Starting phenix.real_space_refine on Fri Aug 9 09:36:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/08_2024/7xbk_33104.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/08_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_33104/08_2024/7xbk_33104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/08_2024/7xbk_33104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/08_2024/7xbk_33104.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/08_2024/7xbk_33104.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-5409/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: 13.02, per 1000 atoms: 0.51 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: 8.96 Conformation dependent library (CDL) restraints added in 4.1 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: 2.84 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: 8.36 Time building geometry restraints manager: 9.80 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 Time spend for trying shortcut: 0.00 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: 1.340 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: 0.050 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 62.000 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.160 ------------------------------------------------------------------------------- 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 : 2.784 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: 0.4625 time to fit residues: 720.9030 Evaluate side-chains 965 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 965 time to evaluate : 2.389 ------------------------------------------------------------------------------- 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: 0.8980 chunk 235 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 chunk 125 optimal weight: 0.0060 chunk 243 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 181 optimal weight: 0.0770 chunk 282 optimal weight: 7.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- 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 D 369 HIS D 418 ASN D 430 HIS D 594 HIS D 603 GLN ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 GLN E 439 GLN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 ASN G 320 GLN H 586 HIS H 594 HIS I 316 HIS I 466 ASN I 475 HIS ** I 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26184 Z= 0.204 Angle : 0.598 9.798 35244 Z= 0.316 Chirality : 0.043 0.203 3860 Planarity : 0.005 0.076 4540 Dihedral : 10.776 89.899 3706 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % Rotamer: Outliers : 1.72 % Allowed : 12.90 % Favored : 85.38 % 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: -0.44 (0.14), residues: 3096 helix: -0.25 (0.13), residues: 1537 sheet: 0.01 (0.23), residues: 494 loop : -0.20 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 571 HIS 0.009 0.001 HIS H 430 PHE 0.041 0.002 PHE I 556 TYR 0.019 0.002 TYR G 339 ARG 0.008 0.001 ARG I 560 *********************** 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 1048 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1001 time to evaluate : 2.794 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 333 ARG cc_start: 0.5863 (mtm110) cc_final: 0.5600 (ttm110) REVERT: A 383 GLU cc_start: 0.5181 (mt-10) cc_final: 0.4924 (mt-10) REVERT: A 392 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7437 (ttpt) REVERT: A 401 VAL cc_start: 0.8432 (m) cc_final: 0.8187 (p) REVERT: A 479 LEU cc_start: 0.7617 (mt) cc_final: 0.7168 (mt) REVERT: A 512 GLU cc_start: 0.6241 (tp30) cc_final: 0.5591 (tp30) REVERT: A 529 LEU cc_start: 0.7307 (mt) cc_final: 0.7056 (mt) REVERT: A 534 GLU cc_start: 0.5787 (tp30) cc_final: 0.5291 (tp30) REVERT: B 346 VAL cc_start: 0.7877 (m) cc_final: 0.7485 (p) REVERT: B 389 GLU cc_start: 0.5960 (mp0) cc_final: 0.5360 (tp30) REVERT: B 392 LYS cc_start: 0.8025 (ttmm) cc_final: 0.6897 (ttpt) REVERT: B 404 GLU cc_start: 0.6854 (mp0) cc_final: 0.6614 (pm20) REVERT: B 408 GLN cc_start: 0.7174 (mp10) cc_final: 0.6947 (mp10) REVERT: B 427 ASP cc_start: 0.6917 (p0) cc_final: 0.6496 (p0) REVERT: B 445 ARG cc_start: 0.7885 (tmm-80) cc_final: 0.7587 (ttp80) REVERT: B 557 TRP cc_start: 0.6743 (m100) cc_final: 0.6104 (m100) REVERT: B 590 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7853 (mtt180) REVERT: B 599 ARG cc_start: 0.7231 (tpp-160) cc_final: 0.6945 (tpp80) REVERT: B 608 TYR cc_start: 0.6686 (t80) cc_final: 0.6191 (t80) REVERT: C 363 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6762 (mm-40) REVERT: C 374 LYS cc_start: 0.7019 (ttmm) cc_final: 0.6689 (mtpp) REVERT: C 522 HIS cc_start: 0.7309 (t70) cc_final: 0.6985 (t-90) REVERT: C 595 GLU cc_start: 0.5839 (tm-30) cc_final: 0.5564 (tm-30) REVERT: D 314 LYS cc_start: 0.7378 (ttpt) cc_final: 0.7155 (ttpt) REVERT: D 315 GLU cc_start: 0.6123 (tm-30) cc_final: 0.5639 (tm-30) REVERT: D 317 ILE cc_start: 0.7903 (tt) cc_final: 0.7656 (tt) REVERT: D 355 ILE cc_start: 0.8032 (mm) cc_final: 0.7819 (mm) REVERT: D 411 LYS cc_start: 0.6990 (ptmt) cc_final: 0.6562 (ptmt) REVERT: D 412 LYS cc_start: 0.8177 (mttp) cc_final: 0.7781 (mttm) REVERT: D 427 ASP cc_start: 0.7125 (t70) cc_final: 0.6667 (t0) REVERT: D 432 ASP cc_start: 0.6926 (m-30) cc_final: 0.6591 (m-30) REVERT: D 467 VAL cc_start: 0.8334 (t) cc_final: 0.8005 (t) REVERT: D 511 LYS cc_start: 0.8318 (mttt) cc_final: 0.7987 (mttt) REVERT: D 522 HIS cc_start: 0.7509 (t-90) cc_final: 0.7230 (t-90) REVERT: D 533 ASN cc_start: 0.6898 (m-40) cc_final: 0.6497 (m-40) REVERT: D 537 TYR cc_start: 0.6983 (m-80) cc_final: 0.6761 (m-80) REVERT: D 539 LEU cc_start: 0.7737 (mt) cc_final: 0.7499 (mt) REVERT: D 546 LEU cc_start: 0.7408 (mt) cc_final: 0.7145 (mt) REVERT: D 555 ASN cc_start: 0.7513 (t0) cc_final: 0.7101 (t0) REVERT: D 587 TYR cc_start: 0.7179 (m-80) cc_final: 0.6968 (m-80) REVERT: E 340 ASP cc_start: 0.7664 (t0) cc_final: 0.7361 (t0) REVERT: E 380 ASP cc_start: 0.7128 (t70) cc_final: 0.6702 (t0) REVERT: E 385 GLN cc_start: 0.7896 (mt0) cc_final: 0.7496 (mt0) REVERT: E 390 VAL cc_start: 0.7814 (t) cc_final: 0.7568 (p) REVERT: E 428 LYS cc_start: 0.7455 (mmtm) cc_final: 0.6942 (mptt) REVERT: E 471 GLU cc_start: 0.6782 (mp0) cc_final: 0.6511 (mp0) REVERT: E 554 LEU cc_start: 0.7778 (mt) cc_final: 0.7484 (mm) REVERT: E 602 ASN cc_start: 0.7064 (m-40) cc_final: 0.6795 (m-40) REVERT: E 604 LEU cc_start: 0.8143 (mt) cc_final: 0.7936 (tp) REVERT: F 341 GLU cc_start: 0.5655 (mm-30) cc_final: 0.5373 (mm-30) REVERT: F 363 GLN cc_start: 0.7648 (mm110) cc_final: 0.7379 (mm-40) REVERT: F 366 LYS cc_start: 0.7178 (mtmt) cc_final: 0.6926 (mtmt) REVERT: F 389 GLU cc_start: 0.6216 (mm-30) cc_final: 0.5879 (mm-30) REVERT: F 437 MET cc_start: 0.6111 (mmp) cc_final: 0.5886 (mmp) REVERT: F 438 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7791 (tt) REVERT: F 448 ASP cc_start: 0.5999 (m-30) cc_final: 0.5770 (m-30) REVERT: F 559 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7526 (ttmt) REVERT: F 594 HIS cc_start: 0.7215 (m90) cc_final: 0.6896 (m90) REVERT: G 347 PHE cc_start: 0.7680 (m-80) cc_final: 0.7091 (m-80) REVERT: G 369 HIS cc_start: 0.6060 (m-70) cc_final: 0.5832 (m-70) REVERT: G 381 MET cc_start: 0.6168 (mmp) cc_final: 0.5878 (mmp) REVERT: G 392 LYS cc_start: 0.7460 (mttm) cc_final: 0.7165 (ttmm) REVERT: G 414 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7325 (ttmm) REVERT: G 440 LEU cc_start: 0.8447 (tp) cc_final: 0.8218 (tp) REVERT: G 531 ARG cc_start: 0.7144 (mtt90) cc_final: 0.6733 (tpp-160) REVERT: G 590 ARG cc_start: 0.6348 (ptp90) cc_final: 0.5994 (mtm-85) REVERT: G 599 ARG cc_start: 