Starting phenix.real_space_refine on Wed Jul 24 11:14:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/07_2024/7xbk_33104_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/07_2024/7xbk_33104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/07_2024/7xbk_33104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/07_2024/7xbk_33104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/07_2024/7xbk_33104_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/07_2024/7xbk_33104_neut.cif" } resolution = 3.7 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= 0.003 sd= 0.037 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 24 5.49 5 Mg 8 5.21 5 S 80 5.16 5 C 16177 2.51 5 N 4674 2.21 5 O 4782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 545": "OE1" <-> "OE2" Residue "E TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 597": "OE1" <-> "OE2" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "F ASP 371": "OD1" <-> "OD2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F GLU 553": "OE1" <-> "OE2" Residue "F TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 342": "OE1" <-> "OE2" Residue "G GLU 359": "OE1" <-> "OE2" Residue "G GLU 386": "OE1" <-> "OE2" Residue "G TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 432": "OD1" <-> "OD2" Residue "G PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 526": "OD1" <-> "OD2" Residue "G GLU 527": "OE1" <-> "OE2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "H PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 25745 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2968 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2842 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 10, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2822 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 10, 'TRANS': 338} Chain breaks: 3 Chain: "D" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2857 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 10, 'TRANS': 342} Chain breaks: 2 Chain: "E" Number of atoms: 2813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2813 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 10, 'TRANS': 337} Chain breaks: 2 Chain: "F" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2766 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 9, 'TRANS': 332} Chain breaks: 1 Chain: "G" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2690 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 9, 'TRANS': 322} Chain breaks: 2 Chain: "H" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 1 Chain: "I" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2850 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 10, 'TRANS': 341} Chain breaks: 1 Chain: "L" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.43, per 1000 atoms: 0.52 Number of scatterers: 25745 At special positions: 0 Unit cell: (166.32, 132.84, 153.36, 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 80 16.00 P 24 15.00 Mg 8 11.99 O 4782 8.00 N 4674 7.00 C 16177 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.78 Conformation dependent library (CDL) restraints added in 4.8 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5938 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 27 sheets defined 55.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 320 through 337 removed outlier: 3.604A pdb=" N GLY A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.648A pdb=" N ALA A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 392 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 Processing helix chain 'A' and resid 430 through 444 removed outlier: 3.777A pdb=" N LEU A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 493 Processing helix chain 'A' and resid 507 through 524 removed outlier: 3.649A pdb=" N LYS A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Proline residue: A 517 - end of helix Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.808A pdb=" N LEU A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 566 removed outlier: 4.052A pdb=" N TRP A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.970A pdb=" N GLY A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 removed outlier: 4.192A pdb=" N ILE A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASN A 602 " --> pdb=" O ARG A 598 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 632 removed outlier: 4.107A pdb=" N GLN A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.814A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 336 Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.630A pdb=" N PHE B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 416 removed outlier: 3.705A pdb=" N CYS B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 429 removed outlier: 3.744A pdb=" N ALA B 429 " --> pdb=" O VAL B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 430 through 444 removed outlier: 3.547A pdb=" N LEU B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 493 Processing helix chain 'B' and resid 507 through 514 Processing helix chain 'B' and resid 514 through 524 Processing helix chain 'B' and resid 525 through 532 removed outlier: 3.638A pdb=" N LEU B 529 " --> pdb=" O ARG B 525 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 532 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 588 through 600 removed outlier: 3.846A pdb=" N ILE B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLU B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG B 598 " --> pdb=" O HIS B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 removed outlier: 3.794A pdb=" N GLU B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 307 Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.572A pdb=" N ARG C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 336 Processing helix chain 'C' and resid 356 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 407 through 416 Processing helix chain 'C' and resid 433 through 435 No H-bonds generated for 'chain 'C' and resid 433 through 435' Processing helix chain 'C' and resid 436 through 443 removed outlier: 4.051A pdb=" N LEU C 440 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 492 Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 514 through 524 removed outlier: 3.995A pdb=" N ILE C 518 " --> pdb=" O VAL C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 531 removed outlier: 3.856A pdb=" N LEU C 529 " --> pdb=" O ARG C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 561 removed outlier: 3.570A pdb=" N GLN C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 581 Processing helix chain 'C' and resid 588 through 594 removed outlier: 3.709A pdb=" N ILE C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 600 Processing helix chain 'C' and resid 600 through 611 removed outlier: 3.664A pdb=" N LEU C 604 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.782A pdb=" N ARG D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 336 Processing helix chain 'D' and resid 356 through 369 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 395 removed outlier: 3.999A pdb=" N PHE D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.567A pdb=" N LYS D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 435 Processing helix chain 'D' and resid 435 through 443 removed outlier: 4.418A pdb=" N GLN D 439 " --> pdb=" O THR D 435 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU D 443 " --> pdb=" O GLN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 493 Processing helix chain 'D' and resid 507 through 514 Processing helix chain 'D' and resid 514 through 524 Processing helix chain 'D' and resid 542 through 566 Processing helix chain 'D' and resid 572 through 579 removed outlier: 3.769A pdb=" N ALA D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 600 removed outlier: 3.534A pdb=" N ILE D 592 " --> pdb=" O GLY D 588 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 610 Processing helix chain 'E' and resid 300 through 301 No H-bonds generated for 'chain 'E' and resid 300 through 301' Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 308 through 317 removed outlier: 3.696A pdb=" N GLU E 315 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS E 316 " --> pdb=" O ARG E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 336 Processing helix chain 'E' and resid 356 through 369 Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 390 through 395 removed outlier: 3.794A pdb=" N ILE E 394 " --> pdb=" O VAL E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 416 Processing helix chain 'E' and resid 435 through 443 removed outlier: 4.447A pdb=" N GLN E 439 " --> pdb=" O THR E 435 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU E 440 " --> pdb=" O ILE E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 493 Processing helix chain 'E' and resid 507 through 514 Processing helix chain 'E' and resid 514 through 524 removed outlier: 3.641A pdb=" N ILE E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 531 removed outlier: 3.679A pdb=" N LEU E 529 " --> pdb=" O ARG E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 566 Processing helix chain 'E' and resid 572 through 581 removed outlier: 3.821A pdb=" N ALA E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 600 removed outlier: 3.701A pdb=" N ILE E 592 " --> pdb=" O GLY E 588 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 600 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 610 Processing helix chain 'E' and resid 625 through 631 removed outlier: 3.603A pdb=" N LYS E 628 " --> pdb=" O ASP E 625 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN E 629 " --> pdb=" O SER E 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 317 Processing helix chain 'F' and resid 320 through 336 Processing helix chain 'F' and resid 356 through 369 Processing helix chain 'F' and resid 386 through 389 removed outlier: 3.518A pdb=" N GLU F 389 " --> pdb=" O GLU F 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 386 through 389' Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 407 through 416 removed outlier: 3.603A pdb=" N CYS F 416 " --> pdb=" O LYS F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 Processing helix chain 'F' and resid 433 through 443 removed outlier: 4.025A pdb=" N MET F 437 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU F 443 " --> pdb=" O GLN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 494 Processing helix chain 'F' and resid 507 through 514 removed outlier: 4.013A pdb=" N VAL F 514 " --> pdb=" O PHE F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 524 Processing helix chain 'F' and resid 525 through 532 removed outlier: 3.943A pdb=" N LEU F 529 " --> pdb=" O ARG F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 566 Processing helix chain 'F' and resid 572 through 582 removed outlier: 3.686A pdb=" N GLY F 582 " --> pdb=" O VAL F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 600 removed outlier: 3.709A pdb=" N ILE F 592 " --> pdb=" O GLY F 588 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU F 595 " --> pdb=" O SER F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 610 removed outlier: 3.908A pdb=" N GLN F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 307 Processing helix chain 'G' and resid 308 through 317 Processing helix chain 'G' and resid 320 through 336 removed outlier: 3.518A pdb=" N ALA G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 369 Processing helix chain 'G' and resid 371 through 375 Processing helix chain 'G' and resid 387 through 393 removed outlier: 3.786A pdb=" N VAL G 390 " --> pdb=" O ARG G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 416 Processing helix chain 'G' and resid 430 through 437 removed outlier: 3.694A pdb=" N LEU G 434 " --> pdb=" O HIS G 430 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 435 " --> pdb=" O PRO G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 443 Processing helix chain 'G' and resid 469 through 481 Processing helix chain 'G' and resid 509 through 514 Processing helix chain 'G' and resid 514 through 523 removed outlier: 3.729A pdb=" N ILE G 518 " --> pdb=" O VAL G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 532 removed outlier: 3.764A pdb=" N LEU G 529 " --> pdb=" O ARG G 525 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 532 " --> pdb=" O PHE G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 566 removed outlier: 3.532A pdb=" N ASN G 566 " --> pdb=" O LYS G 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 574 through 581 removed outlier: 4.541A pdb=" N VAL G 578 " --> pdb=" O GLU G 574 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 579 " --> pdb=" O VAL G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 600 removed outlier: 3.917A pdb=" N ILE G 592 " --> pdb=" O GLY G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 600 through 610 Processing helix chain 'H' and resid 299 through 307 Processing helix chain 'H' and resid 308 through 317 removed outlier: 3.809A pdb=" N ARG H 312 " --> pdb=" O PRO H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 336 Processing helix chain 'H' and resid 357 through 369 Processing helix chain 'H' and resid 371 through 375 Processing helix chain 'H' and resid 387 through 389 No H-bonds generated for 'chain 'H' and resid 387 through 389' Processing helix chain 'H' and resid 390 through 395 removed outlier: 3.530A pdb=" N ILE H 394 " --> pdb=" O VAL H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 416 Processing helix chain 'H' and resid 425 through 429 Processing helix chain 'H' and resid 433 through 438 Processing helix chain 'H' and resid 468 through 479 removed outlier: 3.912A pdb=" N ILE H 472 " --> pdb=" O ALA H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 507 through 514 Processing helix chain 'H' and resid 514 through 524 removed outlier: 3.925A pdb=" N ILE H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 525 through 532 removed outlier: 3.897A pdb=" N LEU H 529 " --> pdb=" O ARG H 525 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 532 " --> pdb=" O PHE H 528 " (cutoff:3.500A) Processing helix chain 'H' and resid 542 through 566 Processing helix chain 'H' and resid 572 through 582 Processing helix chain 'H' and resid 588 through 610 removed outlier: 3.920A pdb=" N ILE H 592 " --> pdb=" O GLY H 588 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL H 601 " --> pdb=" O GLU H 597 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN H 602 " --> pdb=" O ARG H 598 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN H 603 " --> pdb=" O ARG H 599 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR H 608 " --> pdb=" O LEU H 604 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN H 610 " --> pdb=" O ALA H 606 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 632 Processing helix chain 'I' and resid 299 through 307 Processing helix chain 'I' and resid 308 through 317 removed outlier: 3.954A pdb=" N ARG I 312 " --> pdb=" O PRO I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 336 removed outlier: 3.891A pdb=" N LYS I 334 " --> pdb=" O ALA I 330 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU I 335 " --> pdb=" O ILE I 331 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN I 336 " --> pdb=" O ARG I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 369 Processing helix chain 'I' and resid 386 through 388 No H-bonds generated for 'chain 'I' and resid 386 through 388' Processing helix chain 'I' and resid 389 through 394 Processing helix chain 'I' and resid 407 through 416 Processing helix chain 'I' and resid 426 through 429 Processing helix chain 'I' and resid 430 through 443 removed outlier: 3.760A pdb=" N LEU I 440 " --> pdb=" O ILE I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 468 through 493 removed outlier: 3.754A pdb=" N ASN I 489 " --> pdb=" O GLU I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 514 Processing helix chain 'I' and resid 514 through 524 removed outlier: 3.632A pdb=" N ILE I 518 " --> pdb=" O VAL I 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 531 removed outlier: 3.888A pdb=" N LEU I 529 " --> pdb=" O ARG I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 542 through 566 Processing helix chain 'I' and resid 572 through 582 Processing helix chain 'I' and resid 588 through 610 removed outlier: 4.125A pdb=" N ILE I 592 " --> pdb=" O GLY I 588 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL I 601 " --> pdb=" O GLU I 597 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN I 602 " --> pdb=" O ARG I 598 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN I 603 " --> pdb=" O ARG I 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.270A pdb=" N ILE A 377 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASP A 424 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A 379 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A 421 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR A 464 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 423 " --> pdb=" O THR A 464 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA3, first strand: chain 'A' and resid 568 through 570 removed outlier: 6.239A pdb=" N THR A 568 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A 621 " --> pdb=" O THR A 568 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU A 570 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N VAL A 623 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR A 618 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU A 650 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 662 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 376 through 380 removed outlier: 6.489A pdb=" N ILE B 377 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP B 424 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 379 " --> pdb=" O ASP B 424 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 421 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR B 464 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE B 423 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 345 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N MET B 463 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE B 347 " --> pdb=" O MET B 463 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER B 465 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE B 349 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 346 " --> pdb=" O GLU B 534 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL B 536 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B 348 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE B 538 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 350 " --> pdb=" O PHE B 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AA6, first strand: chain 'B' and resid 568 through 570 removed outlier: 6.555A pdb=" N THR B 568 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE B 621 " --> pdb=" O THR B 568 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 570 " --> pdb=" O ILE B 621 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N VAL B 623 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B 618 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 376 through 380 removed outlier: 6.377A pdb=" N VAL C 421 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR C 464 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE C 423 " --> pdb=" O THR C 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 445 through 447 removed outlier: 3.939A pdb=" N LEU C 446 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 568 through 571 removed outlier: 7.326A pdb=" N THR C 568 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE C 621 " --> pdb=" O THR C 568 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU C 570 " --> pdb=" O ILE C 621 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N VAL C 623 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR C 618 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 376 through 380 removed outlier: 6.697A pdb=" N ILE D 377 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP D 424 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU D 379 " --> pdb=" O ASP D 424 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL D 421 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N THR D 464 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE D 423 " --> pdb=" O THR D 464 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 445 through 447 Processing sheet with id=AB3, first strand: chain 'D' and resid 568 through 571 removed outlier: 6.523A pdb=" N THR D 568 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE D 621 " --> pdb=" O THR D 568 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU D 570 " --> pdb=" O ILE D 621 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N VAL D 623 " --> pdb=" O LEU D 570 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR D 618 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 376 through 380 removed outlier: 6.731A pdb=" N ILE E 377 " --> pdb=" O LEU E 422 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP E 424 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU E 379 " --> pdb=" O ASP E 424 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU E 345 " --> pdb=" O PHE E 461 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N MET E 463 " --> pdb=" O LEU E 345 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE E 347 " --> pdb=" O MET E 463 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N SER E 465 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE E 349 " --> pdb=" O SER E 465 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 445 through 447 removed outlier: 3.744A pdb=" N LEU E 446 " --> pdb=" O ILE E 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 568 through 571 removed outlier: 4.314A pdb=" N THR E 618 " --> pdb=" O ILE E 653 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 376 through 380 removed outlier: 6.278A pdb=" N VAL F 421 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR F 464 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE F 423 " --> pdb=" O THR F 464 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL F 346 " --> pdb=" O GLU F 534 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL F 536 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU F 348 " --> pdb=" O VAL F 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 445 through 446 Processing sheet with id=AB9, first strand: chain 'F' and resid 568 through 570 removed outlier: 6.973A pdb=" N THR F 568 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ILE F 621 " --> pdb=" O THR F 568 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU F 570 " --> pdb=" O ILE F 621 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR F 618 " --> pdb=" O ILE F 653 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU F 650 " --> pdb=" O LEU F 662 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 376 through 380 removed outlier: 6.147A pdb=" N VAL G 421 " --> pdb=" O ILE G 462 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR G 464 " --> pdb=" O VAL G 421 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE G 423 " --> pdb=" O THR G 464 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU G 345 " --> pdb=" O PHE G 461 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N MET G 463 " --> pdb=" O LEU G 345 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE G 347 " --> pdb=" O MET G 463 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N SER G 465 " --> pdb=" O PHE G 347 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE G 349 " --> pdb=" O SER G 465 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL G 346 " --> pdb=" O GLU G 534 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL G 536 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU G 348 " --> pdb=" O VAL G 536 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 445 through 447 Processing sheet with id=AC3, first strand: chain 'G' and resid 568 through 571 removed outlier: 6.437A pdb=" N THR G 568 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE G 621 " --> pdb=" O THR G 568 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU G 570 " --> pdb=" O ILE G 621 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL G 623 " --> pdb=" O LEU G 570 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR G 618 " --> pdb=" O ILE G 653 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 376 through 380 removed outlier: 6.611A pdb=" N LEU H 345 " --> pdb=" O PHE H 461 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N MET H 463 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE H 347 " --> pdb=" O MET H 463 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER H 465 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE H 349 " --> pdb=" O SER H 465 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL H 346 " --> pdb=" O GLU H 534 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL H 536 " --> pdb=" O VAL H 346 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU H 348 " --> pdb=" O VAL H 536 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 445 through 446 removed outlier: 3.630A pdb=" N LEU H 446 " --> pdb=" O ILE H 454 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 568 through 571 removed outlier: 6.437A pdb=" N THR H 568 " --> pdb=" O LEU H 619 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE H 621 " --> pdb=" O THR H 568 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU H 570 " --> pdb=" O ILE H 621 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N VAL H 623 " --> pdb=" O LEU H 570 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N THR H 618 " --> pdb=" O ILE H 653 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 376 through 380 removed outlier: 6.208A pdb=" N VAL I 421 " --> pdb=" O ILE I 462 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR I 464 " --> pdb=" O VAL I 421 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE I 423 " --> pdb=" O THR I 464 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL I 346 " --> pdb=" O GLU I 534 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL I 536 " --> pdb=" O VAL I 346 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU I 348 " --> pdb=" O VAL I 536 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 445 through 447 Processing sheet with id=AC9, first strand: chain 'I' and resid 568 through 570 removed outlier: 6.315A pdb=" N THR I 568 " --> pdb=" O LEU I 619 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE I 621 " --> pdb=" O THR I 568 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU I 570 " --> pdb=" O ILE I 621 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N VAL I 623 " --> pdb=" O LEU I 570 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR I 618 " --> pdb=" O ILE I 653 " (cutoff:3.500A) 1174 hydrogen bonds defined for protein. 3468 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: 8.88 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6994 1.33 - 1.45: 4572 1.45 - 1.58: 14459 1.58 - 1.70: 35 1.70 - 1.82: 124 Bond restraints: 26184 Sorted by residual: bond pdb=" CB THR B 435 " pdb=" CG2 THR B 435 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.05e+00 bond pdb=" CA ASN H 466 " pdb=" CB ASN H 466 " ideal model delta sigma weight residual 1.528 1.558 -0.031 1.49e-02 4.50e+03 4.29e+00 bond pdb=" CB THR C 435 " pdb=" CG2 THR C 435 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.21e+00 bond pdb=" CG LEU F 438 " pdb=" CD2 LEU F 438 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB MET C 368 " pdb=" CG MET C 368 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.72e+00 ... (remaining 26179 not shown) Histogram of bond angle deviations from ideal: 97.22 - 105.77: 435 105.77 - 114.31: 15429 114.31 - 122.86: 17123 122.86 - 131.40: 2195 131.40 - 139.95: 62 Bond angle restraints: 35244 Sorted by residual: angle pdb=" N ASP F 432 " pdb=" CA ASP F 432 " pdb=" C ASP F 432 " ideal model delta sigma weight residual 114.56 106.70 7.86 1.27e+00 6.20e-01 3.83e+01 angle pdb=" C HIS E 565 " pdb=" N ASN E 566 " pdb=" CA ASN E 566 " ideal model delta sigma weight residual 122.46 130.40 -7.94 1.41e+00 5.03e-01 3.17e+01 angle pdb=" N VAL D 596 " pdb=" CA VAL D 596 " pdb=" C VAL D 596 " ideal model delta sigma weight residual 112.50 105.85 6.65 1.39e+00 5.18e-01 2.29e+01 angle pdb=" N ILE C 355 " pdb=" CA ILE C 355 " pdb=" C ILE C 355 " ideal model delta sigma weight residual 113.43 108.41 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" CB MET B 381 " pdb=" CG MET B 381 " pdb=" SD MET B 381 " ideal model delta sigma weight residual 112.70 125.87 -13.17 3.00e+00 1.11e-01 1.93e+01 ... (remaining 35239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14212 17.98 - 35.95: 1528 35.95 - 53.93: 338 53.93 - 71.91: 82 71.91 - 89.88: 33 Dihedral angle restraints: 16193 sinusoidal: 7059 harmonic: 9134 Sorted by residual: dihedral pdb=" CA PRO H 540 " pdb=" C PRO H 540 " pdb=" N PHE H 541 " pdb=" CA PHE H 541 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA TYR D 400 " pdb=" C TYR D 400 " pdb=" N VAL D 401 " pdb=" CA VAL D 401 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA PHE F 393 " pdb=" C PHE F 393 " pdb=" N ILE F 394 " pdb=" CA ILE F 394 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 16190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3212 0.066 - 0.131: 549 0.131 - 0.197: 80 0.197 - 0.262: 13 0.262 - 0.328: 6 Chirality restraints: 3860 Sorted by residual: chirality pdb=" CB VAL E 580 " pdb=" CA VAL E 580 " pdb=" CG1 VAL E 580 " pdb=" CG2 VAL E 580 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB VAL A 580 " pdb=" CA VAL A 580 " pdb=" CG1 VAL A 580 " pdb=" CG2 VAL A 580 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE B 535 " pdb=" CA ILE B 535 " pdb=" CG1 ILE B 535 " pdb=" CG2 ILE B 535 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 3857 not shown) Planarity restraints: 4540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 516 " 0.054 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO G 517 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO G 517 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 517 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 430 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 431 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 466 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C ASN H 466 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN H 466 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL H 467 " 0.015 2.00e-02 2.50e+03 ... (remaining 4537 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 298 2.66 - 3.22: 22206 3.22 - 3.78: 40468 3.78 - 4.34: 54629 4.34 - 4.90: 88537 Nonbonded interactions: 206138 Sorted by model distance: nonbonded pdb="MG MG C 701 " pdb=" O3G ATP C 702 " model vdw 2.095 2.170 nonbonded pdb="MG MG F 701 " pdb=" O3G ATP F 702 " model vdw 2.109 2.170 nonbonded pdb=" O2B ATP H 703 " pdb="MG MG I 701 " model vdw 2.111 2.170 nonbonded pdb="MG MG D 701 " pdb=" O3G ATP D 702 " model vdw 2.112 2.170 nonbonded pdb="MG MG E 701 " pdb=" O3G ATP E 702 " model vdw 2.114 2.170 ... (remaining 206133 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' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'B' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'C' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'D' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'E' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'F' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'G' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'H' and (resid 304 through 625 or resid 648 through 662)) selection = (chain 'I' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) } 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 group one per residue 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: 0.820 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: 0.040 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 65.970 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 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 : 0.005 0.074 26184 Z= 0.315 Angle : 0.863 13.166 35244 Z= 0.476 Chirality : 0.053 0.328 3860 Planarity : 0.007 0.081 4540 Dihedral : 16.043 89.885 10255 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.71 (0.14), residues: 3096 helix: -1.64 (0.11), residues: 1497 sheet: -0.13 (0.23), residues: 509 loop : -0.52 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 571 HIS 0.020 0.002 HIS I 475 PHE 0.044 0.003 PHE G 510 TYR 0.039 0.003 TYR H 608 ARG 0.015 0.001 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1078 time to evaluate : 2.672 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 VAL cc_start: 0.7224 (p) cc_final: 0.6996 (p) REVERT: A 347 PHE cc_start: 0.6514 (m-80) cc_final: 0.6271 (m-80) REVERT: A 383 GLU cc_start: 0.5031 (mt-10) cc_final: 0.4813 (mt-10) REVERT: A 392 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7623 (ttpt) REVERT: A 401 VAL cc_start: 0.8368 (m) cc_final: 0.8097 (p) REVERT: A 445 ARG cc_start: 0.6838 (ptm160) cc_final: 0.6589 (ptm-80) REVERT: A 462 ILE cc_start: 0.7929 (mt) cc_final: 0.7715 (mt) REVERT: A 512 GLU cc_start: 0.6119 (tp30) cc_final: 0.5472 (tp30) REVERT: A 527 GLU cc_start: 0.5463 (mp0) cc_final: 0.5223 (mt-10) REVERT: A 534 GLU cc_start: 0.5658 (tp30) cc_final: 0.5235 (tp30) REVERT: B 333 ARG cc_start: 0.6849 (mtp180) cc_final: 0.6521 (ttp80) REVERT: B 334 LYS cc_start: 0.7876 (tttm) cc_final: 0.7618 (tptm) REVERT: B 408 GLN cc_start: 0.7042 (mp10) cc_final: 0.6784 (mp10) REVERT: B 427 ASP cc_start: 0.6737 (p0) cc_final: 0.6436 (p0) REVERT: B 428 LYS cc_start: 0.7530 (mttp) cc_final: 0.7312 (mtmm) REVERT: B 433 VAL cc_start: 0.7908 (t) cc_final: 0.7601 (t) REVERT: B 442 ASP cc_start: 0.6727 (t0) cc_final: 0.6311 (t0) REVERT: B 514 VAL cc_start: 0.7623 (t) cc_final: 0.7400 (t) REVERT: B 539 LEU cc_start: 0.8263 (mt) cc_final: 0.8060 (mt) REVERT: B 587 TYR cc_start: 0.7794 (m-80) cc_final: 0.7522 (m-80) REVERT: B 608 TYR cc_start: 0.6755 (t80) cc_final: 0.6301 (t80) REVERT: C 333 ARG cc_start: 0.7209 (ttm170) cc_final: 0.6963 (ttp80) REVERT: C 363 GLN cc_start: 0.7061 (mm-40) cc_final: 0.6699 (mm-40) REVERT: C 412 LYS cc_start: 0.7733 (mttt) cc_final: 0.7390 (mttm) REVERT: C 445 ARG cc_start: 0.7254 (ttt-90) cc_final: 0.7023 (ttp80) REVERT: C 509 ASN cc_start: 0.6725 (t0) cc_final: 0.6488 (t0) REVERT: C 586 HIS cc_start: 0.7202 (m-70) cc_final: 0.6977 (m90) REVERT: C 592 ILE cc_start: 0.7672 (mm) cc_final: 0.7349 (mm) REVERT: C 595 GLU cc_start: 0.6156 (tm-30) cc_final: 0.5618 (tm-30) REVERT: D 315 GLU cc_start: 0.6269 (tm-30) cc_final: 0.5736 (tm-30) REVERT: D 317 ILE cc_start: 0.7933 (tt) cc_final: 0.7635 (tt) REVERT: D 336 ASN cc_start: 0.7863 (m-40) cc_final: 0.7638 (m110) REVERT: D 355 ILE cc_start: 0.8205 (mm) cc_final: 0.7837 (mm) REVERT: D 424 ASP cc_start: 0.6577 (t70) cc_final: 0.6243 (t70) REVERT: D 427 ASP cc_start: 0.7291 (t70) cc_final: 0.6901 (t70) REVERT: D 439 GLN cc_start: 0.6568 (pt0) cc_final: 0.6208 (pt0) REVERT: D 466 ASN cc_start: 0.6970 (m-40) cc_final: 0.6718 (m-40) REVERT: D 511 LYS cc_start: 0.8295 (mttt) cc_final: 0.8093 (mttp) REVERT: D 518 ILE cc_start: 0.7844 (tt) cc_final: 0.7515 (tp) REVERT: D 531 ARG cc_start: 0.7087 (mtt180) cc_final: 0.6788 (mtt180) REVERT: D 533 ASN cc_start: 0.6821 (m-40) cc_final: 0.6408 (m-40) REVERT: D 537 TYR cc_start: 0.6996 (m-80) cc_final: 0.6634 (m-80) REVERT: D 539 LEU cc_start: 0.7746 (mt) cc_final: 0.7488 (mt) REVERT: D 546 LEU cc_start: 0.7176 (mt) cc_final: 0.6950 (mt) REVERT: D 549 LEU cc_start: 0.7300 (tp) cc_final: 0.7066 (tp) REVERT: D 570 LEU cc_start: 0.7312 (tp) cc_final: 0.7070 (tp) REVERT: E 309 LEU cc_start: 0.6987 (tp) cc_final: 0.6550 (tp) REVERT: E 340 ASP cc_start: 0.7711 (t0) cc_final: 0.7406 (t0) REVERT: E 377 ILE cc_start: 0.8425 (mt) cc_final: 0.8186 (mt) REVERT: E 381 MET cc_start: 0.7417 (mmm) cc_final: 0.7062 (mmm) REVERT: E 385 GLN cc_start: 0.7905 (mt0) cc_final: 0.7575 (mt0) REVERT: E 390 VAL cc_start: 0.7803 (t) cc_final: 0.7408 (p) REVERT: E 418 ASN cc_start: 0.7371 (p0) cc_final: 0.6788 (p0) REVERT: E 427 ASP cc_start: 0.6382 (p0) cc_final: 0.5751 (p0) REVERT: E 428 LYS cc_start: 0.7412 (mmtm) cc_final: 0.6996 (mmtm) REVERT: E 436 ILE cc_start: 0.8258 (tt) cc_final: 0.8044 (tp) REVERT: E 443 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6526 (mm-30) REVERT: E 463 MET cc_start: 0.7901 (mtm) cc_final: 0.7662 (mtm) REVERT: E 466 ASN cc_start: 0.7222 (m-40) cc_final: 0.6916 (m-40) REVERT: E 471 GLU cc_start: 0.6690 (mp0) cc_final: 0.6407 (mp0) REVERT: E 515 ILE cc_start: 0.8162 (mm) cc_final: 0.7950 (mm) REVERT: F 363 GLN cc_start: 0.7457 (mm110) cc_final: 0.7170 (mm-40) REVERT: F 366 LYS cc_start: 0.6983 (mtmt) cc_final: 0.6781 (mtmt) REVERT: F 389 GLU cc_start: 0.6236 (mm-30) cc_final: 0.5762 (mm-30) REVERT: F 424 ASP cc_start: 0.6938 (t70) cc_final: 0.6688 (t70) REVERT: F 425 GLN cc_start: 0.7357 (mm-40) cc_final: 0.7132 (mm110) REVERT: F 448 ASP cc_start: 0.6196 (m-30) cc_final: 0.5921 (m-30) REVERT: F 547 ILE cc_start: 0.7864 (mm) cc_final: 0.7587 (mm) REVERT: F 580 VAL cc_start: 0.7960 (t) cc_final: 0.7670 (p) REVERT: F 594 HIS cc_start: 0.7274 (m90) cc_final: 0.7034 (m90) REVERT: G 377 ILE cc_start: 0.8499 (mt) cc_final: 0.8296 (mm) REVERT: G 381 MET cc_start: 0.6522 (mmp) cc_final: 0.6269 (mmp) REVERT: G 392 LYS cc_start: 0.7586 (mttm) cc_final: 0.7383 (mtmm) REVERT: G 425 GLN cc_start: 0.6856 (mt0) cc_final: 0.6086 (mt0) REVERT: G 440 LEU cc_start: 0.8482 (tp) cc_final: 0.8191 (tp) REVERT: G 516 ARG cc_start: 0.6842 (ttp-170) cc_final: 0.6534 (ttt180) REVERT: G 531 ARG cc_start: 0.7316 (mtt90) cc_final: 0.6455 (mtt90) REVERT: G 599 ARG cc_start: 0.7072 (tpp80) cc_final: 0.6466 (mmm-85) REVERT: G 608 TYR cc_start: 0.7072 (t80) cc_final: 0.6414 (t80) REVERT: H 327 VAL cc_start: 0.7501 (t) cc_final: 0.7077 (t) REVERT: H 334 LYS cc_start: 0.7647 (mtpp) cc_final: 0.7346 (mtpp) REVERT: H 357 LYS cc_start: 0.7554 (mtmm) cc_final: 0.7224 (mtmm) REVERT: H 362 LYS cc_start: 0.6768 (mmtt) cc_final: 0.6396 (mmtt) REVERT: H 363 GLN cc_start: 0.6567 (mm-40) cc_final: 0.6270 (mm-40) REVERT: H 392 LYS cc_start: 0.7575 (mtpt) cc_final: 0.7085 (mtpt) REVERT: H 438 LEU cc_start: 0.7758 (pt) cc_final: 0.7508 (pp) REVERT: H 552 LYS cc_start: 0.7472 (tmtt) cc_final: 0.7124 (tptp) REVERT: H 585 VAL cc_start: 0.8099 (t) cc_final: 0.7540 (p) REVERT: H 592 ILE cc_start: 0.7867 (tt) cc_final: 0.7572 (mm) REVERT: I 597 GLU cc_start: 0.4845 (tt0) cc_final: 0.4563 (tt0) outliers start: 0 outliers final: 0 residues processed: 1078 average time/residue: 0.4577 time to fit residues: 715.9154 Evaluate side-chains 965 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 965 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.7980 chunk 235 optimal weight: 0.4980 chunk 130 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 125 optimal weight: 0.0050 chunk 243 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 181 optimal weight: 0.0870 chunk 282 optimal weight: 7.9990 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS B 316 HIS B 320 GLN B 551 ASN C 439 GLN C 475 HIS C 533 ASN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS D 408 GLN D 418 ASN D 594 HIS D 603 GLN E 316 HIS E 320 GLN E 439 GLN E 522 HIS ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 594 HIS F 584 ASN G 320 GLN ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 HIS I 430 HIS I 466 ASN I 475 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26184 Z= 0.175 Angle : 0.569 10.520 35244 Z= 0.300 Chirality : 0.042 0.192 3860 Planarity : 0.005 0.071 4540 Dihedral : 10.677 88.712 3706 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 1.94 % Allowed : 12.90 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.39 (0.14), residues: 3096 helix: -0.22 (0.13), residues: 1549 sheet: 0.13 (0.23), residues: 481 loop : -0.19 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 571 HIS 0.008 0.001 HIS A 475 PHE 0.044 0.002 PHE I 556 TYR 0.021 0.002 TYR G 339 ARG 0.006 0.000 ARG F 516 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1007 time to evaluate : 2.986 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.5573 (ttm110) REVERT: A 383 GLU cc_start: 0.5213 (mt-10) cc_final: 0.5005 (mt-10) REVERT: A 392 LYS cc_start: 0.7604 (ptpt) cc_final: 0.7306 (ttpt) REVERT: A 401 VAL cc_start: 0.8429 (m) cc_final: 0.8175 (p) REVERT: A 471 GLU cc_start: 0.5923 (mp0) cc_final: 0.5347 (mp0) REVERT: A 479 LEU cc_start: 0.7613 (mt) cc_final: 0.7193 (mt) REVERT: A 512 GLU cc_start: 0.6233 (tp30) cc_final: 0.5551 (tp30) REVERT: A 529 LEU cc_start: 0.7247 (mt) cc_final: 0.7009 (mt) REVERT: A 534 GLU cc_start: 0.5705 (tp30) cc_final: 0.5236 (tp30) REVERT: B 346 VAL cc_start: 0.7821 (m) cc_final: 0.7403 (p) REVERT: B 362 LYS cc_start: 0.7605 (ttmm) cc_final: 0.7313 (mttp) REVERT: B 392 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7074 (ttpt) REVERT: B 427 ASP cc_start: 0.6675 (p0) cc_final: 0.6220 (p0) REVERT: B 445 ARG cc_start: 0.7828 (tmm-80) cc_final: 0.7568 (ttp80) REVERT: B 465 SER cc_start: 0.7471 (t) cc_final: 0.7123 (t) REVERT: B 557 TRP cc_start: 0.6718 (m100) cc_final: 0.6107 (m100) REVERT: B 599 ARG cc_start: 0.7155 (tpp-160) cc_final: 0.6909 (tpp80) REVERT: B 608 TYR cc_start: 0.6626 (t80) cc_final: 0.6260 (t80) REVERT: C 363 GLN cc_start: 0.7016 (mm-40) cc_final: 0.6725 (mm-40) REVERT: C 392 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7604 (mtpp) REVERT: C 541 PHE cc_start: 0.7788 (m-80) cc_final: 0.7578 (m-10) REVERT: C 592 ILE cc_start: 0.7582 (mm) cc_final: 0.7322 (mm) REVERT: D 314 LYS cc_start: 0.7344 (ttpt) cc_final: 0.7130 (ttpt) REVERT: D 315 GLU cc_start: 0.6056 (tm-30) cc_final: 0.5559 (tm-30) REVERT: D 317 ILE cc_start: 0.7921 (tt) cc_final: 0.7658 (tt) REVERT: D 411 LYS cc_start: 0.6943 (ptmt) cc_final: 0.6528 (ptmt) REVERT: D 412 LYS cc_start: 0.8131 (mttp) cc_final: 0.7741 (mttm) REVERT: D 427 ASP cc_start: 0.7016 (t70) cc_final: 0.6813 (t0) REVERT: D 434 LEU cc_start: 0.7190 (mt) cc_final: 0.6814 (mt) REVERT: D 437 MET cc_start: 0.6179 (mpp) cc_final: 0.5795 (mpp) REVERT: D 467 VAL cc_start: 0.8248 (t) cc_final: 0.7986 (t) REVERT: D 511 LYS cc_start: 0.8299 (mttt) cc_final: 0.7937 (mttt) REVERT: D 533 ASN cc_start: 0.6921 (m-40) cc_final: 0.6555 (m-40) REVERT: D 537 TYR cc_start: 0.6962 (m-80) cc_final: 0.6654 (m-80) REVERT: D 546 LEU cc_start: 0.7372 (mt) cc_final: 0.7091 (mt) REVERT: D 555 ASN cc_start: 0.7487 (t0) cc_final: 0.7072 (t0) REVERT: D 557 TRP cc_start: 0.7598 (m100) cc_final: 0.7349 (m100) REVERT: E 340 ASP cc_start: 0.7755 (t0) cc_final: 0.7428 (t0) REVERT: E 380 ASP cc_start: 0.7084 (t70) cc_final: 0.6557 (t0) REVERT: E 385 GLN cc_start: 0.7835 (mt0) cc_final: 0.7561 (mt0) REVERT: E 390 VAL cc_start: 0.7753 (t) cc_final: 0.7546 (p) REVERT: E 428 LYS cc_start: 0.7225 (mmtm) cc_final: 0.6837 (mptt) REVERT: E 471 GLU cc_start: 0.6786 (mp0) cc_final: 0.6527 (mp0) REVERT: E 554 LEU cc_start: 0.7752 (mt) cc_final: 0.7466 (mm) REVERT: E 575 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7133 (p) REVERT: E 602 ASN cc_start: 0.7018 (m-40) cc_final: 0.6756 (m-40) REVERT: F 341 GLU cc_start: 0.5516 (mm-30) cc_final: 0.5208 (mm-30) REVERT: F 363 GLN cc_start: 0.7623 (mm110) cc_final: 0.7334 (mm-40) REVERT: F 432 ASP cc_start: 0.6507 (m-30) cc_final: 0.5632 (m-30) REVERT: F 518 ILE cc_start: 0.8561 (tt) cc_final: 0.8353 (tp) REVERT: F 525 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6524 (tpp80) REVERT: G 347 PHE cc_start: 0.7648 (m-80) cc_final: 0.7094 (m-80) REVERT: G 357 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7539 (mtmt) REVERT: G 381 MET cc_start: 0.6280 (mmp) cc_final: 0.5965 (mmp) REVERT: G 392 LYS cc_start: 0.7395 (mttm) cc_final: 0.6934 (ttmm) REVERT: G 414 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7342 (ttmm) REVERT: G 428 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7439 (mmtt) REVERT: G 440 LEU cc_start: 0.8461 (tp) cc_final: 0.8237 (tp) REVERT: G 531 ARG cc_start: 0.7047 (mtt90) cc_final: 0.6797 (mtt-85) REVERT: G 590 ARG cc_start: 0.6344 (ptp90) cc_final: 0.5594 (ptp90) REVERT: G 593 LYS cc_start: 0.7764 (mtpp) cc_final: 0.7479 (mtmm) REVERT: H 326 THR cc_start: 0.7151 (m) cc_final: 0.6510 (t) REVERT: H 331 ILE cc_start: 0.7192 (mt) cc_final: 0.6977 (mm) REVERT: H 334 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7463 (mtpp) REVERT: H 357 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7312 (mtmm) REVERT: H 363 GLN cc_start: 0.6607 (mm-40) cc_final: 0.6261 (mm-40) REVERT: H 392 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7443 (ttmm) REVERT: H 414 LYS cc_start: 0.6838 (tmmt) cc_final: 0.6293 (ptmm) REVERT: H 415 GLN cc_start: 0.6306 (tp40) cc_final: 0.5895 (tp40) REVERT: H 552 LYS cc_start: 0.7576 (tmtt) cc_final: 0.7145 (tptp) REVERT: H 595 GLU cc_start: 0.6786 (pp20) cc_final: 0.5645 (tm-30) REVERT: I 357 LYS cc_start: 0.5628 (pttm) cc_final: 0.5180 (pttm) outliers start: 53 outliers final: 29 residues processed: 1018 average time/residue: 0.4930 time to fit residues: 736.2242 Evaluate side-chains 973 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 941 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 652 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 525 ARG Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 380 ASP Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 604 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 0.0870 chunk 305 optimal weight: 0.7980 chunk 251 optimal weight: 0.9980 chunk 280 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 GLN B 385 GLN B 513 ASN C 466 ASN C 551 ASN D 418 ASN D 430 HIS D 466 ASN D 603 GLN E 316 HIS E 522 HIS E 555 ASN ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 GLN F 548 GLN F 584 ASN ** G 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 GLN ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26184 Z= 0.213 Angle : 0.566 8.897 35244 Z= 0.301 Chirality : 0.043 0.195 3860 Planarity : 0.004 0.071 4540 Dihedral : 10.299 88.676 3706 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 2.71 % Allowed : 16.09 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.11 (0.15), residues: 3096 helix: 0.31 (0.13), residues: 1540 sheet: 0.03 (0.23), residues: 507 loop : 0.03 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 571 HIS 0.010 0.001 HIS A 475 PHE 0.039 0.002 PHE I 556 TYR 0.021 0.002 TYR G 608 ARG 0.010 0.000 ARG G 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 975 time to evaluate : 2.630 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.7676 (ptpt) cc_final: 0.7256 (ttpt) REVERT: A 401 VAL cc_start: 0.8504 (m) cc_final: 0.8210 (p) REVERT: A 512 GLU cc_start: 0.6335 (tp30) cc_final: 0.5589 (tp30) REVERT: A 534 GLU cc_start: 0.5635 (tp30) cc_final: 0.5274 (tp30) REVERT: B 310 GLU cc_start: 0.7394 (mp0) cc_final: 0.7085 (mp0) REVERT: B 316 HIS cc_start: 0.6688 (t-90) cc_final: 0.6439 (t70) REVERT: B 392 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7804 (ttpt) REVERT: B 427 ASP cc_start: 0.6696 (p0) cc_final: 0.6256 (p0) REVERT: B 428 LYS cc_start: 0.7532 (mtpt) cc_final: 0.7122 (mtpp) REVERT: B 465 SER cc_start: 0.7474 (t) cc_final: 0.7248 (t) REVERT: B 485 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6043 (tm-30) REVERT: C 320 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6809 (mm110) REVERT: C 363 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6810 (mm110) REVERT: C 428 LYS cc_start: 0.7545 (mmtm) cc_final: 0.7320 (mmtm) REVERT: C 594 HIS cc_start: 0.5347 (p90) cc_final: 0.4806 (p90) REVERT: C 595 GLU cc_start: 0.5919 (tm-30) cc_final: 0.5632 (tm-30) REVERT: D 315 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5753 (tm-30) REVERT: D 317 ILE cc_start: 0.7968 (tt) cc_final: 0.7695 (tt) REVERT: D 389 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6509 (mm-30) REVERT: D 411 LYS cc_start: 0.6710 (ptmt) cc_final: 0.6049 (ptmt) REVERT: D 415 GLN cc_start: 0.6729 (mt0) cc_final: 0.6400 (mp10) REVERT: D 533 ASN cc_start: 0.7031 (m-40) cc_final: 0.6707 (m-40) REVERT: D 557 TRP cc_start: 0.7615 (m100) cc_final: 0.7374 (m100) REVERT: D 587 TYR cc_start: 0.7294 (m-80) cc_final: 0.6751 (m-80) REVERT: E 340 ASP cc_start: 0.7915 (t0) cc_final: 0.7569 (t0) REVERT: E 390 VAL cc_start: 0.7855 (t) cc_final: 0.7635 (p) REVERT: E 428 LYS cc_start: 0.7671 (mmtm) cc_final: 0.6909 (mptt) REVERT: E 458 ASP cc_start: 0.7056 (p0) cc_final: 0.6673 (p0) REVERT: E 471 GLU cc_start: 0.6924 (mp0) cc_final: 0.6626 (mp0) REVERT: E 554 LEU cc_start: 0.7830 (mt) cc_final: 0.7469 (mm) REVERT: E 567 ILE cc_start: 0.7230 (mt) cc_final: 0.6803 (mt) REVERT: F 341 GLU cc_start: 0.5681 (mm-30) cc_final: 0.5263 (mm-30) REVERT: F 518 ILE cc_start: 0.8564 (tt) cc_final: 0.8267 (tp) REVERT: G 347 PHE cc_start: 0.7541 (m-80) cc_final: 0.7221 (m-80) REVERT: G 357 LYS cc_start: 0.7924 (mtmm) cc_final: 0.7685 (mtmt) REVERT: G 381 MET cc_start: 0.6389 (mmp) cc_final: 0.6090 (mmp) REVERT: G 392 LYS cc_start: 0.7450 (mttm) cc_final: 0.7126 (ttmm) REVERT: G 440 LEU cc_start: 0.8496 (tp) cc_final: 0.8244 (tp) REVERT: G 593 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7602 (mtmm) REVERT: H 334 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7371 (mtpp) REVERT: H 392 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7459 (ttmm) REVERT: H 414 LYS cc_start: 0.6994 (tmmt) cc_final: 0.6458 (ptmm) REVERT: H 415 GLN cc_start: 0.6142 (tp40) cc_final: 0.5834 (tp40) REVERT: H 437 MET cc_start: 0.4934 (tpp) cc_final: 0.4695 (tpp) REVERT: H 460 ILE cc_start: 0.7761 (mp) cc_final: 0.7467 (mm) REVERT: H 545 GLU cc_start: 0.6462 (mp0) cc_final: 0.5374 (mt-10) REVERT: H 552 LYS cc_start: 0.7551 (tmtt) cc_final: 0.7202 (tptp) REVERT: H 553 GLU cc_start: 0.5741 (tp30) cc_final: 0.5420 (tp30) REVERT: I 357 LYS cc_start: 0.5705 (pttm) cc_final: 0.5234 (pttm) outliers start: 74 outliers final: 42 residues processed: 1000 average time/residue: 0.4469 time to fit residues: 650.0168 Evaluate side-chains 990 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 948 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 552 LYS Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 525 ARG Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 512 GLU Chi-restraints excluded: chain H residue 604 LEU Chi-restraints excluded: chain H residue 611 ASP Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 601 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 31 optimal weight: 30.0000 chunk 135 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 300 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS B 316 HIS B 320 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS D 363 GLN D 385 GLN D 418 ASN D 566 ASN D 603 GLN F 548 GLN H 316 HIS H 425 GLN ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 26184 Z= 0.311 Angle : 0.629 10.392 35244 Z= 0.333 Chirality : 0.046 0.196 3860 Planarity : 0.004 0.058 4540 Dihedral : 10.248 88.025 3706 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.25 % Rotamer: Outliers : 3.48 % Allowed : 18.25 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.13 (0.15), residues: 3096 helix: 0.40 (0.13), residues: 1532 sheet: -0.16 (0.23), residues: 509 loop : 0.02 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 338 HIS 0.017 0.002 HIS E 403 PHE 0.037 0.002 PHE I 556 TYR 0.021 0.002 TYR I 587 ARG 0.010 0.001 ARG G 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 987 time to evaluate : 2.672 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 GLU cc_start: 0.5810 (pt0) cc_final: 0.5513 (pt0) REVERT: A 392 LYS cc_start: 0.7947 (ptpt) cc_final: 0.7681 (ttpp) REVERT: A 401 VAL cc_start: 0.8453 (m) cc_final: 0.8217 (p) REVERT: A 471 GLU cc_start: 0.6099 (mp0) cc_final: 0.5049 (mp0) REVERT: A 512 GLU cc_start: 0.6301 (tp30) cc_final: 0.5594 (tp30) REVERT: A 534 GLU cc_start: 0.6016 (tp30) cc_final: 0.5563 (tp30) REVERT: A 573 ARG cc_start: 0.7397 (ttm110) cc_final: 0.7145 (ttm110) REVERT: B 392 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7961 (ttpt) REVERT: B 411 LYS cc_start: 0.6878 (pttt) cc_final: 0.6638 (pttm) REVERT: B 427 ASP cc_start: 0.6950 (p0) cc_final: 0.6698 (p0) REVERT: B 428 LYS cc_start: 0.7435 (mtpt) cc_final: 0.7121 (mtpp) REVERT: B 458 ASP cc_start: 0.6508 (p0) cc_final: 0.6247 (p0) REVERT: B 524 ARG cc_start: 0.6587 (ptp90) cc_final: 0.6358 (ptp-170) REVERT: B 557 TRP cc_start: 0.6939 (m100) cc_final: 0.6575 (m100) REVERT: C 320 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6589 (mm-40) REVERT: C 363 GLN cc_start: 0.7340 (mm-40) cc_final: 0.6852 (mm110) REVERT: C 522 HIS cc_start: 0.7453 (t70) cc_final: 0.7189 (t-90) REVERT: D 389 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6485 (tp30) REVERT: D 411 LYS cc_start: 0.6782 (ptmt) cc_final: 0.6206 (ptmt) REVERT: D 414 LYS cc_start: 0.8369 (tptm) cc_final: 0.8151 (tptp) REVERT: D 415 GLN cc_start: 0.6706 (mt0) cc_final: 0.6409 (mp10) REVERT: D 511 LYS cc_start: 0.8409 (mttt) cc_final: 0.8178 (mttt) REVERT: D 519 LEU cc_start: 0.8057 (mt) cc_final: 0.7792 (mp) REVERT: D 533 ASN cc_start: 0.7348 (m-40) cc_final: 0.6871 (m-40) REVERT: D 545 GLU cc_start: 0.7128 (pm20) cc_final: 0.6441 (mp0) REVERT: D 555 ASN cc_start: 0.7681 (t0) cc_final: 0.7206 (t0) REVERT: E 340 ASP cc_start: 0.8183 (t0) cc_final: 0.7738 (t0) REVERT: E 368 MET cc_start: 0.7681 (mmm) cc_final: 0.7408 (tpp) REVERT: E 374 LYS cc_start: 0.7614 (tmtt) cc_final: 0.7403 (tmtt) REVERT: E 425 GLN cc_start: 0.7365 (mm-40) cc_final: 0.7096 (mm-40) REVERT: E 428 LYS cc_start: 0.7733 (mmtm) cc_final: 0.7044 (mptt) REVERT: E 471 GLU cc_start: 0.6953 (mp0) cc_final: 0.6692 (mp0) REVERT: E 524 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6679 (ttm-80) REVERT: E 554 LEU cc_start: 0.7935 (mt) cc_final: 0.7581 (mm) REVERT: E 569 LEU cc_start: 0.8199 (tp) cc_final: 0.7984 (tt) REVERT: E 575 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7908 (p) REVERT: F 317 ILE cc_start: 0.8204 (tp) cc_final: 0.7926 (tp) REVERT: F 341 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5657 (mm-30) REVERT: F 425 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7134 (mm110) REVERT: F 580 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.8036 (p) REVERT: F 623 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7670 (m) REVERT: G 381 MET cc_start: 0.6632 (mmp) cc_final: 0.6342 (mmp) REVERT: G 392 LYS cc_start: 0.7563 (mttm) cc_final: 0.7291 (ttmm) REVERT: G 401 VAL cc_start: 0.7858 (m) cc_final: 0.7636 (p) REVERT: G 434 LEU cc_start: 0.6908 (mt) cc_final: 0.6692 (mt) REVERT: G 440 LEU cc_start: 0.8511 (tp) cc_final: 0.8223 (tp) REVERT: G 442 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6625 (m-30) REVERT: G 590 ARG cc_start: 0.6432 (ptp90) cc_final: 0.6184 (mtm110) REVERT: H 334 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7350 (mtpp) REVERT: H 377 ILE cc_start: 0.8300 (mt) cc_final: 0.7973 (mt) REVERT: H 392 LYS cc_start: 0.7672 (mtpt) cc_final: 0.7348 (tttp) REVERT: H 394 ILE cc_start: 0.8275 (pt) cc_final: 0.7901 (mm) REVERT: H 414 LYS cc_start: 0.7091 (tmmt) cc_final: 0.6503 (ptmm) REVERT: H 415 GLN cc_start: 0.6295 (tp40) cc_final: 0.5975 (tp40) REVERT: H 427 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7737 (p0) REVERT: H 437 MET cc_start: 0.5002 (tpp) cc_final: 0.4714 (tpp) REVERT: H 460 ILE cc_start: 0.7965 (mp) cc_final: 0.7641 (mm) REVERT: H 552 LYS cc_start: 0.7697 (tmtt) cc_final: 0.7314 (tptp) outliers start: 95 outliers final: 55 residues processed: 1011 average time/residue: 0.4409 time to fit residues: 648.2219 Evaluate side-chains 1030 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 970 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 512 GLU Chi-restraints excluded: chain H residue 546 LEU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 611 ASP Chi-restraints excluded: chain H residue 617 CYS Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 601 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 0.4980 chunk 170 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 256 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 0 optimal weight: 70.0000 chunk 153 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN B 513 ASN B 584 ASN C 439 GLN ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 GLN D 418 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN E 555 ASN F 522 HIS F 548 GLN ** G 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 HIS ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26184 Z= 0.242 Angle : 0.603 10.282 35244 Z= 0.317 Chirality : 0.044 0.189 3860 Planarity : 0.004 0.050 4540 Dihedral : 9.918 84.712 3706 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 3.77 % Allowed : 19.42 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.28 (0.15), residues: 3096 helix: 0.56 (0.13), residues: 1533 sheet: -0.17 (0.23), residues: 500 loop : 0.07 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 338 HIS 0.019 0.001 HIS A 475 PHE 0.036 0.002 PHE I 556 TYR 0.023 0.002 TYR B 367 ARG 0.007 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 994 time to evaluate : 2.587 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TRP cc_start: 0.6380 (m-10) cc_final: 0.5738 (m-10) REVERT: A 401 VAL cc_start: 0.8446 (m) cc_final: 0.8195 (p) REVERT: A 471 GLU cc_start: 0.5969 (mp0) cc_final: 0.4776 (mp0) REVERT: A 512 GLU cc_start: 0.6162 (tp30) cc_final: 0.5508 (tp30) REVERT: A 515 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6886 (mm) REVERT: A 534 GLU cc_start: 0.5993 (tp30) cc_final: 0.5593 (tp30) REVERT: B 310 GLU cc_start: 0.7458 (mp0) cc_final: 0.7197 (mp0) REVERT: B 392 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7888 (ttpt) REVERT: B 427 ASP cc_start: 0.6865 (p0) cc_final: 0.6639 (p0) REVERT: B 450 LYS cc_start: 0.6591 (mtpt) cc_final: 0.6181 (mtpt) REVERT: B 458 ASP cc_start: 0.6327 (p0) cc_final: 0.6098 (p0) REVERT: B 511 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7659 (mtpt) REVERT: B 534 GLU cc_start: 0.6460 (mp0) cc_final: 0.6212 (mp0) REVERT: B 595 GLU cc_start: 0.6911 (pp20) cc_final: 0.6047 (tm-30) REVERT: C 320 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6584 (mm-40) REVERT: C 363 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7040 (mm-40) REVERT: C 393 PHE cc_start: 0.8538 (m-10) cc_final: 0.8266 (m-10) REVERT: C 437 MET cc_start: 0.7787 (mmt) cc_final: 0.7520 (mmt) REVERT: C 555 ASN cc_start: 0.7696 (t0) cc_final: 0.7441 (t0) REVERT: D 389 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6309 (tp30) REVERT: D 411 LYS cc_start: 0.6773 (ptmt) cc_final: 0.6307 (ptmt) REVERT: D 414 LYS cc_start: 0.8458 (tptm) cc_final: 0.8155 (tttm) REVERT: D 415 GLN cc_start: 0.6683 (mt0) cc_final: 0.6405 (mp10) REVERT: D 533 ASN cc_start: 0.7352 (m-40) cc_final: 0.6615 (m-40) REVERT: D 545 GLU cc_start: 0.7076 (pm20) cc_final: 0.6195 (mp0) REVERT: D 566 ASN cc_start: 0.7842 (t0) cc_final: 0.7477 (t0) REVERT: D 592 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7489 (mt) REVERT: D 598 ARG cc_start: 0.7846 (ptt-90) cc_final: 0.7531 (ptp-170) REVERT: D 599 ARG cc_start: 0.7231 (mmm-85) cc_final: 0.6815 (mmm160) REVERT: D 609 GLU cc_start: 0.6377 (tt0) cc_final: 0.6167 (tt0) REVERT: E 340 ASP cc_start: 0.8193 (t0) cc_final: 0.7389 (t70) REVERT: E 367 TYR cc_start: 0.5762 (OUTLIER) cc_final: 0.5208 (p90) REVERT: E 368 MET cc_start: 0.7701 (mmm) cc_final: 0.7435 (tpp) REVERT: E 425 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7034 (mm110) REVERT: E 428 LYS cc_start: 0.7736 (mmtm) cc_final: 0.7050 (mptt) REVERT: E 471 GLU cc_start: 0.6936 (mp0) cc_final: 0.6676 (mp0) REVERT: E 513 ASN cc_start: 0.7476 (m-40) cc_final: 0.7229 (m-40) REVERT: E 524 ARG cc_start: 0.6980 (ttm-80) cc_final: 0.6722 (ttm-80) REVERT: F 425 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7166 (mm110) REVERT: F 623 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7677 (m) REVERT: G 381 MET cc_start: 0.6585 (mmp) cc_final: 0.6293 (mmp) REVERT: G 392 LYS cc_start: 0.7708 (mttm) cc_final: 0.7373 (ttmm) REVERT: G 440 LEU cc_start: 0.8493 (tp) cc_final: 0.8260 (tp) REVERT: G 590 ARG cc_start: 0.6473 (ptp90) cc_final: 0.5718 (mtm-85) REVERT: G 599 ARG cc_start: 0.7247 (mmm-85) cc_final: 0.7037 (mmm-85) REVERT: H 334 LYS cc_start: 0.7859 (mtpp) cc_final: 0.7369 (mtpp) REVERT: H 377 ILE cc_start: 0.8221 (mt) cc_final: 0.7964 (mt) REVERT: H 392 LYS cc_start: 0.7736 (mtpt) cc_final: 0.7479 (ttmt) REVERT: H 394 ILE cc_start: 0.8233 (pt) cc_final: 0.7876 (mm) REVERT: H 408 GLN cc_start: 0.6318 (pt0) cc_final: 0.6056 (pt0) REVERT: H 414 LYS cc_start: 0.7094 (tmmt) cc_final: 0.6551 (ptmm) REVERT: H 460 ILE cc_start: 0.7964 (mp) cc_final: 0.7633 (mm) REVERT: H 516 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7502 (mtm110) REVERT: H 545 GLU cc_start: 0.6680 (mp0) cc_final: 0.5827 (mt-10) REVERT: H 552 LYS cc_start: 0.7630 (tmtt) cc_final: 0.7281 (tptp) REVERT: I 409 LEU cc_start: 0.6671 (pp) cc_final: 0.6359 (pt) outliers start: 103 outliers final: 72 residues processed: 1027 average time/residue: 0.4743 time to fit residues: 715.0781 Evaluate side-chains 1035 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 959 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 652 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 385 GLN Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 457 LYS Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 534 GLU Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 512 GLU Chi-restraints excluded: chain H residue 532 ILE Chi-restraints excluded: chain H residue 611 ASP Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 548 GLN Chi-restraints excluded: chain I residue 601 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 0.9990 chunk 270 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 300 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN B 548 GLN C 369 HIS ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 ASN D 603 GLN F 522 HIS F 548 GLN ** G 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 369 HIS ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 HIS ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26184 Z= 0.193 Angle : 0.608 10.196 35244 Z= 0.313 Chirality : 0.044 0.355 3860 Planarity : 0.004 0.052 4540 Dihedral : 9.697 87.524 3706 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 3.66 % Allowed : 21.14 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.43 (0.15), residues: 3096 helix: 0.73 (0.13), residues: 1527 sheet: -0.11 (0.23), residues: 507 loop : 0.07 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 557 HIS 0.019 0.001 HIS A 475 PHE 0.040 0.001 PHE I 556 TYR 0.025 0.002 TYR G 367 ARG 0.011 0.000 ARG H 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 980 time to evaluate : 2.667 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TRP cc_start: 0.6411 (m-10) cc_final: 0.6192 (m-10) REVERT: A 362 LYS cc_start: 0.6927 (ttmm) cc_final: 0.6701 (ttmm) REVERT: A 392 LYS cc_start: 0.7660 (ptmm) cc_final: 0.7280 (ttpt) REVERT: A 471 GLU cc_start: 0.5987 (mp0) cc_final: 0.4883 (mp0) REVERT: A 512 GLU cc_start: 0.6058 (tp30) cc_final: 0.5396 (tp30) REVERT: A 515 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6825 (mm) REVERT: A 534 GLU cc_start: 0.5972 (tp30) cc_final: 0.5546 (tp30) REVERT: A 573 ARG cc_start: 0.7350 (ttm110) cc_final: 0.7123 (ttm110) REVERT: B 310 GLU cc_start: 0.7392 (mp0) cc_final: 0.7144 (mp0) REVERT: B 450 LYS cc_start: 0.6553 (mtpt) cc_final: 0.6146 (mtpt) REVERT: B 458 ASP cc_start: 0.6389 (p0) cc_final: 0.6154 (p0) REVERT: B 511 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7675 (mtpt) REVERT: B 534 GLU cc_start: 0.6538 (mp0) cc_final: 0.6236 (mp0) REVERT: C 386 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6300 (mm-30) REVERT: C 458 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6597 (p0) REVERT: C 522 HIS cc_start: 0.7442 (t70) cc_final: 0.7222 (t-90) REVERT: C 555 ASN cc_start: 0.7602 (t0) cc_final: 0.7360 (t0) REVERT: C 610 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7736 (mm-40) REVERT: D 389 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6387 (tp30) REVERT: D 411 LYS cc_start: 0.6790 (ptmt) cc_final: 0.6254 (ptmt) REVERT: D 414 LYS cc_start: 0.8432 (tptm) cc_final: 0.8173 (tttm) REVERT: D 415 GLN cc_start: 0.6668 (mt0) cc_final: 0.6357 (mp10) REVERT: D 511 LYS cc_start: 0.8424 (mttt) cc_final: 0.8069 (mttt) REVERT: D 533 ASN cc_start: 0.6829 (m-40) cc_final: 0.6450 (m-40) REVERT: D 555 ASN cc_start: 0.7652 (t0) cc_final: 0.7086 (t0) REVERT: D 592 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7474 (mt) REVERT: D 599 ARG cc_start: 0.7215 (mmm-85) cc_final: 0.6816 (mmm160) REVERT: E 340 ASP cc_start: 0.8097 (t0) cc_final: 0.7275 (t0) REVERT: E 367 TYR cc_start: 0.5776 (OUTLIER) cc_final: 0.5183 (p90) REVERT: E 368 MET cc_start: 0.7695 (mmm) cc_final: 0.7405 (tpp) REVERT: E 425 GLN cc_start: 0.7255 (mm-40) cc_final: 0.7029 (mm110) REVERT: E 428 LYS cc_start: 0.7682 (mmtm) cc_final: 0.7000 (mptt) REVERT: E 471 GLU cc_start: 0.6885 (mp0) cc_final: 0.6620 (mp0) REVERT: E 511 LYS cc_start: 0.8527 (mttt) cc_final: 0.8284 (mtpp) REVERT: E 513 ASN cc_start: 0.7454 (m-40) cc_final: 0.7225 (m-40) REVERT: E 524 ARG cc_start: 0.6930 (ttm-80) cc_final: 0.6719 (ttm-80) REVERT: F 314 LYS cc_start: 0.7364 (mttp) cc_final: 0.7034 (mttp) REVERT: F 317 ILE cc_start: 0.8142 (tp) cc_final: 0.7729 (tp) REVERT: F 425 GLN cc_start: 0.7389 (mm-40) cc_final: 0.7113 (mm-40) REVERT: F 623 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7675 (m) REVERT: G 392 LYS cc_start: 0.7670 (mttm) cc_final: 0.7340 (ttmm) REVERT: G 418 ASN cc_start: 0.5936 (t0) cc_final: 0.5659 (t0) REVERT: G 427 ASP cc_start: 0.6487 (t0) cc_final: 0.6082 (t0) REVERT: G 440 LEU cc_start: 0.8539 (tp) cc_final: 0.8325 (tp) REVERT: G 445 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6013 (ptt-90) REVERT: H 334 LYS cc_start: 0.7851 (mtpp) cc_final: 0.7545 (mtpp) REVERT: H 414 LYS cc_start: 0.6952 (tmmt) cc_final: 0.6614 (ptmm) REVERT: H 415 GLN cc_start: 0.6246 (tp40) cc_final: 0.6020 (tp40) REVERT: H 424 ASP cc_start: 0.6207 (t70) cc_final: 0.5804 (t70) REVERT: H 516 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7451 (mtm110) REVERT: H 545 GLU cc_start: 0.6726 (mp0) cc_final: 0.5990 (mt-10) REVERT: H 552 LYS cc_start: 0.7594 (tmtt) cc_final: 0.7257 (tptp) REVERT: I 409 LEU cc_start: 0.6856 (pp) cc_final: 0.6536 (pt) outliers start: 100 outliers final: 69 residues processed: 1006 average time/residue: 0.4434 time to fit residues: 646.0569 Evaluate side-chains 1020 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 945 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 374 LYS Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 652 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 385 GLN Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 380 ASP Chi-restraints excluded: chain G residue 425 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 445 ARG Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 535 ILE Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 312 ARG Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 512 GLU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 611 ASP Chi-restraints excluded: chain I residue 381 MET Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 601 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 253 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 138 optimal weight: 0.0570 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS D 418 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN E 555 ASN ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 HIS ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26184 Z= 0.213 Angle : 0.626 10.719 35244 Z= 0.324 Chirality : 0.044 0.283 3860 Planarity : 0.004 0.065 4540 Dihedral : 9.500 88.684 3706 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.25 % Rotamer: Outliers : 3.44 % Allowed : 22.65 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.42 (0.15), residues: 3096 helix: 0.75 (0.13), residues: 1523 sheet: -0.12 (0.23), residues: 501 loop : 0.03 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 557 HIS 0.020 0.001 HIS A 475 PHE 0.042 0.002 PHE I 556 TYR 0.017 0.002 TYR B 367 ARG 0.015 0.001 ARG G 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 982 time to evaluate : 2.819 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TRP cc_start: 0.6357 (m-10) cc_final: 0.6142 (m-10) REVERT: A 362 LYS cc_start: 0.6930 (ttmm) cc_final: 0.6693 (ttmm) REVERT: A 392 LYS cc_start: 0.7791 (ptmm) cc_final: 0.7386 (ttpt) REVERT: A 471 GLU cc_start: 0.6050 (mp0) cc_final: 0.4893 (mp0) REVERT: A 512 GLU cc_start: 0.6032 (tp30) cc_final: 0.5519 (tp30) REVERT: A 515 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6829 (mm) REVERT: A 534 GLU cc_start: 0.5999 (tp30) cc_final: 0.5527 (tp30) REVERT: A 553 GLU cc_start: 0.5054 (pp20) cc_final: 0.4648 (pp20) REVERT: B 392 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7864 (ttpt) REVERT: B 436 ILE cc_start: 0.8047 (tt) cc_final: 0.7845 (tt) REVERT: B 443 GLU cc_start: 0.5542 (pt0) cc_final: 0.5242 (pt0) REVERT: B 450 LYS cc_start: 0.6548 (mtpt) cc_final: 0.6106 (mtpt) REVERT: B 511 LYS cc_start: 0.7922 (ttpt) cc_final: 0.7666 (mtpt) REVERT: B 534 GLU cc_start: 0.6557 (mp0) cc_final: 0.6290 (mp0) REVERT: B 557 TRP cc_start: 0.6738 (m100) cc_final: 0.6447 (m100) REVERT: B 560 ARG cc_start: 0.6413 (ptm160) cc_final: 0.6200 (ptm160) REVERT: C 363 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6776 (mm110) REVERT: C 381 MET cc_start: 0.7251 (mmp) cc_final: 0.6821 (mmp) REVERT: C 389 GLU cc_start: 0.7300 (mp0) cc_final: 0.7036 (mp0) REVERT: C 392 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7610 (mtpp) REVERT: C 437 MET cc_start: 0.7637 (mmt) cc_final: 0.7380 (mmt) REVERT: C 458 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6577 (p0) REVERT: C 522 HIS cc_start: 0.7441 (t70) cc_final: 0.7223 (t-90) REVERT: C 555 ASN cc_start: 0.7633 (t0) cc_final: 0.7400 (t0) REVERT: D 352 SER cc_start: 0.8075 (m) cc_final: 0.7745 (p) REVERT: D 389 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6370 (tp30) REVERT: D 411 LYS cc_start: 0.6805 (ptmt) cc_final: 0.6325 (ptmt) REVERT: D 414 LYS cc_start: 0.8432 (tptm) cc_final: 0.8162 (tttm) REVERT: D 415 GLN cc_start: 0.6666 (mt0) cc_final: 0.6355 (mp10) REVERT: D 425 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7317 (mm-40) REVERT: D 466 ASN cc_start: 0.6903 (m-40) cc_final: 0.6332 (m-40) REVERT: D 533 ASN cc_start: 0.6794 (m-40) cc_final: 0.6456 (m-40) REVERT: D 592 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7465 (mt) REVERT: D 597 GLU cc_start: 0.6053 (tp30) cc_final: 0.5821 (tp30) REVERT: E 340 ASP cc_start: 0.8015 (t0) cc_final: 0.7302 (t0) REVERT: E 367 TYR cc_start: 0.5812 (OUTLIER) cc_final: 0.4968 (p90) REVERT: E 368 MET cc_start: 0.7668 (mmm) cc_final: 0.7303 (tpp) REVERT: E 414 LYS cc_start: 0.7675 (ttpp) cc_final: 0.7356 (tttp) REVERT: E 425 GLN cc_start: 0.7289 (mm-40) cc_final: 0.7048 (mm110) REVERT: E 428 LYS cc_start: 0.7750 (mmtm) cc_final: 0.7103 (mptt) REVERT: E 471 GLU cc_start: 0.6902 (mp0) cc_final: 0.6606 (mp0) REVERT: E 511 LYS cc_start: 0.8538 (mttt) cc_final: 0.8318 (mtpp) REVERT: E 593 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7346 (ttmm) REVERT: E 597 GLU cc_start: 0.6443 (mm-30) cc_final: 0.6222 (tm-30) REVERT: F 317 ILE cc_start: 0.8155 (tp) cc_final: 0.7689 (tp) REVERT: F 425 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7091 (mm-40) REVERT: F 457 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7664 (mttm) REVERT: F 623 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7656 (m) REVERT: G 392 LYS cc_start: 0.7732 (mttm) cc_final: 0.7421 (ttmm) REVERT: G 418 ASN cc_start: 0.6071 (t0) cc_final: 0.5808 (t0) REVERT: G 427 ASP cc_start: 0.6513 (t0) cc_final: 0.6101 (t0) REVERT: G 440 LEU cc_start: 0.8549 (tp) cc_final: 0.8335 (tp) REVERT: H 334 LYS cc_start: 0.7852 (mtpp) cc_final: 0.7535 (mtpp) REVERT: H 414 LYS cc_start: 0.6834 (tmmt) cc_final: 0.6308 (ptmm) REVERT: H 527 GLU cc_start: 0.6432 (pm20) cc_final: 0.6152 (tm-30) REVERT: H 531 ARG cc_start: 0.5511 (tpp-160) cc_final: 0.5222 (tpp-160) REVERT: H 545 GLU cc_start: 0.6657 (mp0) cc_final: 0.5931 (mt-10) REVERT: H 552 LYS cc_start: 0.7566 (tmtt) cc_final: 0.7319 (tptp) outliers start: 94 outliers final: 68 residues processed: 1012 average time/residue: 0.4455 time to fit residues: 653.0762 Evaluate side-chains 1031 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 958 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 374 LYS Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain F residue 597 GLU Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 380 ASP Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 312 ARG Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 512 GLU Chi-restraints excluded: chain H residue 611 ASP Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 601 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN F 548 GLN ** G 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 HIS H 363 GLN H 385 GLN ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26184 Z= 0.347 Angle : 0.704 11.262 35244 Z= 0.370 Chirality : 0.047 0.243 3860 Planarity : 0.005 0.063 4540 Dihedral : 9.721 87.090 3706 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 3.99 % Allowed : 22.98 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.02 (0.15), residues: 3096 helix: 0.43 (0.13), residues: 1530 sheet: -0.25 (0.24), residues: 484 loop : -0.22 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 338 HIS 0.021 0.002 HIS A 475 PHE 0.041 0.002 PHE I 556 TYR 0.021 0.002 TYR D 587 ARG 0.009 0.001 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 987 time to evaluate : 3.098 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TRP cc_start: 0.6766 (m-10) cc_final: 0.6351 (m-10) REVERT: A 392 LYS cc_start: 0.8147 (ptmm) cc_final: 0.7575 (ttpt) REVERT: A 471 GLU cc_start: 0.6428 (mp0) cc_final: 0.5769 (mp0) REVERT: A 512 GLU cc_start: 0.6015 (tp30) cc_final: 0.5550 (tp30) REVERT: A 534 GLU cc_start: 0.6110 (tp30) cc_final: 0.5655 (tp30) REVERT: B 309 LEU cc_start: 0.7482 (tt) cc_final: 0.7211 (tt) REVERT: B 339 TYR cc_start: 0.6284 (t80) cc_final: 0.6013 (t80) REVERT: B 383 GLU cc_start: 0.6983 (pm20) cc_final: 0.6662 (pm20) REVERT: B 386 GLU cc_start: 0.6452 (mp0) cc_final: 0.6185 (mp0) REVERT: B 411 LYS cc_start: 0.6737 (pttt) cc_final: 0.6467 (pttm) REVERT: B 412 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8176 (mttp) REVERT: B 436 ILE cc_start: 0.8119 (tt) cc_final: 0.7911 (tt) REVERT: B 534 GLU cc_start: 0.6616 (mp0) cc_final: 0.6278 (mp0) REVERT: B 583 TYR cc_start: 0.7380 (t80) cc_final: 0.7164 (t80) REVERT: C 363 GLN cc_start: 0.7290 (mm-40) cc_final: 0.7001 (mm-40) REVERT: C 381 MET cc_start: 0.7391 (mmp) cc_final: 0.7155 (mmp) REVERT: C 437 MET cc_start: 0.7644 (mmt) cc_final: 0.7271 (mmt) REVERT: C 563 GLN cc_start: 0.6582 (tp40) cc_final: 0.6310 (tp40) REVERT: D 340 ASP cc_start: 0.7491 (t0) cc_final: 0.7186 (t0) REVERT: D 352 SER cc_start: 0.8092 (m) cc_final: 0.7212 (p) REVERT: D 355 ILE cc_start: 0.7816 (mm) cc_final: 0.7469 (mt) REVERT: D 389 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6722 (mm-30) REVERT: D 400 TYR cc_start: 0.8332 (m-80) cc_final: 0.8021 (m-80) REVERT: D 411 LYS cc_start: 0.6801 (ptmt) cc_final: 0.6265 (ptmt) REVERT: D 415 GLN cc_start: 0.6776 (mt0) cc_final: 0.6473 (mp10) REVERT: D 526 ASP cc_start: 0.5505 (p0) cc_final: 0.5232 (p0) REVERT: D 533 ASN cc_start: 0.6908 (m-40) cc_final: 0.6481 (m-40) REVERT: D 555 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7244 (t0) REVERT: D 592 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7549 (mt) REVERT: E 340 ASP cc_start: 0.8164 (t0) cc_final: 0.7439 (t70) REVERT: E 367 TYR cc_start: 0.5951 (OUTLIER) cc_final: 0.5548 (p90) REVERT: E 458 ASP cc_start: 0.7190 (p0) cc_final: 0.6989 (p0) REVERT: E 471 GLU cc_start: 0.6932 (mp0) cc_final: 0.6647 (mp0) REVERT: E 552 LYS cc_start: 0.8225 (tttp) cc_final: 0.7976 (tptm) REVERT: F 425 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7173 (mm-40) REVERT: F 623 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7658 (m) REVERT: G 333 ARG cc_start: 0.5970 (tpm170) cc_final: 0.5681 (ttm110) REVERT: G 427 ASP cc_start: 0.6622 (t0) cc_final: 0.6288 (t0) REVERT: G 440 LEU cc_start: 0.8518 (tp) cc_final: 0.8272 (tp) REVERT: G 599 ARG cc_start: 0.7128 (mmm-85) cc_final: 0.6822 (mmm-85) REVERT: H 313 LEU cc_start: 0.7715 (tt) cc_final: 0.7479 (tp) REVERT: H 334 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7639 (mtpp) REVERT: H 414 LYS cc_start: 0.6951 (tmmt) cc_final: 0.6458 (ptmm) REVERT: H 545 GLU cc_start: 0.6885 (mp0) cc_final: 0.5975 (mt-10) REVERT: H 552 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7484 (tptp) outliers start: 109 outliers final: 81 residues processed: 1016 average time/residue: 0.4409 time to fit residues: 654.9729 Evaluate side-chains 1060 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 975 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 555 ASN Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain F residue 316 HIS Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 511 LYS Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain F residue 548 GLN Chi-restraints excluded: chain F residue 597 GLU Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 380 ASP Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 425 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 312 ARG Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 512 GLU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 611 ASP Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 601 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 20.0000 chunk 262 optimal weight: 0.7980 chunk 279 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 252 optimal weight: 0.1980 chunk 264 optimal weight: 0.8980 chunk 278 optimal weight: 5.9990 chunk 183 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN D 418 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 ASN D 602 ASN D 603 GLN D 610 GLN F 408 GLN F 548 GLN ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 HIS ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26184 Z= 0.205 Angle : 0.663 11.864 35244 Z= 0.344 Chirality : 0.044 0.212 3860 Planarity : 0.004 0.082 4540 Dihedral : 9.452 86.506 3706 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 2.86 % Allowed : 25.03 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.27 (0.15), residues: 3096 helix: 0.63 (0.13), residues: 1525 sheet: -0.20 (0.24), residues: 499 loop : -0.05 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 557 HIS 0.022 0.001 HIS A 475 PHE 0.042 0.002 PHE I 556 TYR 0.029 0.002 TYR B 367 ARG 0.014 0.001 ARG G 445 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 955 time to evaluate : 2.879 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TRP cc_start: 0.6709 (m-10) cc_final: 0.6382 (m100) REVERT: A 392 LYS cc_start: 0.7955 (ptmm) cc_final: 0.7341 (ttpt) REVERT: A 512 GLU cc_start: 0.5979 (tp30) cc_final: 0.5596 (tp30) REVERT: A 534 GLU cc_start: 0.5921 (tp30) cc_final: 0.5493 (tp30) REVERT: B 339 TYR cc_start: 0.6193 (t80) cc_final: 0.5935 (t80) REVERT: B 411 LYS cc_start: 0.6662 (pttt) cc_final: 0.6427 (pttm) REVERT: B 450 LYS cc_start: 0.6655 (mtpt) cc_final: 0.6364 (mttt) REVERT: B 531 ARG cc_start: 0.7762 (mtt90) cc_final: 0.7535 (mmt-90) REVERT: B 534 GLU cc_start: 0.6498 (mp0) cc_final: 0.6261 (mp0) REVERT: B 587 TYR cc_start: 0.7878 (m-80) cc_final: 0.7645 (m-80) REVERT: B 590 ARG cc_start: 0.7848 (mtt90) cc_final: 0.7585 (mtt90) REVERT: B 608 TYR cc_start: 0.6596 (t80) cc_final: 0.6346 (t80) REVERT: C 363 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6761 (mm-40) REVERT: C 374 LYS cc_start: 0.7163 (ttmm) cc_final: 0.6671 (mtpp) REVERT: C 381 MET cc_start: 0.7341 (mmp) cc_final: 0.6944 (mmt) REVERT: C 458 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6553 (p0) REVERT: C 479 LEU cc_start: 0.8032 (mt) cc_final: 0.7638 (tp) REVERT: C 555 ASN cc_start: 0.7636 (t0) cc_final: 0.7395 (t0) REVERT: D 352 SER cc_start: 0.7946 (m) cc_final: 0.7679 (p) REVERT: D 411 LYS cc_start: 0.6732 (ptmt) cc_final: 0.6229 (ptmt) REVERT: D 415 GLN cc_start: 0.6716 (mt0) cc_final: 0.6442 (mp10) REVERT: D 526 ASP cc_start: 0.5292 (p0) cc_final: 0.5069 (p0) REVERT: D 533 ASN cc_start: 0.6742 (m-40) cc_final: 0.6370 (m-40) REVERT: D 592 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7487 (mt) REVERT: D 598 ARG cc_start: 0.7658 (ptt-90) cc_final: 0.7375 (ptp-170) REVERT: E 312 ARG cc_start: 0.6408 (tpt170) cc_final: 0.6010 (tpt170) REVERT: E 340 ASP cc_start: 0.8055 (t0) cc_final: 0.7392 (t0) REVERT: E 367 TYR cc_start: 0.5899 (OUTLIER) cc_final: 0.5450 (p90) REVERT: E 456 CYS cc_start: 0.7674 (m) cc_final: 0.7411 (p) REVERT: E 471 GLU cc_start: 0.6740 (mp0) cc_final: 0.6460 (mp0) REVERT: E 552 LYS cc_start: 0.8200 (tttp) cc_final: 0.7905 (tptm) REVERT: E 597 GLU cc_start: 0.6605 (tm-30) cc_final: 0.6213 (tm-30) REVERT: F 425 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7165 (mm110) REVERT: F 511 LYS cc_start: 0.7910 (ttmm) cc_final: 0.7632 (mttm) REVERT: F 531 ARG cc_start: 0.7235 (mtt-85) cc_final: 0.7022 (mtt90) REVERT: F 623 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7656 (m) REVERT: G 427 ASP cc_start: 0.6508 (t0) cc_final: 0.6292 (t0) REVERT: G 599 ARG cc_start: 0.7022 (mmm-85) cc_final: 0.6756 (mmm-85) REVERT: H 334 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7505 (mtpp) REVERT: H 414 LYS cc_start: 0.6932 (tmmt) cc_final: 0.6169 (pttp) REVERT: H 545 GLU cc_start: 0.6673 (mp0) cc_final: 0.6011 (mt-10) REVERT: H 552 LYS cc_start: 0.7720 (tmtt) cc_final: 0.7343 (tptp) outliers start: 78 outliers final: 59 residues processed: 979 average time/residue: 0.4619 time to fit residues: 657.9555 Evaluate side-chains 1015 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 952 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 610 GLN Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 652 ILE Chi-restraints excluded: chain F residue 316 HIS Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain F residue 548 GLN Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 597 GLU Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 380 ASP Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 312 ARG Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 190 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 GLN D 316 HIS ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 HIS E 408 GLN ** F 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 GLN ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.267 26184 Z= 0.364 Angle : 0.799 65.900 35244 Z= 0.427 Chirality : 0.045 0.528 3860 Planarity : 0.006 0.180 4540 Dihedral : 9.446 86.629 3706 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 2.89 % Allowed : 25.25 % Favored : 71.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.28 (0.15), residues: 3096 helix: 0.64 (0.13), residues: 1525 sheet: -0.19 (0.24), residues: 499 loop : -0.05 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 338 HIS 0.018 0.001 HIS A 475 PHE 0.041 0.002 PHE I 556 TYR 0.034 0.002 TYR D 367 ARG 0.068 0.001 ARG F 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 955 time to evaluate : 3.029 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TRP cc_start: 0.6687 (m-10) cc_final: 0.6384 (m100) REVERT: A 392 LYS cc_start: 0.7937 (ptmm) cc_final: 0.7342 (ttpt) REVERT: A 471 GLU cc_start: 0.6068 (mp0) cc_final: 0.4935 (mp0) REVERT: A 512 GLU cc_start: 0.5995 (tp30) cc_final: 0.5606 (tp30) REVERT: A 520 LYS cc_start: 0.7379 (tptt) cc_final: 0.7153 (tptt) REVERT: A 534 GLU cc_start: 0.5906 (tp30) cc_final: 0.5493 (tp30) REVERT: B 339 TYR cc_start: 0.6225 (t80) cc_final: 0.5935 (t80) REVERT: B 411 LYS cc_start: 0.6708 (pttt) cc_final: 0.6433 (pttm) REVERT: B 450 LYS cc_start: 0.6632 (mtpt) cc_final: 0.6392 (mttt) REVERT: B 534 GLU cc_start: 0.6518 (mp0) cc_final: 0.6283 (mp0) REVERT: B 587 TYR cc_start: 0.7889 (m-80) cc_final: 0.7639 (m-80) REVERT: B 608 TYR cc_start: 0.6615 (t80) cc_final: 0.6352 (t80) REVERT: C 363 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6770 (mm-40) REVERT: C 374 LYS cc_start: 0.7213 (ttmm) cc_final: 0.6868 (mtpp) REVERT: C 381 MET cc_start: 0.7302 (mmp) cc_final: 0.6934 (mmt) REVERT: C 458 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6563 (p0) REVERT: C 479 LEU cc_start: 0.8028 (mt) cc_final: 0.7651 (tp) REVERT: C 555 ASN cc_start: 0.7652 (t0) cc_final: 0.7394 (t0) REVERT: D 352 SER cc_start: 0.7984 (m) cc_final: 0.7692 (p) REVERT: D 411 LYS cc_start: 0.6756 (ptmt) cc_final: 0.6304 (ptmt) REVERT: D 414 LYS cc_start: 0.8413 (tptm) cc_final: 0.8186 (tttm) REVERT: D 415 GLN cc_start: 0.6735 (mt0) cc_final: 0.6465 (mp10) REVERT: D 526 ASP cc_start: 0.5311 (p0) cc_final: 0.5092 (p0) REVERT: D 533 ASN cc_start: 0.6791 (m-40) cc_final: 0.6397 (m-40) REVERT: D 592 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7494 (mt) REVERT: D 598 ARG cc_start: 0.7719 (ptt-90) cc_final: 0.7396 (ptp-170) REVERT: D 610 GLN cc_start: 0.7542 (mp-120) cc_final: 0.7274 (tt0) REVERT: E 312 ARG cc_start: 0.6431 (tpt170) cc_final: 0.6006 (tpt170) REVERT: E 340 ASP cc_start: 0.8170 (t0) cc_final: 0.7413 (t0) REVERT: E 367 TYR cc_start: 0.5871 (OUTLIER) cc_final: 0.5468 (p90) REVERT: E 456 CYS cc_start: 0.7728 (m) cc_final: 0.7408 (p) REVERT: E 471 GLU cc_start: 0.6738 (mp0) cc_final: 0.6474 (mp0) REVERT: E 552 LYS cc_start: 0.8218 (tttp) cc_final: 0.7918 (tptm) REVERT: F 425 GLN cc_start: 0.7407 (mm-40) cc_final: 0.7192 (mm110) REVERT: F 511 LYS cc_start: 0.7923 (ttmm) cc_final: 0.7631 (mttm) REVERT: F 603 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7418 (mm110) REVERT: F 623 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7665 (m) REVERT: G 427 ASP cc_start: 0.6508 (t0) cc_final: 0.6273 (t0) REVERT: G 599 ARG cc_start: 0.7033 (mmm-85) cc_final: 0.6755 (mmm-85) REVERT: H 334 LYS cc_start: 0.7757 (mtpp) cc_final: 0.7524 (mtpp) REVERT: H 552 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7346 (tptp) REVERT: I 548 GLN cc_start: 0.7210 (pm20) cc_final: 0.6551 (pm20) outliers start: 79 outliers final: 69 residues processed: 976 average time/residue: 0.4486 time to fit residues: 635.6867 Evaluate side-chains 1024 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 951 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 565 HIS Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 478 GLN Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 652 ILE Chi-restraints excluded: chain F residue 316 HIS Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain F residue 548 GLN Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 597 GLU Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 380 ASP Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 425 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 312 ARG Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 380 ASP Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 548 GLN Chi-restraints excluded: chain H residue 653 ILE Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 227 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 253 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN D 610 GLN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 GLN ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 GLN ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.164392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133172 restraints weight = 46169.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137330 restraints weight = 21569.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140013 restraints weight = 12782.715| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.188 26184 Z= 0.370 Angle : 0.896 59.198 35244 Z= 0.507 Chirality : 0.049 0.757 3860 Planarity : 0.006 0.160 4540 Dihedral : 9.487 86.637 3706 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.35 % Rotamer: Outliers : 3.08 % Allowed : 24.84 % Favored : 72.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.24 (0.15), residues: 3096 helix: 0.59 (0.13), residues: 1523 sheet: -0.19 (0.24), residues: 499 loop : -0.05 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 338 HIS 0.020 0.001 HIS A 475 PHE 0.042 0.002 PHE I 556 TYR 0.029 0.002 TYR G 608 ARG 0.040 0.001 ARG G 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9438.03 seconds wall clock time: 166 minutes 0.12 seconds (9960.12 seconds total)