REVERT: D 252 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7818 (p90) REVERT: D 253 TYR cc_start: 0.7428 (m-10) cc_final: 0.7223 (m-10) REVERT: D 263 ASP cc_start: 0.6793 (t70) cc_final: 0.6545 (t70) REVERT: D 612 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8258 (mmtt) REVERT: D 713 MET cc_start: 0.7590 (tpp) cc_final: 0.7284 (mmt) REVERT: D 791 ASN cc_start: 0.8009 (m110) cc_final: 0.7133 (p0) outliers start: 76 outliers final: 49 residues processed: 402 average time/residue: 0.2999 time to fit residues: 191.4894 Evaluate side-chains 411 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 354 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 709 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 314 MET Chi-restraints excluded: chain B residue 533 PHE 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 614 LEU Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 711 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 366 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 616 ARG Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 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 583 VAL Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 145 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 202 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** A 712 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 252 HIS ** 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 = 0.3880 r_free = 0.3880 target = 0.161092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127106 restraints weight = 29876.136| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.20 r_work: 0.3222 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21270 Z= 0.152 Angle : 0.725 13.485 28800 Z= 0.364 Chirality : 0.043 0.285 3238 Planarity : 0.005 0.046 3584 Dihedral : 9.560 120.022 3076 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.25 % Favored : 89.39 % Rotamer: Outliers : 3.26 % Allowed : 18.50 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2526 helix: -0.09 (0.14), residues: 1446 sheet: -2.45 (0.53), residues: 106 loop : -2.59 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 733 HIS 0.006 0.001 HIS D 252 PHE 0.032 0.001 PHE C 485 TYR 0.019 0.001 TYR D 574 ARG 0.008 0.000 ARG B 336 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 845) hydrogen bonds : angle 4.45136 ( 2445) covalent geometry : bond 0.00354 (21270) covalent geometry : angle 0.72498 (28800) *********************** 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 440 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 367 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8311 (mmt90) REVERT: A 369 ASP cc_start: 0.8913 (t0) cc_final: 0.8572 (t0) REVERT: A 531 ASP cc_start: 0.8072 (m-30) cc_final: 0.7540 (m-30) REVERT: A 587 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7758 (mmm) REVERT: B 156 ASP cc_start: 0.8761 (t70) cc_final: 0.8479 (t0) REVERT: B 219 ARG cc_start: 0.8177 (mmt-90) cc_final: 0.7910 (mmt-90) REVERT: B 257 LEU cc_start: 0.8896 (mt) cc_final: 0.8604 (mp) REVERT: B 541 ASN cc_start: 0.7037 (OUTLIER) cc_final: 0.6131 (m-40) REVERT: B 578 MET cc_start: 0.7099 (mmt) cc_final: 0.6765 (tpt) REVERT: B 609 ILE cc_start: 0.9266 (mm) cc_final: 0.9045 (mt) REVERT: B 625 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.5832 (tmm) REVERT: B 791 ASN cc_start: 0.7921 (m110) cc_final: 0.7057 (p0) REVERT: B 794 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7022 (pt) REVERT: C 156 ASP cc_start: 0.7940 (t0) cc_final: 0.7282 (t0) REVERT: C 215 ASP cc_start: 0.8336 (m-30) cc_final: 0.8066 (m-30) REVERT: C 366 LEU cc_start: 0.9053 (mt) cc_final: 0.8827 (mp) REVERT: C 477 SER cc_start: 0.8641 (m) cc_final: 0.8151 (t) REVERT: C 531 ASP cc_start: 0.7618 (m-30) cc_final: 0.7186 (m-30) REVERT: C 567 TYR cc_start: 0.7702 (t80) cc_final: 0.7472 (t80) REVERT: C 604 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8917 (mm) REVERT: C 685 MET cc_start: 0.8320 (ptp) cc_final: 0.7735 (mmt) REVERT: D 252 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7686 (p90) REVERT: D 263 ASP cc_start: 0.6749 (t70) cc_final: 0.6538 (t70) REVERT: D 612 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8231 (mmtt) REVERT: D 702 TYR cc_start: 0.8049 (t80) cc_final: 0.7724 (t80) REVERT: D 713 MET cc_start: 0.7624 (tpp) cc_final: 0.7361 (mmt) REVERT: D 791 ASN cc_start: 0.7932 (m110) cc_final: 0.7093 (p0) outliers start: 73 outliers final: 50 residues processed: 405 average time/residue: 0.2883 time to fit residues: 185.6536 Evaluate side-chains 413 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 356 time to evaluate : 2.524 ------------------------------------------------------------------------------- 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 587 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 623 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 314 MET Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 711 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 334 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 616 ARG Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 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 612 LYS Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 184 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 128 optimal weight: 0.3980 chunk 137 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 243 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** C 222 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 ** C 712 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 = 0.3902 r_free = 0.3902 target = 0.163177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129472 restraints weight = 29739.187| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.23 r_work: 0.3216 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 21270 Z= 0.131 Angle : 0.721 13.197 28800 Z= 0.360 Chirality : 0.042 0.221 3238 Planarity : 0.005 0.048 3584 Dihedral : 9.393 118.558 3076 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.21 % Favored : 89.43 % Rotamer: Outliers : 2.55 % Allowed : 19.57 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2526 helix: -0.05 (0.14), residues: 1448 sheet: -2.46 (0.53), residues: 106 loop : -2.54 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.009 0.001 HIS D 252 PHE 0.030 0.001 PHE C 485 TYR 0.017 0.001 TYR D 574 ARG 0.008 0.000 ARG D 336 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 845) hydrogen bonds : angle 4.42135 ( 2445) covalent geometry : bond 0.00299 (21270) covalent geometry : angle 0.72091 (28800) ********************** 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 424 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 367 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 ASP cc_start: 0.8939 (t0) cc_final: 0.8595 (t0) REVERT: A 477 SER cc_start: 0.8747 (m) cc_final: 0.8332 (t) REVERT: A 531 ASP cc_start: 0.8031 (m-30) cc_final: 0.7504 (m-30) REVERT: A 587 MET cc_start: 0.8007 (mtm) cc_final: 0.7738 (mmm) REVERT: B 156 ASP cc_start: 0.8779 (t70) cc_final: 0.8515 (t0) REVERT: B 219 ARG cc_start: 0.8154 (mmt-90) cc_final: 0.7908 (mmt-90) REVERT: B 257 LEU cc_start: 0.8855 (mt) cc_final: 0.8584 (mp) REVERT: B 541 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6091 (m-40) REVERT: B 578 MET cc_start: 0.7123 (mmt) cc_final: 0.6764 (tpt) REVERT: B 609 ILE cc_start: 0.9295 (mm) cc_final: 0.9070 (mt) REVERT: B 625 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.5827 (tmm) REVERT: B 791 ASN cc_start: 0.7847 (m110) cc_final: 0.6989 (p0) REVERT: B 794 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7047 (pt) REVERT: C 156 ASP cc_start: 0.7947 (t0) cc_final: 0.7228 (t0) REVERT: C 215 ASP cc_start: 0.8332 (m-30) cc_final: 0.8030 (m-30) REVERT: C 366 LEU cc_start: 0.8956 (mt) cc_final: 0.8667 (mp) REVERT: C 477 SER cc_start: 0.8721 (m) cc_final: 0.8288 (t) REVERT: C 531 ASP cc_start: 0.7499 (m-30) cc_final: 0.7087 (m-30) REVERT: C 604 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8941 (mm) REVERT: C 685 MET cc_start: 0.8349 (ptp) cc_final: 0.7769 (mmt) REVERT: D 253 TYR cc_start: 0.7321 (m-10) cc_final: 0.6877 (m-10) REVERT: D 612 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8260 (mmtt) REVERT: D 702 TYR cc_start: 0.8079 (t80) cc_final: 0.7743 (t80) REVERT: D 791 ASN cc_start: 0.7943 (m110) cc_final: 0.7072 (p0) outliers start: 57 outliers final: 42 residues processed: 397 average time/residue: 0.2890 time to fit residues: 183.8557 Evaluate side-chains 397 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 350 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 748 PHE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 222 ASN Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 616 ARG 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 335 THR Chi-restraints excluded: chain D residue 383 ILE 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 575 LEU Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 725 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 2 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 176 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 112 optimal weight: 5.9990 chunk 213 optimal weight: 0.3980 chunk 184 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 243 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN D 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131681 restraints weight = 30014.854| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.19 r_work: 0.3287 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21270 Z= 0.125 Angle : 0.709 12.857 28800 Z= 0.356 Chirality : 0.042 0.205 3238 Planarity : 0.005 0.049 3584 Dihedral : 9.217 116.836 3076 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.62 % Favored : 90.06 % Rotamer: Outliers : 2.50 % Allowed : 19.75 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2526 helix: 0.05 (0.14), residues: 1458 sheet: -2.44 (0.53), residues: 106 loop : -2.44 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 733 HIS 0.003 0.000 HIS B 309 PHE 0.029 0.001 PHE C 485 TYR 0.023 0.001 TYR C 303 ARG 0.009 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 845) hydrogen bonds : angle 4.35813 ( 2445) covalent geometry : bond 0.00278 (21270) covalent geometry : angle 0.70880 (28800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9543.90 seconds wall clock time: 164 minutes 23.70 seconds (9863.70 seconds total)