0.6963 (tpp80) cc_final: 0.6739 (mmm-85) REVERT: H 334 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7495 (mtpp) REVERT: H 343 HIS cc_start: 0.6799 (m90) cc_final: 0.6510 (m90) REVERT: H 363 GLN cc_start: 0.6634 (mm-40) cc_final: 0.6374 (mm-40) REVERT: H 392 LYS cc_start: 0.7683 (mtpt) cc_final: 0.7402 (ttmm) REVERT: H 414 LYS cc_start: 0.6867 (tmmt) cc_final: 0.6331 (ptmm) REVERT: H 415 GLN cc_start: 0.6323 (tp40) cc_final: 0.5893 (tp40) REVERT: H 552 LYS cc_start: 0.7578 (tmtt) cc_final: 0.7150 (tptp) outliers start: 47 outliers final: 20 residues processed: 1011 average time/residue: 0.3772 time to fit residues: 551.2415 Evaluate side-chains 963 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 942 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 648 LEU Chi-restraints excluded: chain E residue 652 ILE Chi-restraints excluded: chain F residue 438 LEU 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 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: 0.9990 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 0.0870 chunk 305 optimal weight: 8.9990 chunk 251 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS A 548 GLN B 408 GLN B 513 ASN B 522 HIS C 466 ASN D 466 ASN D 603 GLN E 316 HIS ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 555 ASN ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 GLN F 584 ASN G 320 GLN ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 594 HIS H 363 GLN ** H 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 369 HIS ** I 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 26184 Z= 0.291 Angle : 0.618 9.991 35244 Z= 0.332 Chirality : 0.045 0.206 3860 Planarity : 0.005 0.062 4540 Dihedral : 10.300 89.869 3706 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 2.38 % Allowed : 16.53 % Favored : 81.09 % 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: -0.06 (0.15), residues: 3096 helix: 0.20 (0.13), residues: 1531 sheet: -0.22 (0.23), residues: 514 loop : -0.01 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 338 HIS 0.012 0.001 HIS A 475 PHE 0.039 0.002 PHE I 556 TYR 0.019 0.002 TYR B 587 ARG 0.009 0.001 ARG G 445 *********************** 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 1063 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 998 time to evaluate : 3.311 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: A 333 ARG cc_start: 0.6089 (mtm110) cc_final: 0.5881 (ttm110) REVERT: A 340 ASP cc_start: 0.6894 (t0) cc_final: 0.6677 (t0) REVERT: A 392 LYS cc_start: 0.7845 (ptpt) cc_final: 0.7472 (ttpt) REVERT: A 401 VAL cc_start: 0.8521 (m) cc_final: 0.8219 (p) REVERT: A 479 LEU cc_start: 0.7601 (mt) cc_final: 0.7359 (mt) REVERT: A 512 GLU cc_start: 0.6396 (tp30) cc_final: 0.5632 (tp30) REVERT: A 529 LEU cc_start: 0.7513 (mt) cc_final: 0.7294 (mt) REVERT: A 534 GLU cc_start: 0.5973 (tp30) cc_final: 0.5597 (tp30) REVERT: A 553 GLU cc_start: 0.5180 (pp20) cc_final: 0.4882 (pp20) REVERT: B 316 HIS cc_start: 0.6793 (t-90) cc_final: 0.6526 (t70) REVERT: B 383 GLU cc_start: 0.5894 (mt-10) cc_final: 0.5548 (mt-10) REVERT: B 389 GLU cc_start: 0.6302 (mp0) cc_final: 0.5588 (mm-30) REVERT: B 392 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7893 (ttpt) REVERT: B 428 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7059 (mtpp) REVERT: B 443 GLU cc_start: 0.5572 (pt0) cc_final: 0.5371 (pt0) REVERT: B 458 ASP cc_start: 0.6576 (p0) cc_final: 0.6317 (p0) REVERT: C 363 GLN cc_start: 0.7330 (mm-40) cc_final: 0.7046 (mm110) REVERT: C 539 LEU cc_start: 0.8354 (mm) cc_final: 0.8017 (mp) REVERT: C 594 HIS cc_start: 0.5456 (p90) cc_final: 0.4969 (p90) REVERT: C 595 GLU cc_start: 0.6133 (tm-30) cc_final: 0.5739 (tm-30) REVERT: D 314 LYS cc_start: 0.7395 (ttpt) cc_final: 0.7191 (ttpt) REVERT: D 315 