Starting phenix.real_space_refine on Tue Jul 23 03:36:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/07_2024/8t1f_40962.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/07_2024/8t1f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/07_2024/8t1f_40962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/07_2024/8t1f_40962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/07_2024/8t1f_40962.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/07_2024/8t1f_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 Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 757": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 746": "NH1" <-> "NH2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "B ARG 779": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 616": "NH1" <-> "NH2" Residue "C ARG 661": "NH1" <-> "NH2" Residue "C ARG 746": "NH1" <-> "NH2" Residue "C ARG 757": "NH1" <-> "NH2" Residue "C ARG 779": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 616": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 746": "NH1" <-> "NH2" Residue "D ARG 757": "NH1" <-> "NH2" Residue "D ARG 779": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.24, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 8.15 Conformation dependent library (CDL) restraints added in 4.3 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: 1.87 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: 5.41 Time building geometry restraints manager: 8.89 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: 97.75 - 105.52: 423 105.52 - 113.29: 11247 113.29 - 121.06: 11233 121.06 - 128.83: 5710 128.83 - 136.60: 187 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: 12512 35.58 - 71.15: 170 71.15 - 106.73: 8 106.73 - 142.30: 4 142.30 - 177.88: 6 Dihedral angle restraints: 12700 sinusoidal: 5266 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 12697 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 2.440 nonbonded pdb=" O LEU D 686 " pdb=" OG1 THR D 689 " model vdw 2.263 2.440 nonbonded pdb=" O LEU B 686 " pdb=" OG1 THR B 689 " model vdw 2.264 2.440 nonbonded pdb=" O ARG A 206 " pdb=" OH TYR A 253 " model vdw 2.289 2.440 nonbonded pdb=" O ARG C 206 " pdb=" OH TYR C 253 " model vdw 2.290 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 148 through 802 or resid 1201 through 1202)) selection = chain 'C' selection = (chain 'D' and (resid 148 through 802 or resid 1201 through 1202)) } 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: 2.240 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.700 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.400 ------------------------------------------------------------------------------- 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= 0.392 Angle : 1.324 20.302 28800 Z= 0.755 Chirality : 0.058 0.362 3238 Planarity : 0.007 0.065 3584 Dihedral : 13.661 177.877 7912 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 *********************** 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 fitting. rotamer outliers: 19 poor density : 664 time to evaluate : 2.268 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: 0.3366 time to fit residues: 337.2130 Evaluate side-chains 410 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 408 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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: 0.6980 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 102 optimal weight: 0.0970 chunk 197 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 0.0970 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 338 ASN A 361 ASN A 474 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 541 ASN A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 784 ASN B 176 HIS B 204 ASN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS B 338 ASN B 361 ASN B 492 GLN B 550 GLN B 588 ASN B 789 ASN C 176 HIS C 201 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN C 265 HIS ** C 297 GLN ** 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 789 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21270 Z= 0.198 Angle : 0.763 11.452 28800 Z= 0.387 Chirality : 0.043 0.283 3238 Planarity : 0.006 0.051 3584 Dihedral : 12.377 172.601 3062 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.90 % Favored : 89.55 % Rotamer: Outliers : 2.64 % Allowed : 13.76 % Favored : 83.60 % 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: -3.78 (0.15), residues: 2526 helix: -2.19 (0.11), residues: 1440 sheet: -3.00 (0.47), residues: 116 loop : -2.74 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 733 HIS 0.008 0.001 HIS B 176 PHE 0.028 0.002 PHE D 666 TYR 0.019 0.001 TYR D 574 ARG 0.007 0.001 ARG B 510 *********************** 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 538 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 479 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8276 (m-30) cc_final: 0.8019 (m-30) REVERT: A 222 ASN cc_start: 0.7684 (m110) cc_final: 0.7387 (m110) REVERT: A 295 THR cc_start: 0.7859 (p) cc_final: 0.7654 (p) REVERT: A 477 SER cc_start: 0.8411 (m) cc_final: 0.8113 (t) REVERT: A 628 TYR cc_start: 0.7879 (m-80) cc_final: 0.7521 (m-80) REVERT: A 696 ILE cc_start: 0.8349 (tp) cc_final: 0.8108 (pt) REVERT: A 761 MET cc_start: 0.8235 (ttt) cc_final: 0.7969 (ttm) REVERT: B 253 TYR cc_start: 0.7450 (m-10) cc_final: 0.7230 (m-10) REVERT: B 291 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8950 (tp) REVERT: B 345 MET cc_start: 0.7846 (mmm) cc_final: 0.7498 (mmm) REVERT: B 614 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7678 (tm) REVERT: B 625 MET cc_start: 0.7689 (ttm) cc_final: 0.6692 (tmm) REVERT: B 791 ASN cc_start: 0.7843 (m110) cc_final: 0.6538 (p0) REVERT: C 156 ASP cc_start: 0.7979 (t0) cc_final: 0.7355 (t0) REVERT: C 179 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7939 (mmm-85) REVERT: C 303 TYR cc_start: 0.7577 (t80) cc_final: 0.7162 (t80) REVERT: C 345 MET cc_start: 0.9044 (mmm) cc_final: 0.8658 (mmm) REVERT: C 379 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8625 (ttmm) REVERT: C 523 LEU cc_start: 0.8464 (mp) cc_final: 0.7920 (tp) REVERT: C 530 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7905 (tttp) REVERT: C 543 LEU cc_start: 0.8495 (tt) cc_final: 0.8291 (mp) REVERT: C 572 GLU cc_start: 0.7822 (tp30) cc_final: 0.7613 (mt-10) REVERT: C 607 GLN cc_start: 0.7505 (mp10) cc_final: 0.7299 (mp10) REVERT: C 799 PRO cc_start: 0.8474 (Cg_endo) cc_final: 0.8262 (Cg_exo) REVERT: D 156 ASP cc_start: 0.8119 (t70) cc_final: 0.7823 (t0) REVERT: D 250 CYS cc_start: 0.7218 (t) cc_final: 0.6823 (t) REVERT: D 253 TYR cc_start: 0.7435 (m-10) cc_final: 0.7195 (m-10) REVERT: D 263 ASP cc_start: 0.6236 (t0) cc_final: 0.5758 (t0) REVERT: D 395 THR cc_start: 0.8348 (p) cc_final: 0.7995 (m) REVERT: D 612 LYS cc_start: 0.8455 (ttpm) cc_final: 0.8119 (mttt) REVERT: D 614 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7783 (tm) REVERT: D 747 SER cc_start: 0.9140 (m) cc_final: 0.8857 (t) outliers start: 59 outliers final: 27 residues processed: 515 average time/residue: 0.3151 time to fit residues: 248.7003 Evaluate side-chains 417 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 387 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 337 GLU 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 601 THR Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 150 ASN 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 127 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 0.0040 chunk 227 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 183 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 588 ASN B 201 ASN B 228 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN D 176 HIS D 297 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21270 Z= 0.172 Angle : 0.698 11.548 28800 Z= 0.351 Chirality : 0.042 0.244 3238 Planarity : 0.005 0.046 3584 Dihedral : 11.205 177.767 3060 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.70 % Favored : 89.90 % Rotamer: Outliers : 3.89 % Allowed : 15.24 % Favored : 80.88 % 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: -2.80 (0.16), residues: 2526 helix: -1.22 (0.13), residues: 1436 sheet: -2.47 (0.53), residues: 98 loop : -2.66 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 733 HIS 0.004 0.001 HIS D 265 PHE 0.033 0.001 PHE C 751 TYR 0.027 0.001 TYR D 574 ARG 0.005 0.001 ARG C 320 *********************** 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 526 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 439 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8320 (m-30) cc_final: 0.8084 (m-30) REVERT: A 222 ASN cc_start: 0.7633 (m110) cc_final: 0.7294 (m110) REVERT: A 477 SER cc_start: 0.8459 (m) cc_final: 0.8098 (t) REVERT: A 531 ASP cc_start: 0.8361 (m-30) cc_final: 0.7974 (m-30) REVERT: A 534 MET cc_start: 0.7981 (mmp) cc_final: 0.7236 (ptt) REVERT: A 588 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8144 (t0) REVERT: A 635 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7431 (tt) REVERT: A 761 MET cc_start: 0.8195 (ttt) cc_final: 0.7912 (ttm) REVERT: B 614 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7757 (tm) REVERT: B 730 LYS cc_start: 0.8336 (mttm) cc_final: 0.7999 (tttm) REVERT: B 791 ASN cc_start: 0.7774 (m110) cc_final: 0.6624 (p0) REVERT: B 794 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6749 (pt) REVERT: C 156 ASP cc_start: 0.7933 (t0) cc_final: 0.7270 (t0) REVERT: C 179 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.8011 (mmm-85) REVERT: C 287 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8412 (mp) REVERT: C 345 MET cc_start: 0.9152 (mmm) cc_final: 0.8776 (mmt) REVERT: C 411 TYR cc_start: 0.8565 (t80) cc_final: 0.8312 (t80) REVERT: C 523 LEU cc_start: 0.8521 (mp) cc_final: 0.7975 (tp) REVERT: C 567 TYR cc_start: 0.7987 (t80) cc_final: 0.7776 (t80) REVERT: C 588 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8501 (t160) REVERT: D 156 ASP cc_start: 0.8169 (t70) cc_final: 0.7862 (t0) REVERT: D 229 SER cc_start: 0.8957 (t) cc_final: 0.8679 (m) REVERT: D 250 CYS cc_start: 0.7112 (t) cc_final: 0.6825 (t) REVERT: D 253 TYR cc_start: 0.7378 (m-10) cc_final: 0.7115 (m-10) REVERT: D 395 THR cc_start: 0.8411 (p) cc_final: 0.8193 (m) REVERT: D 612 LYS cc_start: 0.8468 (ttpm) cc_final: 0.8069 (mttt) REVERT: D 614 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7753 (tm) REVERT: D 736 GLN cc_start: 0.8300 (mt0) cc_final: 0.7931 (mt0) outliers start: 87 outliers final: 41 residues processed: 491 average time/residue: 0.2925 time to fit residues: 229.4924 Evaluate side-chains 433 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 385 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 380 THR 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 588 ASN 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 635 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 213 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 614 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 264 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 705 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 218 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 588 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21270 Z= 0.224 Angle : 0.700 11.685 28800 Z= 0.351 Chirality : 0.042 0.252 3238 Planarity : 0.005 0.065 3584 Dihedral : 10.708 177.093 3060 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.10 % Favored : 89.51 % Rotamer: Outliers : 4.24 % Allowed : 15.95 % Favored : 79.80 % 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: -2.28 (0.16), residues: 2526 helix: -0.68 (0.13), residues: 1430 sheet: -2.40 (0.53), residues: 98 loop : -2.63 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 733 HIS 0.004 0.001 HIS D 326 PHE 0.025 0.001 PHE D 666 TYR 0.028 0.002 TYR D 574 ARG 0.006 0.000 ARG D 336 *********************** 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 501 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 406 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8282 (m-30) cc_final: 0.8053 (m-30) REVERT: A 222 ASN cc_start: 0.7645 (m110) cc_final: 0.7334 (m110) REVERT: A 477 SER cc_start: 0.8519 (m) cc_final: 0.8083 (t) REVERT: A 531 ASP cc_start: 0.8309 (m-30) cc_final: 0.7966 (m-30) REVERT: A 587 MET cc_start: 0.8244 (mtm) cc_final: 0.7706 (mmm) REVERT: A 635 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 761 MET cc_start: 0.8262 (ttt) cc_final: 0.7985 (ttm) REVERT: B 345 MET cc_start: 0.7992 (mmm) cc_final: 0.7534 (mmm) REVERT: B 612 LYS cc_start: 0.8387 (ttpm) cc_final: 0.8169 (mmtt) REVERT: B 614 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7764 (tm) REVERT: B 791 ASN cc_start: 0.7843 (m110) cc_final: 0.6721 (p0) REVERT: B 794 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.6931 (pt) REVERT: C 156 ASP cc_start: 0.7906 (t0) cc_final: 0.7226 (t0) REVERT: C 179 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.8019 (mmm-85) REVERT: C 287 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 303 TYR cc_start: 0.7614 (t80) cc_final: 0.7306 (t80) REVERT: C 477 SER cc_start: 0.8461 (m) cc_final: 0.7981 (t) REVERT: C 567 TYR cc_start: 0.7907 (t80) cc_final: 0.7397 (t80) REVERT: C 598 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8043 (tm) REVERT: C 604 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8391 (mm) REVERT: D 156 ASP cc_start: 0.8202 (t70) cc_final: 0.7933 (t0) REVERT: D 229 SER cc_start: 0.8988 (t) cc_final: 0.8702 (m) REVERT: D 395 THR cc_start: 0.8324 (p) cc_final: 0.8109 (m) REVERT: D 612 LYS cc_start: 0.8453 (ttpm) cc_final: 0.8042 (mttt) REVERT: D 614 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7797 (tm) REVERT: D 736 GLN cc_start: 0.8683 (mt0) cc_final: 0.8192 (mt0) outliers start: 95 outliers final: 50 residues processed: 463 average time/residue: 0.2871 time to fit residues: 213.1770 Evaluate side-chains 432 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 375 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 380 THR 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 605 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 635 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 717 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 207 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 124 optimal weight: 0.0980 chunk 218 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21270 Z= 0.259 Angle : 0.710 11.743 28800 Z= 0.356 Chirality : 0.043 0.242 3238 Planarity : 0.005 0.060 3584 Dihedral : 10.477 172.186 3060 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.49 % Favored : 89.11 % Rotamer: Outliers : 3.93 % Allowed : 16.98 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (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: -2.10 (0.16), residues: 2526 helix: -0.47 (0.13), residues: 1450 sheet: -2.16 (0.57), residues: 88 loop : -2.72 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 733 HIS 0.005 0.001 HIS D 326 PHE 0.038 0.002 PHE D 617 TYR 0.025 0.001 TYR D 574 ARG 0.004 0.000 ARG B 594 *********************** 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 484 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 396 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8302 (m-30) cc_final: 0.8081 (m-30) REVERT: A 222 ASN cc_start: 0.7639 (m110) cc_final: 0.7391 (m110) REVERT: A 531 ASP cc_start: 0.8319 (m-30) cc_final: 0.7639 (m-30) REVERT: A 534 MET cc_start: 0.7822 (mmp) cc_final: 0.7215 (ptt) REVERT: A 587 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7818 (mmm) REVERT: A 625 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6758 (tmm) REVERT: A 761 MET cc_start: 0.8265 (ttt) cc_final: 0.7991 (ttm) REVERT: B 612 LYS cc_start: 0.8419 (ttpm) cc_final: 0.8156 (mmtt) REVERT: B 614 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7754 (tm) REVERT: B 683 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5411 (tp) REVERT: B 791 ASN cc_start: 0.7878 (m110) cc_final: 0.6773 (p0) REVERT: B 794 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7016 (pt) REVERT: C 156 ASP cc_start: 0.7884 (t0) cc_final: 0.7209 (t0) REVERT: C 287 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8532 (mp) REVERT: C 303 TYR cc_start: 0.7612 (t80) cc_final: 0.7347 (t80) REVERT: C 477 SER cc_start: 0.8462 (m) cc_final: 0.7919 (t) REVERT: C 523 LEU cc_start: 0.8415 (mp) cc_final: 0.7700 (tp) REVERT: C 531 ASP cc_start: 0.8221 (m-30) cc_final: 0.7630 (m-30) REVERT: C 567 TYR cc_start: 0.7873 (t80) cc_final: 0.7436 (t80) REVERT: C 604 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8425 (mm) REVERT: C 684 GLU cc_start: 0.5970 (tm-30) cc_final: 0.5749 (tm-30) REVERT: D 156 ASP cc_start: 0.8216 (t70) cc_final: 0.7853 (t0) REVERT: D 229 SER cc_start: 0.9012 (t) cc_final: 0.8727 (m) REVERT: D 612 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7979 (mmtt) REVERT: D 614 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7804 (tm) REVERT: D 621 TYR cc_start: 0.8307 (t80) cc_final: 0.8059 (t80) REVERT: D 702 TYR cc_start: 0.7506 (t80) cc_final: 0.6931 (t80) outliers start: 88 outliers final: 53 residues processed: 451 average time/residue: 0.2926 time to fit residues: 210.9555 Evaluate side-chains 427 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 365 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 483 VAL 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 625 MET Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 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 717 LEU Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 150 ASN 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 258 VAL Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 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 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 81 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 243 optimal weight: 0.4980 chunk 202 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 0.0010 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21270 Z= 0.173 Angle : 0.674 11.932 28800 Z= 0.336 Chirality : 0.041 0.241 3238 Planarity : 0.004 0.061 3584 Dihedral : 10.193 164.997 3060 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.17 % Favored : 89.47 % Rotamer: Outliers : 3.57 % Allowed : 17.25 % Favored : 79.18 % 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: -0.18 (0.14), residues: 1446 sheet: -2.06 (0.59), residues: 88 loop : -2.59 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 733 HIS 0.002 0.000 HIS D 309 PHE 0.031 0.001 PHE D 617 TYR 0.022 0.001 TYR D 574 ARG 0.007 0.000 ARG D 336 *********************** 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 476 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 396 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8350 (tmmt) cc_final: 0.8119 (tmmt) REVERT: A 215 ASP cc_start: 0.8275 (m-30) cc_final: 0.8056 (m-30) REVERT: A 222 ASN cc_start: 0.7656 (m110) cc_final: 0.7384 (m110) REVERT: A 223 MET cc_start: 0.8766 (mmt) cc_final: 0.8385 (mmt) REVERT: A 260 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: A 477 SER cc_start: 0.8523 (m) cc_final: 0.8079 (t) REVERT: A 531 ASP cc_start: 0.8308 (m-30) cc_final: 0.7597 (m-30) REVERT: A 534 MET cc_start: 0.7624 (mmp) cc_final: 0.7215 (ptt) REVERT: A 587 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7760 (mmm) REVERT: A 604 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8653 (mm) REVERT: A 761 MET cc_start: 0.8221 (ttt) cc_final: 0.7964 (ttm) REVERT: B 612 LYS cc_start: 0.8423 (ttpm) cc_final: 0.8166 (mmtt) REVERT: B 614 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7605 (tm) REVERT: B 791 ASN cc_start: 0.7792 (m110) cc_final: 0.6754 (p0) REVERT: B 794 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7044 (pt) REVERT: C 156 ASP cc_start: 0.7883 (t0) cc_final: 0.7215 (t0) REVERT: C 195 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8468 (tt) REVERT: C 303 TYR cc_start: 0.7489 (t80) cc_final: 0.7283 (t80) REVERT: C 477 SER cc_start: 0.8493 (m) cc_final: 0.7975 (t) REVERT: C 531 ASP cc_start: 0.8116 (m-30) cc_final: 0.7494 (m-30) REVERT: C 567 TYR cc_start: 0.7725 (t80) cc_final: 0.7397 (t80) REVERT: C 588 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8204 (t0) REVERT: C 604 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8427 (mm) REVERT: C 684 GLU cc_start: 0.5950 (tm-30) cc_final: 0.5639 (tm-30) REVERT: D 156 ASP cc_start: 0.8177 (t70) cc_final: 0.7812 (t0) REVERT: D 229 SER cc_start: 0.8990 (t) cc_final: 0.8695 (m) REVERT: D 232 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7942 (ptt180) REVERT: D 612 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8005 (mmtt) REVERT: D 614 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7798 (tm) REVERT: D 702 TYR cc_start: 0.7481 (t80) cc_final: 0.7276 (t80) outliers start: 80 outliers final: 44 residues processed: 446 average time/residue: 0.2871 time to fit residues: 202.7858 Evaluate side-chains 419 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 364 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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 334 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 396 ASP 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 604 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 453 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 205 optimal weight: 0.0470 chunk 136 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 overall best weight: 0.9880 ------------------------------------------------------------------------------- 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS D 267 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21270 Z= 0.191 Angle : 0.690 12.305 28800 Z= 0.341 Chirality : 0.042 0.307 3238 Planarity : 0.004 0.059 3584 Dihedral : 9.936 160.969 3060 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.86 % Favored : 89.79 % Rotamer: Outliers : 3.49 % Allowed : 18.14 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.53 (0.17), residues: 2526 helix: 0.04 (0.14), residues: 1436 sheet: -2.01 (0.59), residues: 88 loop : -2.51 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 733 HIS 0.002 0.001 HIS D 326 PHE 0.026 0.001 PHE B 617 TYR 0.021 0.001 TYR D 574 ARG 0.013 0.000 ARG D 269 *********************** 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 458 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 380 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8273 (m-30) cc_final: 0.8059 (m-30) REVERT: A 222 ASN cc_start: 0.7657 (m110) cc_final: 0.7407 (m110) REVERT: A 260 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: A 477 SER cc_start: 0.8525 (m) cc_final: 0.8072 (t) REVERT: A 531 ASP cc_start: 0.8276 (m-30) cc_final: 0.7607 (m-30) REVERT: A 534 MET cc_start: 0.7571 (mmp) cc_final: 0.7200 (ptt) REVERT: A 587 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7720 (mmm) REVERT: A 588 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8065 (t0) REVERT: A 728 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 761 MET cc_start: 0.8226 (ttt) cc_final: 0.7974 (ttm) REVERT: B 204 ASN cc_start: 0.8339 (t0) cc_final: 0.8134 (t0) REVERT: B 612 LYS cc_start: 0.8450 (ttpm) cc_final: 0.8195 (mmtt) REVERT: B 614 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7563 (tm) REVERT: B 791 ASN cc_start: 0.7780 (m110) cc_final: 0.6763 (p0) REVERT: B 794 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7060 (pt) REVERT: C 156 ASP cc_start: 0.7890 (t0) cc_final: 0.7213 (t0) REVERT: C 195 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8476 (tt) REVERT: C 260 GLN cc_start: 0.8727 (mp10) cc_final: 0.8466 (mp10) REVERT: C 345 MET cc_start: 0.9040 (mmm) cc_final: 0.8713 (mmt) REVERT: C 444 GLU cc_start: 0.7562 (mp0) cc_final: 0.7345 (mp0) REVERT: C 477 SER cc_start: 0.8512 (m) cc_final: 0.8010 (t) REVERT: C 531 ASP cc_start: 0.8002 (m-30) cc_final: 0.7388 (m-30) REVERT: C 553 TYR cc_start: 0.8027 (m-80) cc_final: 0.7672 (m-80) REVERT: C 567 TYR cc_start: 0.7633 (t80) cc_final: 0.7366 (t80) REVERT: C 588 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8311 (t0) REVERT: C 604 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8439 (mm) REVERT: D 156 ASP cc_start: 0.8153 (t70) cc_final: 0.7796 (t0) REVERT: D 229 SER cc_start: 0.9014 (t) cc_final: 0.8717 (m) REVERT: D 232 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7929 (ptt180) REVERT: D 234 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8793 (mt) REVERT: D 269 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7373 (ptp-110) REVERT: D 612 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8019 (mmtt) REVERT: D 614 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7694 (tm) outliers start: 78 outliers final: 48 residues processed: 424 average time/residue: 0.2930 time to fit residues: 198.3575 Evaluate side-chains 421 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 361 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 380 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 698 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 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 614 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 222 ASN Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 150 ASN 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 442 LYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 0.0370 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 190 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21270 Z= 0.174 Angle : 0.694 12.878 28800 Z= 0.342 Chirality : 0.042 0.238 3238 Planarity : 0.004 0.059 3584 Dihedral : 9.752 153.314 3060 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.29 % Favored : 89.39 % Rotamer: Outliers : 3.57 % Allowed : 18.45 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.35 (0.17), residues: 2526 helix: 0.19 (0.14), residues: 1432 sheet: -1.99 (0.59), residues: 88 loop : -2.42 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 733 HIS 0.005 0.000 HIS C 252 PHE 0.022 0.001 PHE C 674 TYR 0.022 0.001 TYR D 628 ARG 0.011 0.000 ARG D 269 *********************** 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 478 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 398 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8370 (tmmt) cc_final: 0.8155 (tmmt) REVERT: A 215 ASP cc_start: 0.8261 (m-30) cc_final: 0.8040 (m-30) REVERT: A 222 ASN cc_start: 0.7745 (m110) cc_final: 0.7501 (m110) REVERT: A 233 ASP cc_start: 0.7942 (t0) cc_final: 0.7727 (t0) REVERT: A 260 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: A 477 SER cc_start: 0.8512 (m) cc_final: 0.8072 (t) REVERT: A 528 ASN cc_start: 0.7988 (t0) cc_final: 0.7777 (t0) REVERT: A 531 ASP cc_start: 0.8224 (m-30) cc_final: 0.7576 (m-30) REVERT: A 534 MET cc_start: 0.7668 (mmp) cc_final: 0.7334 (ptt) REVERT: A 587 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7640 (mmm) REVERT: A 669 PHE cc_start: 0.7310 (m-10) cc_final: 0.6979 (m-10) REVERT: A 685 MET cc_start: 0.6287 (mmt) cc_final: 0.6038 (ptp) REVERT: A 728 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8241 (tm-30) REVERT: A 761 MET cc_start: 0.8222 (ttt) cc_final: 0.7943 (ttm) REVERT: B 156 ASP cc_start: 0.8556 (t70) cc_final: 0.8169 (t0) REVERT: B 612 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8201 (mmtt) REVERT: B 614 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7521 (tm) REVERT: B 685 MET cc_start: 0.6333 (mpp) cc_final: 0.5881 (mmt) REVERT: B 791 ASN cc_start: 0.7746 (m110) cc_final: 0.6700 (p0) REVERT: B 794 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7086 (pt) REVERT: C 156 ASP cc_start: 0.7923 (t0) cc_final: 0.7223 (t0) REVERT: C 195 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8552 (tt) REVERT: C 260 GLN cc_start: 0.8774 (mp10) cc_final: 0.8398 (mp10) REVERT: C 345 MET cc_start: 0.9031 (mmm) cc_final: 0.8697 (mmt) REVERT: C 477 SER cc_start: 0.8505 (m) cc_final: 0.8008 (t) REVERT: C 531 ASP cc_start: 0.8013 (m-30) cc_final: 0.7403 (m-30) REVERT: C 567 TYR cc_start: 0.7546 (t80) cc_final: 0.7324 (t80) REVERT: C 588 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8326 (t0) REVERT: C 604 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8466 (mm) REVERT: D 156 ASP cc_start: 0.8164 (t70) cc_final: 0.7806 (t0) REVERT: D 229 SER cc_start: 0.8980 (t) cc_final: 0.8684 (m) REVERT: D 232 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7878 (ptt180) REVERT: D 234 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8781 (mt) REVERT: D 269 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7384 (ptp-110) REVERT: D 612 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8021 (mmtt) REVERT: D 614 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7645 (tm) outliers start: 80 outliers final: 51 residues processed: 442 average time/residue: 0.2845 time to fit residues: 199.6991 Evaluate side-chains 433 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 370 time to evaluate : 2.491 ------------------------------------------------------------------------------- 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 380 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 575 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 693 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 699 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 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 612 LYS 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 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 150 ASN 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 258 VAL Chi-restraints excluded: chain D residue 335 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.7980 chunk 212 optimal weight: 0.0980 chunk 226 optimal weight: 0.9980 chunk 136 optimal weight: 0.0770 chunk 98 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21270 Z= 0.171 Angle : 0.686 13.124 28800 Z= 0.341 Chirality : 0.041 0.228 3238 Planarity : 0.004 0.061 3584 Dihedral : 9.516 137.858 3060 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.98 % Favored : 89.75 % Rotamer: Outliers : 3.31 % Allowed : 19.12 % Favored : 77.57 % 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: -1.21 (0.17), residues: 2526 helix: 0.31 (0.14), residues: 1432 sheet: -1.97 (0.58), residues: 88 loop : -2.37 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 733 HIS 0.002 0.000 HIS D 309 PHE 0.021 0.001 PHE D 666 TYR 0.026 0.001 TYR D 253 ARG 0.010 0.000 ARG D 269 *********************** 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 460 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 386 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8385 (tmmt) cc_final: 0.8170 (tmmt) REVERT: A 215 ASP cc_start: 0.8311 (m-30) cc_final: 0.8071 (m-30) REVERT: A 222 ASN cc_start: 0.7687 (m110) cc_final: 0.7299 (m110) REVERT: A 260 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: A 345 MET cc_start: 0.8995 (tpp) cc_final: 0.8631 (mmt) REVERT: A 477 SER cc_start: 0.8490 (m) cc_final: 0.8078 (t) REVERT: A 523 LEU cc_start: 0.7787 (pp) cc_final: 0.7501 (tp) REVERT: A 531 ASP cc_start: 0.8206 (m-30) cc_final: 0.7544 (m-30) REVERT: A 534 MET cc_start: 0.7654 (mmp) cc_final: 0.7323 (ptt) REVERT: A 587 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7558 (mmm) REVERT: A 588 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8062 (t0) REVERT: A 669 PHE cc_start: 0.7425 (m-10) cc_final: 0.7077 (m-10) REVERT: A 685 MET cc_start: 0.6318 (mmt) cc_final: 0.6072 (ptp) REVERT: A 728 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 761 MET cc_start: 0.8231 (ttt) cc_final: 0.7947 (ttm) REVERT: B 156 ASP cc_start: 0.8553 (t70) cc_final: 0.8232 (t0) REVERT: B 551 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8358 (mt) REVERT: B 602 TYR cc_start: 0.8367 (t80) cc_final: 0.8109 (t80) REVERT: B 612 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8202 (mmtt) REVERT: B 614 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7538 (tm) REVERT: B 718 MET cc_start: 0.7388 (mmm) cc_final: 0.6904 (tpt) REVERT: B 761 MET cc_start: 0.8353 (mmt) cc_final: 0.8117 (mmm) REVERT: B 791 ASN cc_start: 0.7703 (m110) cc_final: 0.6709 (p0) REVERT: B 794 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7081 (pt) REVERT: C 156 ASP cc_start: 0.7915 (t0) cc_final: 0.7207 (t0) REVERT: C 219 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8573 (mmt90) REVERT: C 260 GLN cc_start: 0.8718 (mp10) cc_final: 0.8312 (mp10) REVERT: C 345 MET cc_start: 0.8999 (mmm) cc_final: 0.8671 (mmt) REVERT: C 477 SER cc_start: 0.8566 (m) cc_final: 0.8044 (t) REVERT: C 531 ASP cc_start: 0.7935 (m-30) cc_final: 0.7347 (m-30) REVERT: C 588 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8374 (t0) REVERT: D 156 ASP cc_start: 0.8163 (t70) cc_final: 0.7801 (t0) REVERT: D 229 SER cc_start: 0.8945 (t) cc_final: 0.8663 (m) REVERT: D 234 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8769 (mt) REVERT: D 612 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8021 (mmtt) REVERT: D 614 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7667 (tm) REVERT: D 625 MET cc_start: 0.6714 (mmp) cc_final: 0.5356 (tmm) outliers start: 74 outliers final: 47 residues processed: 422 average time/residue: 0.2877 time to fit residues: 193.7118 Evaluate side-chains 432 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 374 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 575 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 635 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 264 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 453 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 158 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21270 Z= 0.206 Angle : 0.708 12.776 28800 Z= 0.353 Chirality : 0.042 0.234 3238 Planarity : 0.004 0.059 3584 Dihedral : 9.401 127.800 3058 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.45 % Favored : 89.23 % Rotamer: Outliers : 2.77 % Allowed : 20.06 % Favored : 77.17 % 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: -1.20 (0.17), residues: 2526 helix: 0.34 (0.14), residues: 1434 sheet: -1.95 (0.57), residues: 88 loop : -2.39 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 733 HIS 0.005 0.001 HIS D 252 PHE 0.029 0.001 PHE C 669 TYR 0.027 0.001 TYR D 253 ARG 0.009 0.000 ARG D 269 ********************** 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 442 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 380 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8427 (tmmt) cc_final: 0.8207 (tmmt) REVERT: A 215 ASP cc_start: 0.8326 (m-30) cc_final: 0.8091 (m-30) REVERT: A 222 ASN cc_start: 0.7618 (m110) cc_final: 0.7367 (m110) REVERT: A 260 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: A 455 ILE cc_start: 0.8317 (mm) cc_final: 0.7410 (mt) REVERT: A 523 LEU cc_start: 0.7764 (pp) cc_final: 0.7522 (tp) REVERT: A 531 ASP cc_start: 0.8135 (m-30) cc_final: 0.7512 (m-30) REVERT: A 534 MET cc_start: 0.7653 (mmp) cc_final: 0.7338 (ptt) REVERT: A 553 TYR cc_start: 0.7663 (m-80) cc_final: 0.7284 (m-80) REVERT: A 587 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7637 (mmm) REVERT: A 604 ILE cc_start: 0.8890 (mm) cc_final: 0.8659 (mm) REVERT: A 669 PHE cc_start: 0.7414 (m-10) cc_final: 0.7073 (m-10) REVERT: A 685 MET cc_start: 0.6411 (mmt) cc_final: 0.6154 (ptp) REVERT: A 728 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8283 (tm-30) REVERT: A 761 MET cc_start: 0.8222 (ttt) cc_final: 0.7958 (ttm) REVERT: B 156 ASP cc_start: 0.8580 (t70) cc_final: 0.8250 (t0) REVERT: B 551 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8378 (mt) REVERT: B 602 TYR cc_start: 0.8380 (t80) cc_final: 0.8147 (t80) REVERT: B 612 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8210 (mmtt) REVERT: B 614 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7602 (tm) REVERT: B 718 MET cc_start: 0.7397 (mmm) cc_final: 0.6882 (tpt) REVERT: B 761 MET cc_start: 0.8311 (mmt) cc_final: 0.8089 (mmm) REVERT: B 791 ASN cc_start: 0.7721 (m110) cc_final: 0.6668 (p0) REVERT: B 794 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7046 (pt) REVERT: C 156 ASP cc_start: 0.7918 (t0) cc_final: 0.7214 (t0) REVERT: C 215 ASP cc_start: 0.8761 (m-30) cc_final: 0.8441 (m-30) REVERT: C 219 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8585 (mmt90) REVERT: C 260 GLN cc_start: 0.8758 (mp10) cc_final: 0.8386 (mp10) REVERT: C 345 MET cc_start: 0.9039 (mmm) cc_final: 0.8717 (mmt) REVERT: C 477 SER cc_start: 0.8486 (m) cc_final: 0.7955 (t) REVERT: C 531 ASP cc_start: 0.7955 (m-30) cc_final: 0.7355 (m-30) REVERT: C 588 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8326 (t0) REVERT: C 604 ILE cc_start: 0.8757 (mm) cc_final: 0.8483 (mm) REVERT: D 156 ASP cc_start: 0.8182 (t70) cc_final: 0.7832 (t0) REVERT: D 229 SER cc_start: 0.8971 (t) cc_final: 0.8687 (m) REVERT: D 234 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8776 (mt) REVERT: D 612 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8062 (mmtt) REVERT: D 614 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7683 (tm) REVERT: D 625 MET cc_start: 0.6739 (mmp) cc_final: 0.5392 (tmm) outliers start: 62 outliers final: 42 residues processed: 417 average time/residue: 0.2777 time to fit residues: 185.8457 Evaluate side-chains 423 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 371 time to evaluate : 2.055 ------------------------------------------------------------------------------- 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 693 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 639 CYS 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 337 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 258 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 29 optimal weight: 0.0470 chunk 55 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3925 r_free = 0.3925 target = 0.165516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131774 restraints weight = 29815.742| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.22 r_work: 0.3265 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21270 Z= 0.172 Angle : 0.694 12.773 28800 Z= 0.346 Chirality : 0.042 0.231 3238 Planarity : 0.004 0.061 3584 Dihedral : 9.270 121.362 3058 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.17 % Favored : 89.55 % Rotamer: Outliers : 2.41 % Allowed : 20.38 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (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: -1.14 (0.17), residues: 2526 helix: 0.41 (0.14), residues: 1432 sheet: -2.38 (0.52), residues: 106 loop : -2.33 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 733 HIS 0.003 0.000 HIS D 252 PHE 0.026 0.001 PHE C 669 TYR 0.025 0.001 TYR D 253 ARG 0.009 0.000 ARG B 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4867.29 seconds wall clock time: 87 minutes 10.60 seconds (5230.60 seconds total)