Starting phenix.real_space_refine on Wed Apr 10 22:54:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/04_2024/8t1f_40962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/04_2024/8t1f_40962.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/04_2024/8t1f_40962_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/04_2024/8t1f_40962_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/04_2024/8t1f_40962_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/04_2024/8t1f_40962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/04_2024/8t1f_40962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/04_2024/8t1f_40962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/04_2024/8t1f_40962_updated.pdb" } 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-5288/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: 10.64, per 1000 atoms: 0.51 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: 8.40 Conformation dependent library (CDL) restraints added in 3.7 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... running ksdssp... Secondary structure from input PDB file: 118 helices and 4 sheets defined 50.7% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.568A pdb=" N SER A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 removed outlier: 4.135A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 210 through 220 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 242 through 247 Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.702A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.804A pdb=" N LEU A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 355 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 373 through 379 removed outlier: 3.608A pdb=" N ALA A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.838A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 466 through 490 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 508 through 532 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 548 through 569 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 572 through 585 removed outlier: 3.813A pdb=" N LEU A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 579 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 582 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 583 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 585 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 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 600 through 612 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 618 through 625 removed outlier: 3.855A pdb=" N PHE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 666 through 678 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 692 through 719 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) Processing helix chain 'A' and resid 726 through 745 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) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'B' and resid 151 through 159 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 169 through 175 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 251 through 259 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 288 through 294 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 338 through 356 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 375 through 379 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 446 through 449 No H-bonds generated for 'chain 'B' and resid 446 through 449' Processing helix chain 'B' and resid 453 through 465 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) Processing helix chain 'B' and resid 467 through 481 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) removed outlier: 3.981A pdb=" N CYS B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 Processing helix chain 'B' and resid 505 through 534 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 548 through 567 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 573 through 593 removed outlier: 3.582A pdb=" N ALA B 576 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL B 577 " --> pdb=" O TYR B 574 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 582 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 583 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 585 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP B 586 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 588 " --> pdb=" O GLY B 585 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 589 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 591 " --> pdb=" O ASN B 588 " (cutoff:3.500A) 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 597 through 611 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 615 through 624 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 628 through 632 Processing helix chain 'B' and resid 666 through 677 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) Processing helix chain 'B' and resid 692 through 720 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 725 through 747 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) Processing helix chain 'B' and resid 750 through 753 No H-bonds generated for 'chain 'B' and resid 750 through 753' Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.569A pdb=" N SER C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 4.135A pdb=" N LEU C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 210 through 220 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 242 through 247 Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.702A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.805A pdb=" N LEU C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 355 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 373 through 379 removed outlier: 3.609A pdb=" N ALA C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 removed outlier: 3.837A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 399 No H-bonds generated for 'chain 'C' and resid 397 through 399' Processing helix chain 'C' and resid 433 through 439 Processing helix chain 'C' and resid 446 through 449 No H-bonds generated for 'chain 'C' and resid 446 through 449' Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 466 through 490 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 508 through 532 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 548 through 569 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 572 through 585 removed outlier: 3.814A pdb=" N LEU C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 579 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 582 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 583 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 584 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY C 585 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 593 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 600 through 612 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 618 through 625 removed outlier: 3.855A pdb=" N PHE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 666 through 678 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 692 through 719 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) Processing helix chain 'C' and resid 726 through 745 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) Processing helix chain 'C' and resid 750 through 755 Processing helix chain 'D' and resid 151 through 159 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 169 through 175 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 241 through 247 Processing helix chain 'D' and resid 251 through 259 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 288 through 294 Processing helix chain 'D' and resid 298 through 304 Processing helix chain 'D' and resid 326 through 330 Processing helix chain 'D' and resid 338 through 356 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 375 through 379 Processing helix chain 'D' and resid 385 through 390 Processing helix chain 'D' and resid 400 through 402 No H-bonds generated for 'chain 'D' and resid 400 through 402' Processing helix chain 'D' and resid 433 through 439 Processing helix chain 'D' and resid 446 through 449 No H-bonds generated for 'chain 'D' and resid 446 through 449' Processing helix chain 'D' and resid 453 through 465 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) Processing helix chain 'D' and resid 467 through 481 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) removed outlier: 3.981A pdb=" N CYS D 480 " --> pdb=" O VAL D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 490 Processing helix chain 'D' and resid 505 through 534 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 548 through 567 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 573 through 593 removed outlier: 3.582A pdb=" N ALA D 576 " --> pdb=" O ALA D 573 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL D 577 " --> pdb=" O TYR D 574 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET D 578 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 582 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 583 " --> pdb=" O PHE D 580 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY D 585 " --> pdb=" O LEU D 582 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TRP D 586 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN D 588 " --> pdb=" O GLY D 585 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA D 589 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 591 " --> pdb=" O ASN D 588 " (cutoff:3.500A) 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 597 through 611 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 615 through 624 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 628 through 632 Processing helix chain 'D' and resid 666 through 677 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) Processing helix chain 'D' and resid 692 through 720 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 725 through 747 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) Processing helix chain 'D' and resid 750 through 753 No H-bonds generated for 'chain 'D' and resid 750 through 753' Processing sheet with id= A, first strand: chain 'A' and resid 405 through 407 Processing sheet with id= B, first strand: chain 'B' and resid 778 through 782 removed outlier: 3.790A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 405 through 407 Processing sheet with id= D, first strand: chain 'D' and resid 778 through 782 removed outlier: 3.791A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1917 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: 5.91 Time building geometry restraints manager: 9.02 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=" C4 X7N A1201 " pdb=" N5 X7N A1201 " ideal model delta sigma weight residual 1.456 1.367 0.089 2.00e-02 2.50e+03 1.97e+01 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=" C4 X7N C1201 " pdb=" N5 X7N C1201 " ideal model delta sigma weight residual 1.456 1.369 0.087 2.00e-02 2.50e+03 1.90e+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 ... (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: 12450 35.58 - 71.15: 171 71.15 - 106.73: 12 106.73 - 142.30: 9 142.30 - 177.88: 6 Dihedral angle restraints: 12648 sinusoidal: 5214 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 12645 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: 1138 2.72 - 3.26: 20341 3.26 - 3.81: 33221 3.81 - 4.35: 42696 4.35 - 4.90: 70195 Nonbonded interactions: 167591 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 167586 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.080 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 55.410 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.350 ------------------------------------------------------------------------------- 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 : 0.007 0.089 21270 Z= 0.431 Angle : 1.372 20.302 28800 Z= 0.765 Chirality : 0.058 0.362 3238 Planarity : 0.007 0.065 3584 Dihedral : 14.138 177.877 7860 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 : 2.372 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: 0.3550 time to fit residues: 355.4913 Evaluate side-chains 410 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 408 time to evaluate : 2.391 ------------------------------------------------------------------------------- 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: 0.7980 chunk 191 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 0.0970 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 228 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 252 HIS ** 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21270 Z= 0.262 Angle : 0.795 11.303 28800 Z= 0.396 Chirality : 0.044 0.234 3238 Planarity : 0.005 0.050 3584 Dihedral : 13.498 170.102 3010 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.53 % Favored : 88.92 % Rotamer: Outliers : 2.77 % Allowed : 13.90 % Favored : 83.33 % 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: -3.86 (0.14), residues: 2526 helix: -2.28 (0.11), residues: 1410 sheet: -3.04 (0.47), residues: 116 loop : -2.73 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 733 HIS 0.006 0.001 HIS B 176 PHE 0.025 0.002 PHE D 617 TYR 0.021 0.002 TYR D 574 ARG 0.007 0.001 ARG C 269 *********************** 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 522 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 460 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8227 (m-30) cc_final: 0.7978 (m-30) REVERT: A 222 ASN cc_start: 0.7833 (m110) cc_final: 0.7535 (m-40) REVERT: A 477 SER cc_start: 0.8492 (m) cc_final: 0.8099 (t) REVERT: A 530 LYS cc_start: 0.8430 (mtpt) cc_final: 0.7996 (tttp) REVERT: A 534 MET cc_start: 0.8202 (mpm) cc_final: 0.7865 (mpm) REVERT: A 575 LEU cc_start: 0.8731 (pp) cc_final: 0.8269 (pt) REVERT: A 628 TYR cc_start: 0.8101 (m-80) cc_final: 0.7641 (m-80) REVERT: A 696 ILE cc_start: 0.8406 (tp) cc_final: 0.8154 (pt) REVERT: A 761 MET cc_start: 0.8279 (ttt) cc_final: 0.8016 (ttm) REVERT: A 773 ASP cc_start: 0.8463 (t0) cc_final: 0.8248 (t0) REVERT: B 253 TYR cc_start: 0.7726 (m-10) cc_final: 0.7506 (m-10) REVERT: B 291 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8990 (tp) REVERT: B 345 MET cc_start: 0.8039 (mmm) cc_final: 0.7736 (mmm) REVERT: B 473 ILE cc_start: 0.8463 (mm) cc_final: 0.8261 (mt) REVERT: B 614 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7697 (tm) REVERT: B 791 ASN cc_start: 0.7910 (m110) cc_final: 0.6610 (p0) REVERT: C 156 ASP cc_start: 0.8041 (t0) cc_final: 0.7417 (t0) REVERT: C 179 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.8007 (mmm-85) REVERT: C 287 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8478 (mp) REVERT: C 303 TYR cc_start: 0.7598 (t80) cc_final: 0.7271 (t80) REVERT: C 379 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8710 (ttmm) REVERT: C 477 SER cc_start: 0.8329 (m) cc_final: 0.7915 (t) REVERT: C 523 LEU cc_start: 0.8521 (mp) cc_final: 0.7967 (tp) REVERT: C 543 LEU cc_start: 0.8615 (tt) cc_final: 0.8328 (mp) REVERT: C 572 GLU cc_start: 0.7839 (tp30) cc_final: 0.7487 (mt-10) REVERT: C 703 ILE cc_start: 0.8819 (mm) cc_final: 0.8601 (pt) REVERT: C 799 PRO cc_start: 0.8549 (Cg_endo) cc_final: 0.8333 (Cg_exo) REVERT: D 156 ASP cc_start: 0.8279 (t70) cc_final: 0.7917 (t0) REVERT: D 253 TYR cc_start: 0.7655 (m-10) cc_final: 0.7418 (m-10) REVERT: D 263 ASP cc_start: 0.6810 (t0) cc_final: 0.6324 (t0) REVERT: D 473 ILE cc_start: 0.8528 (mm) cc_final: 0.8295 (mt) REVERT: D 607 GLN cc_start: 0.7728 (mt0) cc_final: 0.7401 (mm110) REVERT: D 612 LYS cc_start: 0.8432 (ttpm) cc_final: 0.8085 (mttt) REVERT: D 614 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7774 (tm) REVERT: D 730 LYS cc_start: 0.8485 (ptmm) cc_final: 0.8265 (pttm) REVERT: D 747 SER cc_start: 0.9141 (m) cc_final: 0.8849 (t) REVERT: D 791 ASN cc_start: 0.7908 (m110) cc_final: 0.7143 (p0) outliers start: 62 outliers final: 33 residues processed: 495 average time/residue: 0.3212 time to fit residues: 246.4832 Evaluate side-chains 426 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 389 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 483 VAL 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 704 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 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 636 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 337 GLU 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 C residue 694 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 442 LYS 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 Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 746 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.0060 chunk 71 optimal weight: 0.3980 chunk 190 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 0.0020 chunk 227 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 overall best weight: 0.4004 ------------------------------------------------------------------------------- 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 228 ASN B 252 HIS B 338 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN D 176 HIS D 204 ASN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21270 Z= 0.157 Angle : 0.697 11.792 28800 Z= 0.345 Chirality : 0.041 0.235 3238 Planarity : 0.004 0.047 3584 Dihedral : 12.541 171.803 3008 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.66 % Favored : 89.87 % Rotamer: Outliers : 3.84 % Allowed : 15.28 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.15), residues: 2526 helix: -1.34 (0.13), residues: 1412 sheet: -2.49 (0.54), residues: 98 loop : -2.65 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 733 HIS 0.003 0.001 HIS D 265 PHE 0.024 0.001 PHE D 666 TYR 0.026 0.001 TYR D 574 ARG 0.004 0.000 ARG B 271 *********************** 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 531 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 445 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8233 (m-30) cc_final: 0.8032 (m-30) REVERT: A 222 ASN cc_start: 0.7783 (m110) cc_final: 0.7394 (m110) REVERT: A 477 SER cc_start: 0.8471 (m) cc_final: 0.8060 (t) REVERT: A 530 LYS cc_start: 0.8395 (mtpt) cc_final: 0.7970 (tttp) REVERT: A 534 MET cc_start: 0.8101 (mpm) cc_final: 0.7737 (mpm) REVERT: A 635 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7423 (tt) REVERT: A 696 ILE cc_start: 0.8389 (tp) cc_final: 0.8174 (pt) REVERT: A 761 MET cc_start: 0.8206 (ttt) cc_final: 0.7919 (ttm) REVERT: A 773 ASP cc_start: 0.8481 (t0) cc_final: 0.8240 (t0) REVERT: B 237 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7891 (ttp-110) REVERT: B 252 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7392 (p90) REVERT: B 291 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 414 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8277 (m) REVERT: B 551 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8376 (mt) REVERT: B 614 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7735 (tm) REVERT: B 625 MET cc_start: 0.7512 (ttm) cc_final: 0.6717 (tmm) REVERT: B 691 TYR cc_start: 0.7472 (m-80) cc_final: 0.7238 (m-80) REVERT: B 736 GLN cc_start: 0.8240 (mt0) cc_final: 0.7840 (mt0) REVERT: B 761 MET cc_start: 0.8109 (tpp) cc_final: 0.7890 (mmt) REVERT: B 791 ASN cc_start: 0.7856 (m110) cc_final: 0.6680 (p0) REVERT: B 794 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7068 (pt) REVERT: C 156 ASP cc_start: 0.8019 (t0) cc_final: 0.7431 (t0) REVERT: C 179 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7849 (mmm-85) REVERT: C 411 TYR cc_start: 0.8540 (t80) cc_final: 0.8287 (t80) REVERT: C 523 LEU cc_start: 0.8499 (mp) cc_final: 0.8117 (tp) REVERT: C 567 TYR cc_start: 0.8079 (t80) cc_final: 0.7776 (t80) REVERT: C 572 GLU cc_start: 0.7932 (tp30) cc_final: 0.7631 (mt-10) REVERT: C 607 GLN cc_start: 0.7720 (mp10) cc_final: 0.7394 (mm-40) REVERT: C 703 ILE cc_start: 0.8825 (mm) cc_final: 0.8501 (pt) REVERT: C 799 PRO cc_start: 0.8552 (Cg_endo) cc_final: 0.8341 (Cg_exo) REVERT: D 156 ASP cc_start: 0.8275 (t70) cc_final: 0.7895 (t0) REVERT: D 229 SER cc_start: 0.8956 (t) cc_final: 0.8671 (m) REVERT: D 395 THR cc_start: 0.8349 (p) cc_final: 0.8045 (m) REVERT: D 607 GLN cc_start: 0.7779 (mt0) cc_final: 0.7382 (mm110) REVERT: D 612 LYS cc_start: 0.8447 (ttpm) cc_final: 0.8206 (mmtt) REVERT: D 614 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7735 (tm) REVERT: D 730 LYS cc_start: 0.8414 (ptmm) cc_final: 0.8194 (pttm) REVERT: D 747 SER cc_start: 0.9079 (m) cc_final: 0.8851 (t) REVERT: D 791 ASN cc_start: 0.7793 (m110) cc_final: 0.6949 (p0) outliers start: 86 outliers final: 34 residues processed: 498 average time/residue: 0.3004 time to fit residues: 235.7258 Evaluate side-chains 423 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 381 time to evaluate : 2.335 ------------------------------------------------------------------------------- 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 551 LEU Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 414 VAL 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 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 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 693 VAL Chi-restraints excluded: chain C residue 721 THR 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 551 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 717 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 243 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 218 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 252 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 297 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21270 Z= 0.170 Angle : 0.687 13.575 28800 Z= 0.339 Chirality : 0.041 0.239 3238 Planarity : 0.004 0.046 3584 Dihedral : 12.015 174.698 3008 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.90 % Favored : 89.71 % Rotamer: Outliers : 4.07 % Allowed : 15.86 % Favored : 80.07 % 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: -2.40 (0.16), residues: 2526 helix: -0.83 (0.13), residues: 1426 sheet: -2.32 (0.55), residues: 98 loop : -2.57 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 733 HIS 0.015 0.001 HIS B 252 PHE 0.023 0.001 PHE D 666 TYR 0.028 0.001 TYR D 574 ARG 0.005 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 512 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 421 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 SER cc_start: 0.7254 (m) cc_final: 0.6899 (p) REVERT: A 215 ASP cc_start: 0.8243 (m-30) cc_final: 0.8031 (m-30) REVERT: A 222 ASN cc_start: 0.7799 (m110) cc_final: 0.7450 (m110) REVERT: A 223 MET cc_start: 0.8721 (mmt) cc_final: 0.8496 (mmp) REVERT: A 444 GLU cc_start: 0.7680 (mp0) cc_final: 0.7458 (mp0) REVERT: A 477 SER cc_start: 0.8490 (m) cc_final: 0.8070 (t) REVERT: A 530 LYS cc_start: 0.8353 (mtpt) cc_final: 0.7980 (tttp) REVERT: A 534 MET cc_start: 0.8074 (mpm) cc_final: 0.7738 (mpm) REVERT: A 635 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7423 (tt) REVERT: A 761 MET cc_start: 0.8199 (ttt) cc_final: 0.7891 (ttm) REVERT: A 773 ASP cc_start: 0.8502 (t0) cc_final: 0.8238 (t0) REVERT: B 237 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7953 (ttp-110) REVERT: B 291 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9010 (tp) REVERT: B 551 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8411 (mt) REVERT: B 614 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7657 (tm) REVERT: B 625 MET cc_start: 0.7341 (ttm) cc_final: 0.6581 (tmm) REVERT: B 791 ASN cc_start: 0.7802 (m110) cc_final: 0.6694 (p0) REVERT: B 794 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7126 (pt) REVERT: C 156 ASP cc_start: 0.8033 (t0) cc_final: 0.7430 (t0) REVERT: C 179 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7864 (mmm-85) REVERT: C 287 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 411 TYR cc_start: 0.8541 (t80) cc_final: 0.8332 (t80) REVERT: C 477 SER cc_start: 0.8359 (m) cc_final: 0.7935 (t) REVERT: C 607 GLN cc_start: 0.7730 (mp10) cc_final: 0.7424 (mm-40) REVERT: C 703 ILE cc_start: 0.8828 (mm) cc_final: 0.8476 (pt) REVERT: C 773 ASP cc_start: 0.8457 (t0) cc_final: 0.8232 (t0) REVERT: D 156 ASP cc_start: 0.8304 (t70) cc_final: 0.7907 (t0) REVERT: D 229 SER cc_start: 0.8908 (t) cc_final: 0.8621 (m) REVERT: D 395 THR cc_start: 0.8378 (p) cc_final: 0.8144 (m) REVERT: D 602 TYR cc_start: 0.8168 (t80) cc_final: 0.7826 (t80) REVERT: D 607 GLN cc_start: 0.7804 (mt0) cc_final: 0.7386 (mm110) REVERT: D 612 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8014 (mmtt) REVERT: D 614 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7714 (tm) REVERT: D 730 LYS cc_start: 0.8387 (ptmm) cc_final: 0.8182 (pttm) REVERT: D 791 ASN cc_start: 0.7822 (m110) cc_final: 0.6968 (p0) outliers start: 91 outliers final: 48 residues processed: 469 average time/residue: 0.3057 time to fit residues: 227.4496 Evaluate side-chains 425 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 369 time to evaluate : 2.528 ------------------------------------------------------------------------------- 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 366 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 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 635 LEU Chi-restraints excluded: chain A residue 693 VAL 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 291 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 575 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 ASP 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 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 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 335 THR Chi-restraints excluded: chain D residue 351 LEU 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 579 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 674 PHE 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: 3.9990 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 588 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 21270 Z= 0.209 Angle : 0.691 12.548 28800 Z= 0.342 Chirality : 0.042 0.255 3238 Planarity : 0.004 0.056 3584 Dihedral : 11.779 177.497 3008 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.37 % Favored : 89.23 % Rotamer: Outliers : 3.62 % Allowed : 16.76 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2526 helix: -0.53 (0.14), residues: 1418 sheet: -2.42 (0.52), residues: 98 loop : -2.55 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 733 HIS 0.005 0.001 HIS D 252 PHE 0.025 0.001 PHE B 617 TYR 0.031 0.001 TYR C 574 ARG 0.007 0.000 ARG C 237 *********************** 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 468 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 387 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7796 (m110) cc_final: 0.7546 (m110) REVERT: A 295 THR cc_start: 0.8252 (p) cc_final: 0.7552 (t) REVERT: A 530 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7949 (tttp) REVERT: A 534 MET cc_start: 0.8114 (mpm) cc_final: 0.7732 (mpm) REVERT: A 587 MET cc_start: 0.8045 (mtm) cc_final: 0.7698 (mmm) REVERT: A 628 TYR cc_start: 0.8026 (m-80) cc_final: 0.7654 (m-80) REVERT: A 761 MET cc_start: 0.8243 (ttt) cc_final: 0.7928 (ttm) REVERT: A 773 ASP cc_start: 0.8549 (t0) cc_final: 0.8277 (t0) REVERT: B 204 ASN cc_start: 0.8314 (t0) cc_final: 0.8031 (t0) REVERT: B 237 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8048 (ttp-110) REVERT: B 291 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9064 (tp) REVERT: B 551 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8379 (mt) REVERT: B 614 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7669 (tm) REVERT: B 625 MET cc_start: 0.7244 (ttm) cc_final: 0.6468 (tmm) REVERT: B 683 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.5403 (tp) REVERT: B 791 ASN cc_start: 0.7823 (m110) cc_final: 0.6716 (p0) REVERT: B 794 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7229 (pt) REVERT: C 156 ASP cc_start: 0.7993 (t0) cc_final: 0.7389 (t0) REVERT: C 260 GLN cc_start: 0.8759 (mp10) cc_final: 0.8506 (mp10) REVERT: C 287 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8563 (mp) REVERT: C 477 SER cc_start: 0.8425 (m) cc_final: 0.7963 (t) REVERT: C 523 LEU cc_start: 0.8531 (mp) cc_final: 0.7864 (tp) REVERT: C 567 TYR cc_start: 0.8385 (t80) cc_final: 0.7938 (t80) REVERT: C 607 GLN cc_start: 0.7801 (mp10) cc_final: 0.7502 (mm-40) REVERT: C 773 ASP cc_start: 0.8421 (t0) cc_final: 0.8194 (t0) REVERT: D 156 ASP cc_start: 0.8341 (t70) cc_final: 0.7889 (t0) REVERT: D 229 SER cc_start: 0.8903 (t) cc_final: 0.8641 (m) REVERT: D 232 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7992 (ptt180) REVERT: D 247 GLU cc_start: 0.8243 (tp30) cc_final: 0.7855 (tp30) REVERT: D 253 TYR cc_start: 0.7460 (m-10) cc_final: 0.7190 (m-10) REVERT: D 607 GLN cc_start: 0.7831 (mt0) cc_final: 0.7376 (mm110) REVERT: D 612 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8102 (mmtt) REVERT: D 614 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7794 (tm) REVERT: D 636 LEU cc_start: 0.7419 (mm) cc_final: 0.7197 (pp) REVERT: D 730 LYS cc_start: 0.8403 (ptmm) cc_final: 0.8189 (pttm) REVERT: D 761 MET cc_start: 0.8101 (tpp) cc_final: 0.7881 (mmt) REVERT: D 791 ASN cc_start: 0.8001 (m110) cc_final: 0.7093 (p0) outliers start: 81 outliers final: 50 residues processed: 439 average time/residue: 0.3142 time to fit residues: 217.1828 Evaluate side-chains 415 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 356 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 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 B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 291 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 626 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 639 CYS Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 ASP 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 365 VAL 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 598 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 579 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: 0.9990 chunk 219 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 0.0370 chunk 243 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 128 optimal weight: 0.5980 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 588 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21270 Z= 0.159 Angle : 0.662 11.632 28800 Z= 0.327 Chirality : 0.041 0.235 3238 Planarity : 0.004 0.046 3584 Dihedral : 11.458 176.271 3008 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.90 % Favored : 89.75 % Rotamer: Outliers : 3.80 % Allowed : 16.98 % Favored : 79.22 % 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: -1.92 (0.16), residues: 2526 helix: -0.38 (0.14), residues: 1444 sheet: -2.47 (0.51), residues: 102 loop : -2.48 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 733 HIS 0.003 0.000 HIS B 309 PHE 0.028 0.001 PHE D 617 TYR 0.025 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 484 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 399 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7680 (m110) cc_final: 0.7420 (m110) REVERT: A 295 THR cc_start: 0.8120 (p) cc_final: 0.7478 (t) REVERT: A 444 GLU cc_start: 0.7708 (mp0) cc_final: 0.7427 (mp0) REVERT: A 477 SER cc_start: 0.8501 (m) cc_final: 0.8066 (t) REVERT: A 530 LYS cc_start: 0.8370 (mtpt) cc_final: 0.8008 (tttp) REVERT: A 534 MET cc_start: 0.8092 (mpm) cc_final: 0.7740 (mpm) REVERT: A 587 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7733 (mmm) REVERT: A 728 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 761 MET cc_start: 0.8225 (ttt) cc_final: 0.7901 (ttm) REVERT: A 773 ASP cc_start: 0.8542 (t0) cc_final: 0.8273 (t0) REVERT: B 291 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9053 (tp) REVERT: B 541 ASN cc_start: 0.6924 (OUTLIER) cc_final: 0.6065 (m-40) REVERT: B 614 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7625 (tm) REVERT: B 622 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7801 (mp) REVERT: B 683 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5355 (tp) REVERT: B 791 ASN cc_start: 0.7760 (m110) cc_final: 0.6702 (p0) REVERT: B 794 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7330 (pt) REVERT: C 156 ASP cc_start: 0.7963 (t0) cc_final: 0.7368 (t0) REVERT: C 195 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8490 (tt) REVERT: C 223 MET cc_start: 0.9118 (mmt) cc_final: 0.8915 (mmt) REVERT: C 260 GLN cc_start: 0.8760 (mp10) cc_final: 0.8318 (mp10) REVERT: C 477 SER cc_start: 0.8393 (m) cc_final: 0.7961 (t) REVERT: C 523 LEU cc_start: 0.8471 (mp) cc_final: 0.7829 (tp) REVERT: C 607 GLN cc_start: 0.7756 (mp10) cc_final: 0.7456 (mm-40) REVERT: C 702 TYR cc_start: 0.8702 (t80) cc_final: 0.8477 (t80) REVERT: C 773 ASP cc_start: 0.8410 (t0) cc_final: 0.8207 (t0) REVERT: D 156 ASP cc_start: 0.8323 (t70) cc_final: 0.7879 (t0) REVERT: D 229 SER cc_start: 0.8879 (t) cc_final: 0.8598 (m) REVERT: D 232 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7916 (ptt180) REVERT: D 234 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8849 (mt) REVERT: D 247 GLU cc_start: 0.8167 (tp30) cc_final: 0.7812 (tp30) REVERT: D 253 TYR cc_start: 0.7372 (m-10) cc_final: 0.7155 (m-10) REVERT: D 607 GLN cc_start: 0.7815 (mt0) cc_final: 0.7361 (mm110) REVERT: D 612 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8107 (mmtt) REVERT: D 636 LEU cc_start: 0.7581 (mm) cc_final: 0.7223 (pp) REVERT: D 791 ASN cc_start: 0.8083 (m110) cc_final: 0.7232 (p0) outliers start: 85 outliers final: 49 residues processed: 446 average time/residue: 0.3405 time to fit residues: 242.5238 Evaluate side-chains 416 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 356 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 335 THR 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 614 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 ASP 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 337 GLU Chi-restraints excluded: chain C residue 365 VAL 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 598 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 732 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 351 LEU 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 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 717 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 205 optimal weight: 0.0670 chunk 136 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 148 optimal weight: 0.0040 chunk 112 optimal weight: 20.0000 overall best weight: 0.6132 ------------------------------------------------------------------------------- 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 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN C 550 GLN C 588 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21270 Z= 0.161 Angle : 0.667 12.080 28800 Z= 0.329 Chirality : 0.041 0.232 3238 Planarity : 0.004 0.070 3584 Dihedral : 11.169 166.585 3008 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.34 % Favored : 90.34 % Rotamer: Outliers : 3.62 % Allowed : 18.05 % Favored : 78.33 % 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: -1.80 (0.16), residues: 2526 helix: -0.24 (0.14), residues: 1426 sheet: -2.23 (0.55), residues: 92 loop : -2.47 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 737 HIS 0.003 0.000 HIS B 309 PHE 0.022 0.001 PHE D 666 TYR 0.036 0.001 TYR C 574 ARG 0.009 0.000 ARG A 391 *********************** 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 461 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 380 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7778 (tp30) REVERT: A 222 ASN cc_start: 0.7693 (m110) cc_final: 0.7444 (m110) REVERT: A 295 THR cc_start: 0.8155 (p) cc_final: 0.7502 (t) REVERT: A 444 GLU cc_start: 0.7680 (mp0) cc_final: 0.7424 (mp0) REVERT: A 477 SER cc_start: 0.8499 (m) cc_final: 0.8078 (t) REVERT: A 587 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7681 (mmm) REVERT: A 588 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7987 (t0) REVERT: A 628 TYR cc_start: 0.7984 (m-80) cc_final: 0.7733 (m-80) REVERT: A 728 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8517 (tm-30) REVERT: A 761 MET cc_start: 0.8223 (ttt) cc_final: 0.7898 (ttm) REVERT: A 773 ASP cc_start: 0.8548 (t0) cc_final: 0.8269 (t0) REVERT: B 156 ASP cc_start: 0.8596 (t70) cc_final: 0.8237 (t0) REVERT: B 291 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9070 (tp) REVERT: B 541 ASN cc_start: 0.6883 (OUTLIER) cc_final: 0.5974 (m-40) REVERT: B 551 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8423 (mt) REVERT: B 625 MET cc_start: 0.7841 (tpp) cc_final: 0.7564 (mmp) REVERT: B 791 ASN cc_start: 0.7696 (m110) cc_final: 0.6704 (p0) REVERT: B 794 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7371 (pt) REVERT: C 156 ASP cc_start: 0.7932 (t0) cc_final: 0.7341 (t0) REVERT: C 195 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8465 (tt) REVERT: C 477 SER cc_start: 0.8437 (m) cc_final: 0.8026 (t) REVERT: C 531 ASP cc_start: 0.8247 (m-30) cc_final: 0.7712 (m-30) REVERT: D 156 ASP cc_start: 0.8304 (t70) cc_final: 0.7854 (t0) REVERT: D 229 SER cc_start: 0.8870 (t) cc_final: 0.8608 (m) REVERT: D 232 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7969 (ptt180) REVERT: D 234 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8818 (mt) REVERT: D 247 GLU cc_start: 0.8190 (tp30) cc_final: 0.7838 (tp30) REVERT: D 607 GLN cc_start: 0.7841 (mt0) cc_final: 0.7361 (mm110) REVERT: D 612 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8107 (mmtt) REVERT: D 791 ASN cc_start: 0.8136 (m110) cc_final: 0.7274 (p0) outliers start: 81 outliers final: 48 residues processed: 425 average time/residue: 0.2984 time to fit residues: 202.3231 Evaluate side-chains 412 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 353 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 222 ASN 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 365 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 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: 0.6980 chunk 145 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 190 optimal weight: 0.0570 chunk 220 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN D 228 ASN D 252 HIS ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21270 Z= 0.161 Angle : 0.672 12.271 28800 Z= 0.331 Chirality : 0.041 0.238 3238 Planarity : 0.004 0.071 3584 Dihedral : 10.976 155.712 3008 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.22 % Favored : 90.42 % Rotamer: Outliers : 3.26 % Allowed : 18.72 % Favored : 78.02 % 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: -1.63 (0.17), residues: 2526 helix: -0.08 (0.14), residues: 1432 sheet: -2.22 (0.55), residues: 92 loop : -2.44 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 733 HIS 0.003 0.000 HIS B 309 PHE 0.021 0.001 PHE D 666 TYR 0.029 0.001 TYR C 574 ARG 0.008 0.000 ARG B 336 *********************** 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 452 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 379 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: A 233 ASP cc_start: 0.7940 (t0) cc_final: 0.7737 (t0) REVERT: A 444 GLU cc_start: 0.7694 (mp0) cc_final: 0.7426 (mp0) REVERT: A 477 SER cc_start: 0.8499 (m) cc_final: 0.8081 (t) REVERT: A 523 LEU cc_start: 0.8394 (mp) cc_final: 0.8183 (pp) REVERT: A 531 ASP cc_start: 0.8292 (m-30) cc_final: 0.7720 (m-30) REVERT: A 553 TYR cc_start: 0.7394 (m-80) cc_final: 0.7182 (m-80) REVERT: A 591 TYR cc_start: 0.8316 (t80) cc_final: 0.7702 (t80) REVERT: A 628 TYR cc_start: 0.7993 (m-80) cc_final: 0.7741 (m-80) REVERT: A 761 MET cc_start: 0.8243 (ttt) cc_final: 0.7910 (ttm) REVERT: A 773 ASP cc_start: 0.8550 (t0) cc_final: 0.8289 (t0) REVERT: B 156 ASP cc_start: 0.8607 (t70) cc_final: 0.8241 (t0) REVERT: B 291 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9087 (tp) REVERT: B 541 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6097 (m-40) REVERT: B 551 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8434 (mt) REVERT: B 622 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7617 (mp) REVERT: B 625 MET cc_start: 0.7965 (tpp) cc_final: 0.7670 (mmp) REVERT: B 791 ASN cc_start: 0.7692 (m110) cc_final: 0.6708 (p0) REVERT: B 794 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7368 (pt) REVERT: C 156 ASP cc_start: 0.7938 (t0) cc_final: 0.7331 (t0) REVERT: C 179 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7789 (mmt90) REVERT: C 195 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8508 (tt) REVERT: C 477 SER cc_start: 0.8442 (m) cc_final: 0.8053 (t) REVERT: D 156 ASP cc_start: 0.8299 (t70) cc_final: 0.7853 (t0) REVERT: D 229 SER cc_start: 0.8855 (t) cc_final: 0.8589 (m) REVERT: D 234 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8817 (mt) REVERT: D 247 GLU cc_start: 0.8219 (tp30) cc_final: 0.7922 (tp30) REVERT: D 607 GLN cc_start: 0.7842 (mt0) cc_final: 0.7343 (mm110) REVERT: D 612 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8142 (mmtt) outliers start: 73 outliers final: 47 residues processed: 418 average time/residue: 0.3101 time to fit residues: 205.4238 Evaluate side-chains 413 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 357 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 0.5980 chunk 226 optimal weight: 8.9990 chunk 136 optimal weight: 0.0570 chunk 98 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 69 optimal weight: 0.0050 chunk 204 optimal weight: 0.8980 chunk 214 optimal weight: 0.0070 chunk 225 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.3130 ------------------------------------------------------------------------------- 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 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 588 ASN D 252 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 21270 Z= 0.155 Angle : 0.667 14.313 28800 Z= 0.328 Chirality : 0.041 0.225 3238 Planarity : 0.004 0.072 3584 Dihedral : 10.703 145.102 3008 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.50 % Favored : 90.18 % Rotamer: Outliers : 2.99 % Allowed : 19.66 % Favored : 77.35 % 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: -1.44 (0.17), residues: 2526 helix: 0.09 (0.14), residues: 1412 sheet: -2.19 (0.56), residues: 92 loop : -2.34 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 733 HIS 0.003 0.000 HIS B 309 PHE 0.038 0.001 PHE D 669 TYR 0.028 0.001 TYR C 574 ARG 0.010 0.000 ARG A 336 *********************** 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: 67 poor density : 393 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: A 219 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8314 (mmt90) REVERT: A 444 GLU cc_start: 0.7691 (mp0) cc_final: 0.7480 (mp0) REVERT: A 455 ILE cc_start: 0.8059 (mm) cc_final: 0.7063 (mt) REVERT: A 477 SER cc_start: 0.8494 (m) cc_final: 0.8089 (t) REVERT: A 531 ASP cc_start: 0.8241 (m-30) cc_final: 0.7640 (m-30) REVERT: A 534 MET cc_start: 0.7789 (mmp) cc_final: 0.6750 (ptt) REVERT: A 553 TYR cc_start: 0.7385 (m-80) cc_final: 0.7046 (m-80) REVERT: A 572 GLU cc_start: 0.7244 (tp30) cc_final: 0.6499 (pm20) REVERT: A 587 MET cc_start: 0.7692 (mmm) cc_final: 0.7471 (mmm) REVERT: A 591 TYR cc_start: 0.8263 (t80) cc_final: 0.7678 (t80) REVERT: A 761 MET cc_start: 0.8199 (ttt) cc_final: 0.7846 (ttm) REVERT: A 773 ASP cc_start: 0.8537 (t0) cc_final: 0.8278 (t0) REVERT: B 156 ASP cc_start: 0.8568 (t70) cc_final: 0.8186 (t0) REVERT: B 219 ARG cc_start: 0.8299 (mmt-90) cc_final: 0.7935 (mmt-90) REVERT: B 291 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9077 (tp) REVERT: B 541 ASN cc_start: 0.6926 (OUTLIER) cc_final: 0.6081 (m-40) REVERT: B 602 TYR cc_start: 0.8303 (t80) cc_final: 0.8043 (t80) REVERT: B 625 MET cc_start: 0.7975 (tpp) cc_final: 0.7660 (mmp) REVERT: B 736 GLN cc_start: 0.8289 (mt0) cc_final: 0.7980 (mt0) REVERT: B 791 ASN cc_start: 0.7701 (m110) cc_final: 0.6742 (p0) REVERT: B 794 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7402 (pt) REVERT: C 156 ASP cc_start: 0.7935 (t0) cc_final: 0.7330 (t0) REVERT: C 195 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8497 (tt) REVERT: C 369 ASP cc_start: 0.8471 (m-30) cc_final: 0.8238 (m-30) REVERT: C 477 SER cc_start: 0.8492 (m) cc_final: 0.8061 (t) REVERT: C 531 ASP cc_start: 0.8260 (m-30) cc_final: 0.7695 (m-30) REVERT: C 625 MET cc_start: 0.6981 (mmp) cc_final: 0.6187 (tpp) REVERT: D 156 ASP cc_start: 0.8276 (t70) cc_final: 0.7839 (t0) REVERT: D 234 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8803 (mt) REVERT: D 247 GLU cc_start: 0.8198 (tp30) cc_final: 0.7889 (tp30) REVERT: D 607 GLN cc_start: 0.7801 (mt0) cc_final: 0.7318 (mm110) REVERT: D 612 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8143 (mmtt) outliers start: 67 outliers final: 45 residues processed: 425 average time/residue: 0.3108 time to fit residues: 209.4340 Evaluate side-chains 418 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 366 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 541 ASN 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 626 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 ILE 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 518 LEU Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 251 optimal weight: 0.0770 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN D 252 HIS ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21270 Z= 0.191 Angle : 0.692 13.817 28800 Z= 0.340 Chirality : 0.041 0.222 3238 Planarity : 0.004 0.069 3584 Dihedral : 10.619 138.235 3008 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.82 % Favored : 89.83 % Rotamer: Outliers : 2.50 % Allowed : 20.24 % Favored : 77.26 % 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: -1.45 (0.17), residues: 2526 helix: 0.11 (0.14), residues: 1424 sheet: -2.10 (0.57), residues: 88 loop : -2.42 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 737 HIS 0.005 0.001 HIS A 252 PHE 0.037 0.001 PHE D 669 TYR 0.036 0.001 TYR D 253 ARG 0.010 0.000 ARG C 391 ********************** 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 421 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 365 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8292 (mmt90) REVERT: A 444 GLU cc_start: 0.7711 (mp0) cc_final: 0.7471 (mp0) REVERT: A 477 SER cc_start: 0.8510 (m) cc_final: 0.8090 (t) REVERT: A 531 ASP cc_start: 0.8327 (m-30) cc_final: 0.7721 (m-30) REVERT: A 534 MET cc_start: 0.7786 (mmp) cc_final: 0.6790 (ptt) REVERT: A 553 TYR cc_start: 0.7470 (m-80) cc_final: 0.7080 (m-80) REVERT: A 572 GLU cc_start: 0.7209 (tp30) cc_final: 0.6487 (pm20) REVERT: A 587 MET cc_start: 0.7729 (mmm) cc_final: 0.7525 (mmm) REVERT: A 591 TYR cc_start: 0.8321 (t80) cc_final: 0.7717 (t80) REVERT: A 628 TYR cc_start: 0.7661 (m-80) cc_final: 0.7310 (m-80) REVERT: A 761 MET cc_start: 0.8229 (ttt) cc_final: 0.7886 (ttm) REVERT: A 773 ASP cc_start: 0.8553 (t0) cc_final: 0.8287 (t0) REVERT: B 156 ASP cc_start: 0.8580 (t70) cc_final: 0.8185 (t0) REVERT: B 219 ARG cc_start: 0.8309 (mmt-90) cc_final: 0.7956 (mmt-90) REVERT: B 291 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9090 (tp) REVERT: B 541 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6116 (m-40) REVERT: B 602 TYR cc_start: 0.8283 (t80) cc_final: 0.8045 (t80) REVERT: B 625 MET cc_start: 0.8112 (tpp) cc_final: 0.7786 (mmp) REVERT: B 685 MET cc_start: 0.6291 (mpp) cc_final: 0.5954 (mmt) REVERT: B 761 MET cc_start: 0.8097 (mmt) cc_final: 0.7847 (mmp) REVERT: B 791 ASN cc_start: 0.7724 (m110) cc_final: 0.6737 (p0) REVERT: B 794 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7318 (pt) REVERT: C 156 ASP cc_start: 0.7936 (t0) cc_final: 0.7314 (t0) REVERT: C 195 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 219 ARG cc_start: 0.8835 (mmm-85) cc_final: 0.8576 (mmt90) REVERT: C 260 GLN cc_start: 0.8649 (mp10) cc_final: 0.8329 (mp10) REVERT: C 477 SER cc_start: 0.8479 (m) cc_final: 0.8013 (t) REVERT: C 625 MET cc_start: 0.6945 (mmp) cc_final: 0.6609 (mmp) REVERT: C 677 THR cc_start: 0.8533 (m) cc_final: 0.8265 (m) REVERT: C 685 MET cc_start: 0.5642 (mmt) cc_final: 0.5327 (mmt) REVERT: D 156 ASP cc_start: 0.8294 (t70) cc_final: 0.7856 (t0) REVERT: D 247 GLU cc_start: 0.8225 (tp30) cc_final: 0.7914 (tp30) REVERT: D 607 GLN cc_start: 0.7855 (mt0) cc_final: 0.7329 (mm110) REVERT: D 612 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8138 (mmtt) outliers start: 56 outliers final: 44 residues processed: 394 average time/residue: 0.3083 time to fit residues: 192.9081 Evaluate side-chains 412 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 363 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 541 ASN 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 626 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 622 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 732 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 612 LYS Chi-restraints excluded: chain D residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 83 optimal weight: 0.0470 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 550 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.165607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131761 restraints weight = 29780.941| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.16 r_work: 0.3259 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5176 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 : 0.676 12.897 28800 Z= 0.332 Chirality : 0.041 0.220 3238 Planarity : 0.004 0.068 3584 Dihedral : 10.492 130.343 3008 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.38 % Favored : 90.26 % Rotamer: Outliers : 2.55 % Allowed : 20.33 % Favored : 77.12 % 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: -1.38 (0.17), residues: 2526 helix: 0.17 (0.14), residues: 1426 sheet: -2.05 (0.58), residues: 88 loop : -2.41 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 733 HIS 0.003 0.001 HIS D 252 PHE 0.037 0.001 PHE D 669 TYR 0.028 0.001 TYR C 574 ARG 0.009 0.000 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5084.56 seconds wall clock time: 93 minutes 2.99 seconds (5582.99 seconds total)