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6198 (tm-30) REVERT: D 317 ILE cc_start: 0.7993 (tt) cc_final: 0.7762 (tt) REVERT: D 380 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6580 (m-30) REVERT: D 411 LYS cc_start: 0.6803 (ptmt) cc_final: 0.6136 (ptmt) REVERT: D 415 GLN cc_start: 0.6699 (mt0) cc_final: 0.6388 (mp10) REVERT: D 533 ASN cc_start: 0.7233 (m-40) cc_final: 0.6787 (m-40) REVERT: D 539 LEU cc_start: 0.7877 (mt) cc_final: 0.7537 (mt) REVERT: D 542 CYS cc_start: 0.6692 (p) cc_final: 0.6488 (p) REVERT: D 555 ASN cc_start: 0.7571 (t0) cc_final: 0.7164 (t0) REVERT: E 340 ASP cc_start: 0.7957 (t0) cc_final: 0.7582 (t0) REVERT: E 428 LYS cc_start: 0.7775 (mmtm) cc_final: 0.7149 (mptt) REVERT: E 471 GLU cc_start: 0.6953 (mp0) cc_final: 0.6641 (mp0) REVERT: E 524 ARG cc_start: 0.7060 (ttm-80) cc_final: 0.6859 (ttm-80) REVERT: E 554 LEU cc_start: 0.7869 (mt) cc_final: 0.7593 (mm) REVERT: E 569 LEU cc_start: 0.8110 (tp) cc_final: 0.7892 (tt) REVERT: E 602 ASN cc_start: 0.7256 (m-40) cc_final: 0.7033 (m-40) REVERT: F 341 GLU cc_start: 0.5981 (mm-30) cc_final: 0.5651 (mm-30) REVERT: F 358 THR cc_start: 0.7680 (m) cc_final: 0.7468 (m) REVERT: F 359 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5920 (mp0) REVERT: F 363 GLN cc_start: 0.7720 (mm110) cc_final: 0.7356 (mm-40) REVERT: F 389 GLU cc_start: 0.6310 (mm-30) cc_final: 0.6081 (mm-30) REVERT: F 443 GLU cc_start: 0.5373 (tt0) cc_final: 0.4827 (tt0) REVERT: F 450 LYS cc_start: 0.7461 (mttp) cc_final: 0.7246 (mttp) REVERT: F 531 ARG cc_start: 0.7502 (mtt90) cc_final: 0.7024 (mtt-85) REVERT: F 559 LYS cc_start: 0.7733 (ttmm) cc_final: 0.7521 (ttmt) REVERT: G 381 MET cc_start: 0.6365 (mmp) cc_final: 0.6110 (mmp) REVERT: G 392 LYS cc_start: 0.7560 (mttm) cc_final: 0.7355 (ttmm) REVERT: G 440 LEU cc_start: 0.8491 (tp) cc_final: 0.8200 (tp) REVERT: G 590 ARG cc_start: 0.6460 (ptp90) cc_final: 0.6191 (mtm110) REVERT: H 318 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6625 (pt) REVERT: H 327 VAL cc_start: 0.8037 (t) cc_final: 0.7723 (p) REVERT: H 334 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7559 (mtpp) REVERT: H 378 ARG cc_start: 0.7219 (ttt180) cc_final: 0.6930 (ttt180) REVERT: H 394 ILE cc_start: 0.8223 (pt) cc_final: 0.7947 (mm) REVERT: H 414 LYS cc_start: 0.7086 (tmmt) cc_final: 0.6527 (ptmm) REVERT: H 415 GLN cc_start: 0.6226 (tp40) cc_final: 0.5922 (tp40) REVERT: H 428 LYS cc_start: 0.7663 (mptt) cc_final: 0.7307 (mmtm) REVERT: H 516 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7580 (mtm110) REVERT: H 552 LYS cc_start: 0.7616 (tmtt) cc_final: 0.7281 (tptp) REVERT: I 560 ARG cc_start: 0.6599 (ptm160) cc_final: 0.6327 (mtp-110) outliers start: 65 outliers final: 37 residues processed: 1017 average time/residue: 0.4512 time to fit residues: 667.3684 Evaluate side-chains 1013 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 973 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 565 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 542 CYS 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 D residue 580 VAL Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 322 SER 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 533 ASN Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 652 ILE Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 460 ILE 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 318 ILE Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 512 GLU Chi-restraints excluded: chain I residue 364 THR 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: 0.0040 chunk 212 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 135 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 300 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 269 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: