Starting phenix.real_space_refine on Wed Mar 20 00:25:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/03_2024/7xbk_33104_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/03_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_33104/03_2024/7xbk_33104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/03_2024/7xbk_33104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/03_2024/7xbk_33104_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/03_2024/7xbk_33104_updated.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.38, 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: 10.21 Conformation dependent library (CDL) restraints added in 4.4 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... running ksdssp... Secondary structure from input PDB file: 142 helices and 25 sheets defined 47.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 321 through 336 Processing helix chain 'A' and resid 357 through 368 Processing helix chain 'A' and resid 387 through 394 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) No H-bonds generated for 'chain 'A' and resid 387 through 394' Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 431 through 443 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 469 through 492 Processing helix chain 'A' and resid 508 through 523 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 526 through 530 Processing helix chain 'A' and resid 543 through 565 removed outlier: 4.052A pdb=" N TRP A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 588 through 609 removed outlier: 3.573A pdb=" N SER A 591 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 600 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL A 601 " --> pdb=" O ARG A 598 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 609 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 631 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 306 Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 321 through 335 Processing helix chain 'B' and resid 357 through 368 Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 431 through 443 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 469 through 492 Processing helix chain 'B' and resid 508 through 513 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 543 through 564 Processing helix chain 'B' and resid 573 through 581 Processing helix chain 'B' and resid 589 through 599 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 601 through 606 Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'C' and resid 300 through 306 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 387 through 394 removed outlier: 3.604A pdb=" N VAL C 390 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 415 Processing helix chain 'C' and resid 434 through 442 removed outlier: 4.002A pdb=" N GLN C 439 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 493 removed outlier: 3.834A pdb=" N GLU C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.570A pdb=" N GLN C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 580 Processing helix chain 'C' and resid 588 through 593 Processing helix chain 'C' and resid 596 through 599 No H-bonds generated for 'chain 'C' and resid 596 through 599' Processing helix chain 'C' and resid 601 through 610 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 321 through 335 Processing helix chain 'D' and resid 357 through 368 Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 387 through 394 removed outlier: 4.210A pdb=" N ILE D 394 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.567A pdb=" N LYS D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 442 removed outlier: 4.408A pdb=" N ILE D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET D 437 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN D 439 " --> pdb=" O THR D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 492 Processing helix chain 'D' and resid 508 through 513 Processing helix chain 'D' and resid 515 through 523 Processing helix chain 'D' and resid 543 through 565 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 588 through 599 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 601 through 609 Processing helix chain 'E' and resid 301 through 304 No H-bonds generated for 'chain 'E' and resid 301 through 304' Processing helix chain 'E' and resid 309 through 316 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 321 through 335 Processing helix chain 'E' and resid 357 through 368 Processing helix chain 'E' and resid 372 through 375 No H-bonds generated for 'chain 'E' and resid 372 through 375' Processing helix chain 'E' and resid 387 through 394 removed outlier: 3.816A pdb=" N ALA E 391 " --> pdb=" O HIS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 415 Processing helix chain 'E' and resid 434 through 442 removed outlier: 4.151A pdb=" N GLN E 439 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP E 442 " --> pdb=" O GLN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 492 Processing helix chain 'E' and resid 508 through 513 Processing helix chain 'E' and resid 515 through 523 Processing helix chain 'E' and resid 526 through 530 Processing helix chain 'E' and resid 543 through 565 Processing helix chain 'E' and resid 573 through 580 Processing helix chain 'E' and resid 588 through 599 removed outlier: 4.264A pdb=" N ARG E 599 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 609 Processing helix chain 'E' and resid 628 through 630 No H-bonds generated for 'chain 'E' and resid 628 through 630' Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 321 through 335 Processing helix chain 'F' and resid 357 through 368 Processing helix chain 'F' and resid 387 through 394 removed outlier: 3.711A pdb=" N VAL F 390 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA F 391 " --> pdb=" O HIS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 415 Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 433 through 442 removed outlier: 3.576A pdb=" N PHE F 441 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 442 " --> pdb=" O GLN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 493 Processing helix chain 'F' and resid 508 through 513 Processing helix chain 'F' and resid 515 through 523 Processing helix chain 'F' and resid 526 through 531 Processing helix chain 'F' and resid 543 through 564 Processing helix chain 'F' and resid 573 through 581 Processing helix chain 'F' and resid 588 through 599 removed outlier: 4.799A pdb=" N HIS F 594 " --> pdb=" O SER F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 601 through 609 Processing helix chain 'G' and resid 301 through 306 Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 321 through 335 removed outlier: 3.518A pdb=" N ALA G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 368 Processing helix chain 'G' and resid 372 through 375 No H-bonds generated for 'chain 'G' and resid 372 through 375' Processing helix chain 'G' and resid 388 through 392 Processing helix chain 'G' and resid 408 through 415 Processing helix chain 'G' and resid 431 through 442 removed outlier: 3.552A pdb=" N THR G 435 " --> pdb=" O PRO G 431 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN G 439 " --> pdb=" O THR G 435 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU G 440 " --> pdb=" O ILE G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 480 Processing helix chain 'G' and resid 510 through 513 No H-bonds generated for 'chain 'G' and resid 510 through 513' Processing helix chain 'G' and resid 515 through 522 Processing helix chain 'G' and resid 526 through 531 Processing helix chain 'G' and resid 543 through 564 Processing helix chain 'G' and resid 575 through 580 removed outlier: 3.786A pdb=" N LEU G 579 " --> pdb=" O VAL G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 589 through 599 Processing helix chain 'G' and resid 601 through 609 Processing helix chain 'H' and resid 299 through 306 Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 321 through 335 Processing helix chain 'H' and resid 358 through 368 Processing helix chain 'H' and resid 372 through 375 No H-bonds generated for 'chain 'H' and resid 372 through 375' Processing helix chain 'H' and resid 388 through 394 removed outlier: 3.746A pdb=" N ILE H 394 " --> pdb=" O ALA H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 415 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 431 through 440 removed outlier: 3.982A pdb=" N THR H 435 " --> pdb=" O PRO H 431 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE H 436 " --> pdb=" O ASP H 432 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLN H 439 " --> pdb=" O THR H 435 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU H 440 " --> pdb=" O ILE H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 478 Processing helix chain 'H' and resid 508 through 513 Processing helix chain 'H' and resid 515 through 523 Processing helix chain 'H' and resid 526 through 531 Processing helix chain 'H' and resid 543 through 564 Processing helix chain 'H' and resid 573 through 581 Processing helix chain 'H' and resid 588 through 609 removed outlier: 3.748A pdb=" N ARG H 598 " --> pdb=" O GLU H 595 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 599 " --> pdb=" O VAL H 596 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL H 600 " --> pdb=" O GLU H 597 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 601 " --> pdb=" O ARG H 598 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN H 602 " --> pdb=" O ARG H 599 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN H 603 " --> pdb=" O VAL H 600 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA H 607 " --> pdb=" O LEU H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 626 through 631 removed outlier: 4.072A pdb=" N LEU H 630 " --> pdb=" O SER H 626 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 306 Processing helix chain 'I' and resid 309 through 316 Processing helix chain 'I' and resid 321 through 335 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) Processing helix chain 'I' and resid 358 through 368 Processing helix chain 'I' and resid 387 through 393 removed outlier: 3.645A pdb=" N VAL I 390 " --> pdb=" O ARG I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 415 Processing helix chain 'I' and resid 426 through 428 No H-bonds generated for 'chain 'I' and resid 426 through 428' Processing helix chain 'I' and resid 431 through 442 removed outlier: 3.760A pdb=" N LEU I 440 " --> pdb=" O ILE I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 492 removed outlier: 3.754A pdb=" N ASN I 489 " --> pdb=" O GLU I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 513 No H-bonds generated for 'chain 'I' and resid 510 through 513' Processing helix chain 'I' and resid 515 through 523 Processing helix chain 'I' and resid 526 through 530 Processing helix chain 'I' and resid 543 through 565 Processing helix chain 'I' and resid 573 through 581 Processing helix chain 'I' and resid 588 through 609 removed outlier: 3.700A pdb=" N HIS I 594 " --> pdb=" O SER I 591 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG I 599 " --> pdb=" O VAL I 596 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL I 600 " --> pdb=" O GLU I 597 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL I 601 " --> pdb=" O ARG I 598 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN I 602 " --> pdb=" O ARG I 599 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU I 604 " --> pdb=" O VAL I 601 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU I 609 " --> pdb=" O ALA I 606 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 534 through 537 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= B, first strand: chain 'A' and resid 445 through 447 Processing sheet with id= C, first strand: chain 'A' and resid 568 through 570 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= D, first strand: chain 'B' and resid 534 through 538 removed outlier: 3.928A pdb=" N GLY B 351 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 445 through 447 Processing sheet with id= F, first strand: chain 'B' and resid 568 through 571 removed outlier: 4.554A pdb=" N THR B 618 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 534 through 537 Processing sheet with id= H, 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= I, first strand: chain 'C' and resid 568 through 571 removed outlier: 3.586A pdb=" N LEU C 619 " --> pdb=" O THR C 568 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 621 " --> 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) removed outlier: 3.644A pdb=" N LYS C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 534 through 537 Processing sheet with id= K, first strand: chain 'D' and resid 445 through 447 Processing sheet with id= L, first strand: chain 'D' and resid 568 through 571 removed outlier: 4.204A pdb=" N THR D 618 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 534 through 537 Processing sheet with id= N, 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= O, 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= P, first strand: chain 'F' and resid 534 through 537 Processing sheet with id= Q, first strand: chain 'F' and resid 568 through 570 removed outlier: 3.621A pdb=" N ILE F 621 " --> pdb=" O LEU F 570 " (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= R, first strand: chain 'G' and resid 534 through 537 removed outlier: 3.525A pdb=" N THR G 464 " --> pdb=" O PHE G 423 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 445 through 447 Processing sheet with id= T, first strand: chain 'G' and resid 568 through 571 removed outlier: 4.325A pdb=" N THR G 618 " --> pdb=" O ILE G 653 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 534 through 537 Processing sheet with id= V, first strand: chain 'H' and resid 568 through 571 removed outlier: 5.178A pdb=" N THR H 618 " --> pdb=" O ILE H 653 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 534 through 536 Processing sheet with id= X, first strand: chain 'I' and resid 445 through 447 Processing sheet with id= Y, first strand: chain 'I' and resid 568 through 570 removed outlier: 4.549A pdb=" N THR I 618 " --> pdb=" O ILE I 653 " (cutoff:3.500A) 1097 hydrogen bonds defined for protein. 2961 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: 8.34 Time building geometry restraints manager: 10.94 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: 314 2.66 - 3.22: 22232 3.22 - 3.78: 40496 3.78 - 4.34: 54778 4.34 - 4.90: 88626 Nonbonded interactions: 206446 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 206441 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: 0.850 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: 0.010 Extract box with map and model: 4.820 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 64.940 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.090 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.340 ------------------------------------------------------------------------------- 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= 0.323 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 : 2.916 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: 0.4558 time to fit residues: 712.8182 Evaluate side-chains 965 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 965 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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: 0.9990 chunk 235 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 0.0670 chunk 125 optimal weight: 0.0050 chunk 243 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 181 optimal weight: 0.0870 chunk 282 optimal weight: 1.9990 overall best weight: 0.3510 ------------------------------------------------------------------------------- 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 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 HIS D 603 GLN ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 GLN E 439 GLN E 522 HIS ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 594 HIS F 584 ASN F 594 HIS G 320 GLN G 474 GLN ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN I 475 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26184 Z= 0.172 Angle : 0.552 10.166 35244 Z= 0.289 Chirality : 0.041 0.212 3860 Planarity : 0.005 0.063 4540 Dihedral : 10.653 89.674 3706 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 1.94 % Allowed : 13.12 % Favored : 84.94 % 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: -0.60 (0.14), residues: 3096 helix: -0.42 (0.13), residues: 1513 sheet: -0.07 (0.22), residues: 497 loop : -0.21 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 571 HIS 0.009 0.001 HIS A 475 PHE 0.044 0.001 PHE I 556 TYR 0.019 0.001 TYR G 339 ARG 0.007 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 1036 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 983 time to evaluate : 2.615 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: A 333 ARG cc_start: 0.5753 (mtm110) cc_final: 0.5472 (ttm110) REVERT: A 367 TYR cc_start: 0.6851 (t80) cc_final: 0.6407 (t80) REVERT: A 392 LYS cc_start: 0.7612 (ptpt) cc_final: 0.7289 (ttpt) REVERT: A 401 VAL cc_start: 0.8441 (m) cc_final: 0.8141 (p) REVERT: A 450 LYS cc_start: 0.7150 (ttmt) cc_final: 0.6871 (mtpp) REVERT: A 512 GLU cc_start: 0.6203 (tp30) cc_final: 0.5546 (tp30) REVERT: A 529 LEU cc_start: 0.7274 (mt) cc_final: 0.6968 (mt) REVERT: A 534 GLU cc_start: 0.5677 (tp30) cc_final: 0.5225 (tp30) REVERT: B 346 VAL cc_start: 0.7963 (m) cc_final: 0.7584 (p) REVERT: B 389 GLU cc_start: 0.5970 (mp0) cc_final: 0.5058 (mm-30) REVERT: B 427 ASP cc_start: 0.6686 (p0) cc_final: 0.6319 (p0) REVERT: B 445 ARG cc_start: 0.7881 (tmm-80) cc_final: 0.7640 (ttp80) REVERT: B 557 TRP cc_start: 0.6710 (m100) cc_final: 0.6477 (m100) REVERT: B 599 ARG cc_start: 0.7338 (tpp-160) cc_final: 0.7087 (tpp80) REVERT: C 363 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6737 (mm-40) REVERT: C 541 PHE cc_start: 0.7760 (m-80) cc_final: 0.7545 (m-10) REVERT: D 315 GLU cc_start: 0.6040 (tm-30) cc_final: 0.5778 (tm-30) REVERT: D 317 ILE cc_start: 0.7741 (tt) cc_final: 0.7521 (tt) REVERT: D 389 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6375 (mm-30) REVERT: D 427 ASP cc_start: 0.7026 (t70) cc_final: 0.6583 (t0) REVERT: D 467 VAL cc_start: 0.8256 (t) cc_final: 0.8040 (t) REVERT: D 511 LYS cc_start: 0.8371 (mttt) cc_final: 0.8029 (mttt) REVERT: D 518 ILE cc_start: 0.8058 (tt) cc_final: 0.7663 (tp) REVERT: D 522 HIS cc_start: 0.7116 (t-90) cc_final: 0.6800 (t-90) REVERT: D 533 ASN cc_start: 0.6961 (m-40) cc_final: 0.6649 (m-40) REVERT: D 537 TYR cc_start: 0.7098 (m-80) cc_final: 0.6828 (m-80) REVERT: D 555 ASN cc_start: 0.7491 (t0) cc_final: 0.7073 (t0) REVERT: D 557 TRP cc_start: 0.7601 (m100) cc_final: 0.7357 (m100) REVERT: D 587 TYR cc_start: 0.7440 (m-80) cc_final: 0.7113 (m-80) REVERT: D 621 ILE cc_start: 0.8345 (mp) cc_final: 0.8028 (mm) REVERT: E 309 LEU cc_start: 0.6987 (tp) cc_final: 0.6771 (tp) REVERT: E 340 ASP cc_start: 0.7741 (t0) cc_final: 0.7421 (t0) REVERT: E 380 ASP cc_start: 0.7190 (t70) cc_final: 0.6621 (t0) REVERT: E 385 GLN cc_start: 0.7757 (mt0) cc_final: 0.7518 (mt0) REVERT: E 390 VAL cc_start: 0.7848 (t) cc_final: 0.7623 (p) REVERT: E 428 LYS cc_start: 0.7215 (mmtm) cc_final: 0.6744 (mptt) REVERT: E 471 GLU cc_start: 0.6735 (mp0) cc_final: 0.6496 (mp0) REVERT: E 554 LEU cc_start: 0.7783 (mt) cc_final: 0.7418 (mm) REVERT: E 575 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.7148 (p) REVERT: E 604 LEU cc_start: 0.8129 (mt) cc_final: 0.7835 (tp) REVERT: F 341 GLU cc_start: 0.5486 (mm-30) cc_final: 0.5198 (mm-30) REVERT: F 363 GLN cc_start: 0.7597 (mm110) cc_final: 0.7276 (mm-40) REVERT: F 512 GLU cc_start: 0.6763 (tm-30) cc_final: 0.4776 (tm-30) REVERT: F 518 ILE cc_start: 0.8426 (tt) cc_final: 0.8113 (pt) REVERT: F 525 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6672 (tpp80) REVERT: G 357 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7557 (mtmt) REVERT: G 369 HIS cc_start: 0.6082 (m-70) cc_final: 0.5827 (m-70) REVERT: G 381 MET cc_start: 0.6269 (mmp) cc_final: 0.5995 (mmp) REVERT: G 392 LYS cc_start: 0.7448 (mttm) cc_final: 0.7163 (ttmm) REVERT: G 414 LYS cc_start: 0.7911 (ttmm) cc_final: 0.7363 (ttmm) REVERT: G 440 LEU cc_start: 0.8386 (tp) cc_final: 0.8174 (tp) REVERT: G 441 PHE cc_start: 0.8085 (m-10) cc_final: 0.7863 (m-80) REVERT: G 516 ARG cc_start: 0.6780 (ttp-170) cc_final: 0.6571 (ttp80) REVERT: G 590 ARG cc_start: 0.6363 (ptp90) cc_final: 0.5875 (ttm-80) REVERT: H 331 ILE cc_start: 0.7138 (mt) cc_final: 0.6879 (mm) REVERT: H 334 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7490 (mtpp) REVERT: H 357 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7414 (mtmm) REVERT: H 363 GLN cc_start: 0.6511 (mm-40) cc_final: 0.6198 (mm-40) REVERT: H 392 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7447 (ttmm) REVERT: H 414 LYS cc_start: 0.6838 (tmmt) cc_final: 0.6328 (ptmm) REVERT: H 461 PHE cc_start: 0.7834 (m-80) cc_final: 0.7634 (m-10) REVERT: H 552 LYS cc_start: 0.7600 (tmtt) cc_final: 0.7151 (tptp) REVERT: I 357 LYS cc_start: 0.5598 (pttm) cc_final: 0.5142 (pttm) outliers start: 53 outliers final: 29 residues processed: 993 average time/residue: 0.4763 time to fit residues: 686.7474 Evaluate side-chains 964 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 933 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 623 VAL 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 591 SER 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 322 SER 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 318 ILE Chi-restraints excluded: chain E residue 336 ASN 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 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 440 LEU Chi-restraints excluded: chain H residue 569 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 235 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 0.7980 chunk 305 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 280 optimal weight: 30.0000 chunk 96 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 GLN B 320 GLN B 385 GLN C 439 GLN C 551 ASN D 336 ASN D 418 ASN D 430 HIS D 603 GLN E 316 HIS E 320 GLN ** E 430 HIS ** 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 316 HIS F 548 GLN F 584 ASN G 316 HIS G 320 GLN ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 594 HIS H 363 GLN H 425 GLN ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26184 Z= 0.255 Angle : 0.573 9.248 35244 Z= 0.305 Chirality : 0.043 0.207 3860 Planarity : 0.004 0.055 4540 Dihedral : 10.278 88.707 3706 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.71 % Allowed : 16.23 % Favored : 81.06 % 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: -0.23 (0.15), residues: 3096 helix: -0.00 (0.13), residues: 1509 sheet: -0.25 (0.22), residues: 529 loop : 0.00 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 338 HIS 0.012 0.001 HIS A 475 PHE 0.035 0.002 PHE I 556 TYR 0.026 0.002 TYR F 608 ARG 0.011 0.001 ARG I 560 *********************** 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 1068 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 994 time to evaluate : 2.588 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 377 ILE cc_start: 0.7966 (mm) cc_final: 0.7680 (mt) REVERT: A 392 LYS cc_start: 0.7761 (ptpt) cc_final: 0.7480 (ttpp) REVERT: A 479 LEU cc_start: 0.7639 (mt) cc_final: 0.7415 (mt) REVERT: A 512 GLU cc_start: 0.6378 (tp30) cc_final: 0.5626 (tp30) REVERT: A 515 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.7009 (mm) REVERT: A 529 LEU cc_start: 0.7458 (mt) cc_final: 0.7232 (mt) REVERT: A 534 GLU cc_start: 0.5724 (tp30) cc_final: 0.5390 (tp30) REVERT: B 310 GLU cc_start: 0.7432 (mp0) cc_final: 0.7110 (mp0) REVERT: B 313 LEU cc_start: 0.7806 (mt) cc_final: 0.7530 (mp) REVERT: B 316 HIS cc_start: 0.6794 (t-90) cc_final: 0.6555 (t70) REVERT: B 383 GLU cc_start: 0.6303 (mp0) cc_final: 0.5937 (mp0) REVERT: B 389 GLU cc_start: 0.6294 (mp0) cc_final: 0.5680 (tp30) REVERT: B 392 LYS cc_start: 0.8097 (ptmt) cc_final: 0.7334 (ptmt) REVERT: B 404 GLU cc_start: 0.7075 (mp0) cc_final: 0.6791 (pm20) REVERT: B 428 LYS cc_start: 0.7462 (mtpt) cc_final: 0.7112 (mtpp) REVERT: B 458 ASP cc_start: 0.6553 (p0) cc_final: 0.6280 (p0) REVERT: C 320 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6993 (mm-40) REVERT: C 363 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6807 (mm110) REVERT: C 392 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7688 (mtpp) REVERT: C 437 MET cc_start: 0.7696 (mmt) cc_final: 0.7495 (mmt) REVERT: C 592 ILE cc_start: 0.7608 (mm) cc_final: 0.7323 (mm) REVERT: D 315 GLU cc_start: 0.6465 (tm-30) cc_final: 0.6141 (tm-30) REVERT: D 362 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7574 (mtmm) REVERT: D 389 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6378 (mm-30) REVERT: D 467 VAL cc_start: 0.8422 (t) cc_final: 0.8201 (t) REVERT: D 511 LYS cc_start: 0.8479 (mttt) cc_final: 0.8164 (mttt) REVERT: D 518 ILE cc_start: 0.8206 (tt) cc_final: 0.7803 (tp) REVERT: D 533 ASN cc_start: 0.7138 (m-40) cc_final: 0.6701 (m-40) REVERT: D 537 TYR cc_start: 0.7187 (m-80) cc_final: 0.6981 (m-80) REVERT: D 555 ASN cc_start: 0.7575 (t0) cc_final: 0.7282 (t0) REVERT: E 340 ASP cc_start: 0.8069 (t0) cc_final: 0.7692 (t0) REVERT: E 385 GLN cc_start: 0.7752 (mt0) cc_final: 0.7528 (mt0) REVERT: E 428 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7399 (mptt) REVERT: E 471 GLU cc_start: 0.6909 (mp0) cc_final: 0.6603 (mp0) REVERT: E 553 GLU cc_start: 0.6065 (tp30) cc_final: 0.5857 (tp30) REVERT: E 554 LEU cc_start: 0.7891 (mt) cc_final: 0.7542 (mm) REVERT: F 623 VAL cc_start: 0.7849 (t) cc_final: 0.7639 (m) REVERT: G 381 MET cc_start: 0.6435 (mmp) cc_final: 0.6169 (mmp) REVERT: G 385 GLN cc_start: 0.7390 (mt0) cc_final: 0.7166 (mt0) REVERT: G 392 LYS cc_start: 0.7470 (mttm) cc_final: 0.7207 (ttmm) REVERT: G 440 LEU cc_start: 0.8480 (tp) cc_final: 0.8226 (tp) REVERT: G 590 ARG cc_start: 0.6480 (ptp90) cc_final: 0.6145 (mtm-85) REVERT: G 599 ARG cc_start: 0.6953 (tpp80) cc_final: 0.6749 (tpp80) REVERT: H 327 VAL cc_start: 0.7949 (t) cc_final: 0.7699 (p) REVERT: H 334 LYS cc_start: 0.7876 (mtpp) cc_final: 0.7596 (mtpp) REVERT: H 414 LYS cc_start: 0.7080 (tmmt) cc_final: 0.6605 (ptmm) REVERT: H 461 PHE cc_start: 0.7686 (m-80) cc_final: 0.7123 (m-80) REVERT: H 516 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7576 (mtm110) REVERT: H 545 GLU cc_start: 0.6638 (mp0) cc_final: 0.5386 (mt-10) REVERT: H 552 LYS cc_start: 0.7614 (tmtt) cc_final: 0.7200 (tptp) REVERT: I 346 VAL cc_start: 0.6008 (t) cc_final: 0.5798 (m) outliers start: 74 outliers final: 47 residues processed: 1015 average time/residue: 0.4455 time to fit residues: 656.7720 Evaluate side-chains 1008 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 960 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 309 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 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 542 CYS 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 620 ARG Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 374 LYS 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 568 THR 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 364 THR Chi-restraints excluded: chain F residue 457 LYS Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 534 GLU Chi-restraints excluded: chain H residue 380 ASP Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 604 LEU Chi-restraints excluded: chain I residue 536 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 31 optimal weight: 40.0000 chunk 135 optimal weight: 2.9990 chunk 189 optimal weight: 0.0770 chunk 283 optimal weight: 10.0000 chunk 300 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS B 584 ASN C 425 GLN D 385 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN E 439 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 HIS F 548 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 GLN H 316 HIS ** H 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** 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: 0.6440 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26184 Z= 0.244 Angle : 0.571 10.302 35244 Z= 0.301 Chirality : 0.043 0.208 3860 Planarity : 0.004 0.047 4540 Dihedral : 10.069 89.057 3706 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Rotamer: Outliers : 3.22 % Allowed : 18.65 % Favored : 78.12 % 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: 0.14 (0.13), residues: 1513 sheet: -0.30 (0.22), residues: 520 loop : 0.04 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 571 HIS 0.015 0.001 HIS A 475 PHE 0.040 0.002 PHE I 556 TYR 0.019 0.002 TYR G 608 ARG 0.008 0.000 ARG F 387 *********************** 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 1068 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 980 time to evaluate : 2.910 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: 0.7772 (ptpt) cc_final: 0.7476 (ttpp) REVERT: A 401 VAL cc_start: 0.8477 (m) cc_final: 0.8190 (p) REVERT: A 512 GLU cc_start: 0.6270 (tp30) cc_final: 0.5554 (tp30) REVERT: A 515 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6933 (mm) REVERT: A 534 GLU cc_start: 0.5972 (tp30) cc_final: 0.5553 (tp30) REVERT: B 309 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7140 (tt) REVERT: B 313 LEU cc_start: 0.7800 (mt) cc_final: 0.7488 (mp) REVERT: B 392 LYS cc_start: 0.7942 (ptmt) cc_final: 0.7302 (ptmt) REVERT: B 445 ARG cc_start: 0.7946 (tmm-80) cc_final: 0.7635 (ttm170) REVERT: B 458 ASP cc_start: 0.6577 (p0) cc_final: 0.6294 (p0) REVERT: C 363 GLN cc_start: 0.7297 (mm-40) cc_final: 0.6832 (mm110) REVERT: C 392 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7668 (mtpp) REVERT: C 404 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6499 (mm-30) REVERT: C 437 MET cc_start: 0.7761 (mmt) cc_final: 0.7512 (mmt) REVERT: C 522 HIS cc_start: 0.7408 (t70) cc_final: 0.7117 (t-90) REVERT: C 592 ILE cc_start: 0.7571 (mm) cc_final: 0.7303 (mm) REVERT: C 594 HIS cc_start: 0.5277 (p90) cc_final: 0.4987 (p90) REVERT: D 359 GLU cc_start: 0.5827 (tp30) cc_final: 0.5403 (tp30) REVERT: D 389 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6434 (mm-30) REVERT: D 427 ASP cc_start: 0.7061 (t70) cc_final: 0.6669 (t0) REVERT: D 467 VAL cc_start: 0.8408 (t) cc_final: 0.8165 (t) REVERT: D 518 ILE cc_start: 0.8224 (tt) cc_final: 0.7809 (tp) REVERT: D 533 ASN cc_start: 0.7205 (m-40) cc_final: 0.6744 (m-40) REVERT: D 537 TYR cc_start: 0.7219 (m-80) cc_final: 0.6980 (m-80) REVERT: D 555 ASN cc_start: 0.7645 (t0) cc_final: 0.7201 (t0) REVERT: D 620 ARG cc_start: 0.6236 (ttp80) cc_final: 0.5753 (ttp80) REVERT: E 340 ASP cc_start: 0.8156 (t0) cc_final: 0.7763 (t0) REVERT: E 387 ARG cc_start: 0.7314 (mtp-110) cc_final: 0.7113 (ttm170) REVERT: E 414 LYS cc_start: 0.7731 (tmtt) cc_final: 0.7479 (tttp) REVERT: E 428 LYS cc_start: 0.7594 (mmtm) cc_final: 0.7112 (mptt) REVERT: E 471 GLU cc_start: 0.6935 (mp0) cc_final: 0.6708 (mp0) REVERT: E 554 LEU cc_start: 0.7921 (mt) cc_final: 0.7587 (mm) REVERT: F 427 ASP cc_start: 0.6707 (p0) cc_final: 0.6285 (p0) REVERT: F 439 GLN cc_start: 0.6844 (tt0) cc_final: 0.6584 (tt0) REVERT: F 512 GLU cc_start: 0.6700 (tp30) cc_final: 0.6396 (tp30) REVERT: F 518 ILE cc_start: 0.8535 (tt) cc_final: 0.8333 (tp) REVERT: F 531 ARG cc_start: 0.7533 (mtt90) cc_final: 0.7108 (mtt90) REVERT: F 623 VAL cc_start: 0.7895 (t) cc_final: 0.7674 (m) REVERT: G 357 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7940 (mtmt) REVERT: G 385 GLN cc_start: 0.7289 (mt0) cc_final: 0.7052 (mt0) REVERT: G 392 LYS cc_start: 0.7690 (mttm) cc_final: 0.7393 (ttmm) REVERT: G 440 LEU cc_start: 0.8486 (tp) cc_final: 0.8189 (tp) REVERT: H 327 VAL cc_start: 0.8014 (t) cc_final: 0.7760 (p) REVERT: H 334 LYS cc_start: 0.7792 (mtpp) cc_final: 0.7560 (mtpp) REVERT: H 392 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7562 (tttp) REVERT: H 394 ILE cc_start: 0.8194 (pt) cc_final: 0.7831 (mm) REVERT: H 408 GLN cc_start: 0.6481 (pt0) cc_final: 0.6131 (pt0) REVERT: H 414 LYS cc_start: 0.7175 (tmmt) cc_final: 0.6453 (ptmm) REVERT: H 427 ASP cc_start: 0.8031 (p0) cc_final: 0.7716 (p0) REVERT: H 461 PHE cc_start: 0.7804 (m-80) cc_final: 0.7118 (m-80) REVERT: H 527 GLU cc_start: 0.6703 (pm20) cc_final: 0.6471 (tm-30) REVERT: H 552 LYS cc_start: 0.7618 (tmtt) cc_final: 0.7248 (tptp) REVERT: H 553 GLU cc_start: 0.5787 (tp30) cc_final: 0.5504 (tp30) REVERT: H 585 VAL cc_start: 0.7968 (p) cc_final: 0.7732 (t) outliers start: 88 outliers final: 63 residues processed: 1004 average time/residue: 0.4510 time to fit residues: 653.7330 Evaluate side-chains 1019 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 954 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 455 ASP 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 458 ASP 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 410 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 568 THR 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 336 ASN Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 364 THR 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 439 GLN 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 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 436 ILE Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 SER 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 380 ASP Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 592 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 546 LEU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 592 ILE Chi-restraints excluded: chain H residue 611 ASP Chi-restraints excluded: chain H residue 617 CYS Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 536 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 223 optimal weight: 0.4980 chunk 124 optimal weight: 0.4980 chunk 256 optimal weight: 0.6980 chunk 207 optimal weight: 0.0270 chunk 0 optimal weight: 70.0000 chunk 153 optimal weight: 0.6980 chunk 269 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 GLN D 418 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 GLN ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 GLN H 316 HIS ** H 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 586 HIS ** I 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 603 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26184 Z= 0.172 Angle : 0.561 8.845 35244 Z= 0.291 Chirality : 0.042 0.268 3860 Planarity : 0.004 0.049 4540 Dihedral : 9.673 86.857 3706 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Rotamer: Outliers : 3.26 % Allowed : 20.67 % Favored : 76.07 % 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: 0.12 (0.15), residues: 3096 helix: 0.35 (0.13), residues: 1510 sheet: -0.19 (0.22), residues: 516 loop : 0.11 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 571 HIS 0.019 0.001 HIS A 475 PHE 0.039 0.001 PHE I 556 TYR 0.021 0.001 TYR B 367 ARG 0.013 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 1057 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 968 time to evaluate : 2.971 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: A 401 VAL cc_start: 0.8448 (m) cc_final: 0.8179 (p) REVERT: A 512 GLU cc_start: 0.6169 (tp30) cc_final: 0.5534 (tp30) REVERT: A 515 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6864 (mm) REVERT: A 534 GLU cc_start: 0.5724 (tp30) cc_final: 0.5354 (tp30) REVERT: B 309 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6981 (tt) REVERT: B 310 GLU cc_start: 0.7388 (mp0) cc_final: 0.7172 (mp0) REVERT: B 362 LYS cc_start: 0.7671 (mttp) cc_final: 0.7444 (mttp) REVERT: B 392 LYS cc_start: 0.7909 (ptmt) cc_final: 0.7218 (ptmt) REVERT: B 428 LYS cc_start: 0.7230 (mtpp) cc_final: 0.6978 (mtpp) REVERT: B 458 ASP cc_start: 0.6512 (p0) cc_final: 0.6226 (p0) REVERT: B 485 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6067 (tm-30) REVERT: C 363 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6990 (mm-40) REVERT: C 437 MET cc_start: 0.7700 (mmt) cc_final: 0.7377 (mmt) REVERT: C 592 ILE cc_start: 0.7481 (mm) cc_final: 0.7195 (mm) REVERT: D 389 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6368 (mm-30) REVERT: D 427 ASP cc_start: 0.7231 (t70) cc_final: 0.6990 (t0) REVERT: D 467 VAL cc_start: 0.8254 (t) cc_final: 0.8017 (t) REVERT: D 518 ILE cc_start: 0.8148 (tt) cc_final: 0.7726 (tp) REVERT: D 533 ASN cc_start: 0.7169 (m-40) cc_final: 0.6728 (m-40) REVERT: D 557 TRP cc_start: 0.7755 (m100) cc_final: 0.7350 (m100) REVERT: D 599 ARG cc_start: 0.7054 (mmm-85) cc_final: 0.6607 (mmm160) REVERT: D 601 VAL cc_start: 0.8368 (t) cc_final: 0.8134 (t) REVERT: E 340 ASP cc_start: 0.8108 (t0) cc_final: 0.7708 (t0) REVERT: E 428 LYS cc_start: 0.7604 (mmtm) cc_final: 0.7084 (mptt) REVERT: E 471 GLU cc_start: 0.6890 (mp0) cc_final: 0.6582 (mp0) REVERT: F 317 ILE cc_start: 0.7805 (tp) cc_final: 0.7360 (mm) REVERT: F 425 GLN cc_start: 0.7298 (mm-40) cc_final: 0.7022 (mm110) REVERT: F 427 ASP cc_start: 0.6623 (p0) cc_final: 0.6089 (p0) REVERT: F 457 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7366 (mtmt) REVERT: F 513 ASN cc_start: 0.7064 (p0) cc_final: 0.6821 (p0) REVERT: F 518 ILE cc_start: 0.8473 (tt) cc_final: 0.8194 (tp) REVERT: F 564 ARG cc_start: 0.6857 (ttm170) cc_final: 0.6546 (ttm170) REVERT: G 357 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7849 (mtmt) REVERT: G 381 MET cc_start: 0.6198 (mmp) cc_final: 0.5997 (mmp) REVERT: G 392 LYS cc_start: 0.7705 (mttm) cc_final: 0.7418 (ttmm) REVERT: G 418 ASN cc_start: 0.5909 (t0) cc_final: 0.5705 (t0) REVERT: G 440 LEU cc_start: 0.8407 (tp) cc_final: 0.8135 (tp) REVERT: G 445 ARG cc_start: 0.6862 (ttp80) cc_final: 0.5979 (ptt-90) REVERT: G 590 ARG cc_start: 0.6573 (mtm-85) cc_final: 0.6244 (mtt180) REVERT: H 334 LYS cc_start: 0.7745 (mtpp) cc_final: 0.7516 (mtpp) REVERT: H 378 ARG cc_start: 0.7008 (ttt180) cc_final: 0.6529 (ttt180) REVERT: H 408 GLN cc_start: 0.6454 (pt0) cc_final: 0.6189 (pt0) REVERT: H 414 LYS cc_start: 0.6986 (tmmt) cc_final: 0.6485 (ptmm) REVERT: H 461 PHE cc_start: 0.7741 (m-80) cc_final: 0.7190 (m-80) REVERT: H 527 GLU cc_start: 0.6694 (pm20) cc_final: 0.6477 (tm-30) REVERT: H 552 LYS cc_start: 0.7595 (tmtt) cc_final: 0.7218 (tptp) REVERT: H 649 ARG cc_start: 0.3890 (mtm-85) cc_final: 0.3603 (mtm-85) REVERT: I 603 GLN cc_start: 0.6868 (mm110) cc_final: 0.6424 (mp10) outliers start: 89 outliers final: 62 residues processed: 996 average time/residue: 0.4521 time to fit residues: 653.0835 Evaluate side-chains 1006 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 942 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 309 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 539 LEU 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 458 ASP Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 396 SER 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 542 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 374 LYS Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 439 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 463 MET Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 529 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 316 HIS Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 544 SER 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 436 ILE Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 312 ARG Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 546 LEU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 586 HIS Chi-restraints excluded: chain H residue 592 ILE Chi-restraints excluded: chain H residue 604 LEU Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 548 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 0.6980 chunk 270 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 300 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 HIS D 385 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 555 ASN ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 HIS ** G 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 586 HIS ** I 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 594 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26184 Z= 0.184 Angle : 0.572 9.450 35244 Z= 0.297 Chirality : 0.042 0.233 3860 Planarity : 0.004 0.057 4540 Dihedral : 9.425 89.219 3706 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 3.66 % Allowed : 21.55 % Favored : 74.79 % 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: 0.18 (0.15), residues: 3096 helix: 0.39 (0.13), residues: 1518 sheet: -0.16 (0.22), residues: 516 loop : 0.16 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 557 HIS 0.019 0.001 HIS H 586 PHE 0.042 0.001 PHE I 556 TYR 0.023 0.002 TYR B 367 ARG 0.009 0.000 ARG F 387 *********************** 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 1060 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 960 time to evaluate : 2.942 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 359 GLU cc_start: 0.4844 (mp0) cc_final: 0.4365 (mp0) REVERT: A 392 LYS cc_start: 0.7496 (ptmm) cc_final: 0.7079 (ttpt) REVERT: A 512 GLU cc_start: 0.6119 (tp30) cc_final: 0.5493 (tp30) REVERT: A 515 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6887 (mm) REVERT: A 525 ARG cc_start: 0.7032 (tpp80) cc_final: 0.6711 (ttm-80) REVERT: A 534 GLU cc_start: 0.5756 (tp30) cc_final: 0.5332 (tp30) REVERT: A 553 GLU cc_start: 0.4934 (pp20) cc_final: 0.4702 (pp20) REVERT: B 310 GLU cc_start: 0.7393 (mp0) cc_final: 0.7187 (mp0) REVERT: B 346 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7521 (m) REVERT: B 389 GLU cc_start: 0.6169 (mp0) cc_final: 0.5805 (tp30) REVERT: B 450 LYS cc_start: 0.6425 (mtpt) cc_final: 0.6004 (mtpt) REVERT: B 458 ASP cc_start: 0.6506 (p0) cc_final: 0.6272 (p0) REVERT: B 485 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6006 (tm-30) REVERT: C 363 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6773 (mm-40) REVERT: C 392 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7635 (mtpp) REVERT: C 437 MET cc_start: 0.7625 (mmt) cc_final: 0.7370 (mmt) REVERT: C 522 HIS cc_start: 0.7425 (t70) cc_final: 0.7140 (t-90) REVERT: C 534 GLU cc_start: 0.6498 (mm-30) cc_final: 0.6222 (mm-30) REVERT: D 315 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6083 (tm-30) REVERT: D 389 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6367 (mm-30) REVERT: D 467 VAL cc_start: 0.8283 (t) cc_final: 0.8068 (t) REVERT: D 518 ILE cc_start: 0.8166 (tt) cc_final: 0.7745 (tp) REVERT: D 533 ASN cc_start: 0.7169 (m-40) cc_final: 0.6749 (m-40) REVERT: D 555 ASN cc_start: 0.7538 (t0) cc_final: 0.7036 (t0) REVERT: D 599 ARG cc_start: 0.7113 (mmm-85) cc_final: 0.6666 (mmm160) REVERT: E 340 ASP cc_start: 0.8117 (t0) cc_final: 0.7685 (t0) REVERT: E 428 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7166 (mptt) REVERT: E 471 GLU cc_start: 0.6884 (mp0) cc_final: 0.6595 (mp0) REVERT: E 575 VAL cc_start: 0.8048 (m) cc_final: 0.7800 (p) REVERT: F 317 ILE cc_start: 0.7792 (tp) cc_final: 0.7378 (mm) REVERT: F 425 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6990 (mm110) REVERT: F 427 ASP cc_start: 0.6635 (p0) cc_final: 0.6086 (p0) REVERT: F 513 ASN cc_start: 0.7166 (p0) cc_final: 0.6950 (p0) REVERT: F 518 ILE cc_start: 0.8492 (tt) cc_final: 0.8249 (tp) REVERT: F 564 ARG cc_start: 0.6881 (ttm170) cc_final: 0.6548 (ttm170) REVERT: G 385 GLN cc_start: 0.7438 (mt0) cc_final: 0.7129 (mt0) REVERT: G 392 LYS cc_start: 0.7768 (mttm) cc_final: 0.7564 (ttmm) REVERT: G 418 ASN cc_start: 0.6085 (t0) cc_final: 0.5857 (t0) REVERT: G 440 LEU cc_start: 0.8396 (tp) cc_final: 0.8181 (tp) REVERT: H 334 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7518 (mtpp) REVERT: H 392 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7502 (ttmm) REVERT: H 408 GLN cc_start: 0.6481 (pt0) cc_final: 0.6165 (pt0) REVERT: H 414 LYS cc_start: 0.7021 (tmmt) cc_final: 0.6480 (ptmm) REVERT: H 461 PHE cc_start: 0.7739 (m-80) cc_final: 0.7225 (m-80) REVERT: H 552 LYS cc_start: 0.7587 (tmtt) cc_final: 0.7296 (tptp) REVERT: I 603 GLN cc_start: 0.6847 (mm110) cc_final: 0.6366 (mp10) REVERT: I 651 GLU cc_start: 0.3381 (mp0) cc_final: 0.3101 (mp0) outliers start: 100 outliers final: 67 residues processed: 991 average time/residue: 0.4489 time to fit residues: 646.2781 Evaluate side-chains 1012 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 943 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 539 LEU 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 458 ASP Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 396 SER 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 542 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 374 LYS Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 463 MET Chi-restraints excluded: chain E residue 529 LEU 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 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 652 ILE Chi-restraints excluded: chain F residue 436 ILE 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 453 THR Chi-restraints excluded: chain G residue 475 HIS 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 352 SER Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 546 LEU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 604 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 535 ILE Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 548 GLN Chi-restraints excluded: chain I residue 552 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 10.0000 chunk 33 optimal weight: 0.0040 chunk 171 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 299 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 182 optimal weight: 0.0980 chunk 138 optimal weight: 4.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS D 385 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 594 HIS D 603 GLN E 439 GLN E 555 ASN ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26184 Z= 0.175 Angle : 0.586 10.792 35244 Z= 0.302 Chirality : 0.043 0.382 3860 Planarity : 0.004 0.056 4540 Dihedral : 9.108 89.939 3706 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.80 % Rotamer: Outliers : 3.48 % Allowed : 22.10 % Favored : 74.42 % 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: 0.46 (0.13), residues: 1517 sheet: -0.14 (0.22), residues: 515 loop : 0.23 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 557 HIS 0.015 0.001 HIS A 475 PHE 0.042 0.001 PHE I 556 TYR 0.024 0.002 TYR B 367 ARG 0.010 0.000 ARG F 387 *********************** 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 1040 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 945 time to evaluate : 2.914 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 359 GLU cc_start: 0.4654 (mp0) cc_final: 0.4405 (mp0) REVERT: A 392 LYS cc_start: 0.7449 (ptmm) cc_final: 0.6972 (ttpt) REVERT: A 512 GLU cc_start: 0.6127 (tp30) cc_final: 0.5528 (tp30) REVERT: A 515 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6832 (mm) REVERT: A 525 ARG cc_start: 0.7026 (tpp80) cc_final: 0.6439 (tpp80) REVERT: A 534 GLU cc_start: 0.5782 (tp30) cc_final: 0.5328 (tp30) REVERT: A 550 VAL cc_start: 0.6131 (t) cc_final: 0.5897 (t) REVERT: B 346 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7571 (m) REVERT: B 383 GLU cc_start: 0.6868 (mp0) cc_final: 0.6017 (mp0) REVERT: B 389 GLU cc_start: 0.6069 (mp0) cc_final: 0.5367 (mp0) REVERT: B 392 LYS cc_start: 0.7815 (ptmt) cc_final: 0.7384 (ptmt) REVERT: B 404 GLU cc_start: 0.7033 (mp0) cc_final: 0.6730 (mp0) REVERT: B 450 LYS cc_start: 0.6327 (mtpt) cc_final: 0.5996 (mtpt) REVERT: B 458 ASP cc_start: 0.6636 (p0) cc_final: 0.6211 (p0) REVERT: B 511 LYS cc_start: 0.7672 (mppt) cc_final: 0.7368 (mtpt) REVERT: B 557 TRP cc_start: 0.6618 (m100) cc_final: 0.6062 (m100) REVERT: B 595 GLU cc_start: 0.6732 (pp20) cc_final: 0.5902 (tm-30) REVERT: C 363 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6717 (mm-40) REVERT: C 437 MET cc_start: 0.7607 (mmt) cc_final: 0.7299 (mmt) REVERT: C 534 GLU cc_start: 0.6449 (mm-30) cc_final: 0.6210 (mm-30) REVERT: D 315 GLU cc_start: 0.6622 (tm-30) cc_final: 0.6075 (tm-30) REVERT: D 389 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6346 (mm-30) REVERT: D 418 ASN cc_start: 0.7565 (t0) cc_final: 0.7351 (t0) REVERT: D 518 ILE cc_start: 0.8183 (tt) cc_final: 0.7775 (tp) REVERT: D 533 ASN cc_start: 0.7117 (m-40) cc_final: 0.6688 (m-40) REVERT: D 597 GLU cc_start: 0.5846 (tp30) cc_final: 0.5616 (tp30) REVERT: D 599 ARG cc_start: 0.7105 (mmm-85) cc_final: 0.6730 (mmm160) REVERT: E 340 ASP cc_start: 0.8083 (t0) cc_final: 0.7658 (t0) REVERT: E 428 LYS cc_start: 0.7595 (mmtm) cc_final: 0.7105 (mptt) REVERT: E 471 GLU cc_start: 0.6797 (mp0) cc_final: 0.6522 (mp0) REVERT: E 593 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7222 (ttpp) REVERT: F 317 ILE cc_start: 0.7804 (tp) cc_final: 0.7380 (mm) REVERT: F 420 VAL cc_start: 0.8172 (t) cc_final: 0.7936 (p) REVERT: F 425 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6946 (mm110) REVERT: F 427 ASP cc_start: 0.6572 (p0) cc_final: 0.6071 (p0) REVERT: F 513 ASN cc_start: 0.7166 (p0) cc_final: 0.6923 (p0) REVERT: F 518 ILE cc_start: 0.8458 (tt) cc_final: 0.8247 (tp) REVERT: F 564 ARG cc_start: 0.6691 (ttm170) cc_final: 0.6471 (ttm170) REVERT: G 385 GLN cc_start: 0.7423 (mt0) cc_final: 0.7146 (mt0) REVERT: G 418 ASN cc_start: 0.6099 (t0) cc_final: 0.5851 (t0) REVERT: G 440 LEU cc_start: 0.8511 (tp) cc_final: 0.8227 (tp) REVERT: G 443 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5832 (tm-30) REVERT: H 334 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7505 (mtpp) REVERT: H 378 ARG cc_start: 0.7007 (ttt180) cc_final: 0.6578 (ttt180) REVERT: H 392 LYS cc_start: 0.7829 (ttmt) cc_final: 0.7590 (ttmm) REVERT: H 408 GLN cc_start: 0.6474 (pt0) cc_final: 0.6144 (pt0) REVERT: H 414 LYS cc_start: 0.6979 (tmmt) cc_final: 0.6429 (ptmm) REVERT: H 461 PHE cc_start: 0.7742 (m-80) cc_final: 0.7293 (m-80) REVERT: H 552 LYS cc_start: 0.7535 (tmtt) cc_final: 0.7307 (tptp) REVERT: I 651 GLU cc_start: 0.3333 (mp0) cc_final: 0.2987 (mp0) outliers start: 95 outliers final: 74 residues processed: 976 average time/residue: 0.4485 time to fit residues: 636.6348 Evaluate side-chains 1004 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 927 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 322 SER 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 458 ASP Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 568 THR 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 353 SER 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 439 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 463 MET 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 617 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 652 ILE Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 544 SER 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 390 VAL Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 443 GLU Chi-restraints excluded: chain G residue 475 HIS 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 352 SER Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 440 LEU Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 546 LEU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 592 ILE Chi-restraints excluded: chain H residue 604 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 535 ILE Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 552 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 603 GLN E 439 GLN E 555 ASN ** F 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN G 474 GLN ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 603 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26184 Z= 0.247 Angle : 0.632 10.315 35244 Z= 0.328 Chirality : 0.044 0.271 3860 Planarity : 0.004 0.053 4540 Dihedral : 9.045 86.384 3706 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 3.81 % Allowed : 22.76 % Favored : 73.43 % 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: 0.17 (0.15), residues: 3096 helix: 0.40 (0.13), residues: 1505 sheet: -0.23 (0.22), residues: 519 loop : 0.15 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 338 HIS 0.016 0.001 HIS A 475 PHE 0.042 0.002 PHE I 556 TYR 0.032 0.002 TYR G 367 ARG 0.010 0.001 ARG F 387 *********************** 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 1070 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 966 time to evaluate : 2.674 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 335 GLU cc_start: 0.6102 (pt0) cc_final: 0.5898 (pt0) REVERT: A 392 LYS cc_start: 0.7599 (ptmm) cc_final: 0.7107 (ttpt) REVERT: A 512 GLU cc_start: 0.5985 (tp30) cc_final: 0.5363 (tp30) REVERT: A 515 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6885 (mm) REVERT: A 525 ARG cc_start: 0.6922 (tpp80) cc_final: 0.6365 (tpp80) REVERT: A 534 GLU cc_start: 0.5971 (tp30) cc_final: 0.5507 (tp30) REVERT: B 346 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7527 (m) REVERT: B 382 SER cc_start: 0.8557 (p) cc_final: 0.8019 (m) REVERT: B 392 LYS cc_start: 0.7832 (ptmt) cc_final: 0.7503 (ptmt) REVERT: B 428 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7007 (mtpp) REVERT: B 445 ARG cc_start: 0.8019 (ptm160) cc_final: 0.7728 (ptm160) REVERT: B 450 LYS cc_start: 0.6550 (mtpt) cc_final: 0.6129 (mtpt) REVERT: B 458 ASP cc_start: 0.6628 (p0) cc_final: 0.6199 (p0) REVERT: C 363 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6737 (mm-40) REVERT: C 392 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7572 (mtpp) REVERT: C 437 MET cc_start: 0.7641 (mmt) cc_final: 0.7322 (mmt) REVERT: C 522 HIS cc_start: 0.7384 (t70) cc_final: 0.7090 (t-90) REVERT: C 594 HIS cc_start: 0.4907 (p90) cc_final: 0.4600 (p90) REVERT: D 342 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6122 (mm-30) REVERT: D 352 SER cc_start: 0.7841 (m) cc_final: 0.7334 (p) REVERT: D 389 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6420 (mm-30) REVERT: D 457 LYS cc_start: 0.7522 (mtpt) cc_final: 0.7223 (mtpt) REVERT: D 518 ILE cc_start: 0.8262 (tt) cc_final: 0.7843 (tp) REVERT: D 533 ASN cc_start: 0.7221 (m-40) cc_final: 0.6272 (m-40) REVERT: D 592 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7451 (mt) REVERT: D 598 ARG cc_start: 0.7842 (ptt-90) cc_final: 0.7488 (ptp-170) REVERT: D 599 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6715 (mmm160) REVERT: E 332 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7587 (ttm-80) REVERT: E 340 ASP cc_start: 0.8187 (t0) cc_final: 0.7406 (t0) REVERT: E 367 TYR cc_start: 0.5578 (OUTLIER) cc_final: 0.5216 (p90) REVERT: E 428 LYS cc_start: 0.7674 (mmtm) cc_final: 0.7245 (mptt) REVERT: E 471 GLU cc_start: 0.6902 (mp0) cc_final: 0.6595 (mp0) REVERT: E 513 ASN cc_start: 0.7459 (m-40) cc_final: 0.7237 (m-40) REVERT: F 420 VAL cc_start: 0.8271 (t) cc_final: 0.7987 (p) REVERT: F 425 GLN cc_start: 0.7282 (mm-40) cc_final: 0.6960 (mm110) REVERT: F 427 ASP cc_start: 0.6707 (p0) cc_final: 0.6082 (p0) REVERT: F 564 ARG cc_start: 0.6816 (ttm170) cc_final: 0.6519 (ttm170) REVERT: G 385 GLN cc_start: 0.7352 (mt0) cc_final: 0.7017 (mt0) REVERT: G 418 ASN cc_start: 0.6182 (t0) cc_final: 0.5925 (t0) REVERT: G 440 LEU cc_start: 0.8561 (tp) cc_final: 0.8286 (tp) REVERT: G 590 ARG cc_start: 0.6142 (mtt180) cc_final: 0.5734 (mtt180) REVERT: H 334 LYS cc_start: 0.7801 (mtpp) cc_final: 0.7557 (mtpp) REVERT: H 408 GLN cc_start: 0.6520 (pt0) cc_final: 0.6178 (pt0) REVERT: H 414 LYS cc_start: 0.7043 (tmmt) cc_final: 0.6507 (ptmm) REVERT: H 461 PHE cc_start: 0.7852 (m-80) cc_final: 0.7342 (m-80) REVERT: H 527 GLU cc_start: 0.6989 (pm20) cc_final: 0.6454 (tm-30) REVERT: H 552 LYS cc_start: 0.7647 (tmtt) cc_final: 0.7303 (tptp) outliers start: 104 outliers final: 82 residues processed: 1003 average time/residue: 0.4506 time to fit residues: 653.9268 Evaluate side-chains 1050 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 962 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 464 THR 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 396 SER Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 485 GLU 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 336 ASN 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 439 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 463 MET 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 352 SER Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 465 SER Chi-restraints excluded: chain F residue 544 SER 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 390 VAL Chi-restraints excluded: chain G residue 425 GLN Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 518 ILE Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 310 GLU Chi-restraints excluded: chain H residue 312 ARG Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 592 ILE Chi-restraints excluded: chain H residue 604 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 552 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 7.9990 chunk 262 optimal weight: 0.0370 chunk 279 optimal weight: 8.9990 chunk 168 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 252 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 418 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 603 GLN E 555 ASN ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN ** G 385 GLN ** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26184 Z= 0.192 Angle : 0.628 13.589 35244 Z= 0.323 Chirality : 0.043 0.233 3860 Planarity : 0.004 0.064 4540 Dihedral : 8.777 87.523 3706 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.74 % Rotamer: Outliers : 3.19 % Allowed : 24.22 % Favored : 72.59 % 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: 0.24 (0.15), residues: 3096 helix: 0.47 (0.14), residues: 1504 sheet: -0.20 (0.22), residues: 524 loop : 0.17 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 338 HIS 0.019 0.001 HIS A 475 PHE 0.044 0.001 PHE I 556 TYR 0.025 0.002 TYR G 367 ARG 0.011 0.001 ARG G 531 *********************** 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 1049 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 962 time to evaluate : 2.852 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 392 LYS cc_start: 0.7493 (ptmm) cc_final: 0.6997 (ttpt) REVERT: A 512 GLU cc_start: 0.5949 (tp30) cc_final: 0.5365 (tp30) REVERT: A 515 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6841 (mm) REVERT: A 525 ARG cc_start: 0.6901 (tpp80) cc_final: 0.6615 (ttm-80) REVERT: A 534 GLU cc_start: 0.5972 (tp30) cc_final: 0.5631 (tp30) REVERT: B 346 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7590 (m) REVERT: B 382 SER cc_start: 0.8514 (p) cc_final: 0.8136 (m) REVERT: B 392 LYS cc_start: 0.7813 (ptmt) cc_final: 0.7472 (ptmt) REVERT: B 450 LYS cc_start: 0.6412 (mtpt) cc_final: 0.6032 (mtpt) REVERT: B 458 ASP cc_start: 0.6463 (p0) cc_final: 0.6047 (p0) REVERT: C 363 GLN cc_start: 0.7134 (mm-40) cc_final: 0.6703 (mm-40) REVERT: C 437 MET cc_start: 0.7613 (mmt) cc_final: 0.7300 (mmt) REVERT: C 522 HIS cc_start: 0.7391 (t70) cc_final: 0.7122 (t-90) REVERT: D 352 SER cc_start: 0.7841 (m) cc_final: 0.7293 (p) REVERT: D 389 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6339 (mm-30) REVERT: D 511 LYS cc_start: 0.8566 (mttt) cc_final: 0.8362 (mttt) REVERT: D 518 ILE cc_start: 0.8230 (tt) cc_final: 0.7798 (tp) REVERT: D 533 ASN cc_start: 0.6588 (m-40) cc_final: 0.6196 (m-40) REVERT: D 598 ARG cc_start: 0.7809 (ptt-90) cc_final: 0.7561 (ptp-170) REVERT: D 599 ARG cc_start: 0.7189 (mmm-85) cc_final: 0.6704 (mmm160) REVERT: D 601 VAL cc_start: 0.8315 (t) cc_final: 0.8053 (t) REVERT: E 332 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7602 (ttm-80) REVERT: E 340 ASP cc_start: 0.8153 (t0) cc_final: 0.7389 (t0) REVERT: E 367 TYR cc_start: 0.5545 (OUTLIER) cc_final: 0.5183 (p90) REVERT: E 428 LYS cc_start: 0.7614 (mmtm) cc_final: 0.7176 (mptt) REVERT: E 433 VAL cc_start: 0.8215 (p) cc_final: 0.7942 (p) REVERT: E 471 GLU cc_start: 0.6737 (mp0) cc_final: 0.6461 (mp0) REVERT: F 411 LYS cc_start: 0.7199 (ttpp) cc_final: 0.6950 (tttm) REVERT: F 420 VAL cc_start: 0.8157 (t) cc_final: 0.7871 (p) REVERT: F 425 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6886 (mm110) REVERT: F 427 ASP cc_start: 0.6543 (p0) cc_final: 0.5864 (p0) REVERT: F 516 ARG cc_start: 0.6526 (ttp-170) cc_final: 0.6185 (ttp-170) REVERT: F 564 ARG cc_start: 0.6745 (ttm170) cc_final: 0.6447 (ttm170) REVERT: G 347 PHE cc_start: 0.7503 (m-80) cc_final: 0.7090 (m-80) REVERT: G 357 LYS cc_start: 0.8018 (mtmm) cc_final: 0.7808 (mtmt) REVERT: G 385 GLN cc_start: 0.7358 (mt0) cc_final: 0.7082 (mt0) REVERT: G 418 ASN cc_start: 0.6094 (t0) cc_final: 0.5840 (t0) REVERT: G 440 LEU cc_start: 0.8561 (tp) cc_final: 0.8286 (tp) REVERT: G 531 ARG cc_start: 0.7720 (mtt-85) cc_final: 0.7326 (mtt90) REVERT: G 590 ARG cc_start: 0.6073 (mtt180) cc_final: 0.5559 (mtt180) REVERT: H 334 LYS cc_start: 0.7708 (mtpp) cc_final: 0.7484 (mtpp) REVERT: H 408 GLN cc_start: 0.6460 (pt0) cc_final: 0.6141 (pt0) REVERT: H 414 LYS cc_start: 0.7016 (tmmt) cc_final: 0.6470 (ptmm) REVERT: H 461 PHE cc_start: 0.7849 (m-80) cc_final: 0.7362 (m-80) REVERT: H 552 LYS cc_start: 0.7582 (tmtt) cc_final: 0.7254 (tptp) outliers start: 87 outliers final: 70 residues processed: 991 average time/residue: 0.4620 time to fit residues: 661.2517 Evaluate side-chains 1022 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 949 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 309 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 539 LEU 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 458 ASP Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 555 ASN 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 353 SER 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 439 GLN Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 463 MET 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 352 SER Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 465 SER Chi-restraints excluded: chain F residue 544 SER 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 390 VAL Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 310 GLU Chi-restraints excluded: chain H residue 312 ARG Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 592 ILE Chi-restraints excluded: chain H residue 604 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 20.0000 chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 0.0670 chunk 205 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 chunk 285 optimal weight: 0.0030 chunk 246 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 190 optimal weight: 0.0060 chunk 151 optimal weight: 0.9990 chunk 195 optimal weight: 0.6980 overall best weight: 0.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 ASN C 369 HIS C 388 HIS C 439 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 603 GLN ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 GLN ** F 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN ** H 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 551 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26184 Z= 0.184 Angle : 0.648 14.847 35244 Z= 0.332 Chirality : 0.043 0.229 3860 Planarity : 0.004 0.113 4540 Dihedral : 8.618 87.425 3706 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.42 % Allowed : 25.58 % Favored : 72.00 % 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: 0.29 (0.15), residues: 3096 helix: 0.53 (0.14), residues: 1501 sheet: -0.13 (0.22), residues: 522 loop : 0.14 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 338 HIS 0.016 0.001 HIS A 475 PHE 0.044 0.001 PHE I 556 TYR 0.023 0.002 TYR B 587 ARG 0.010 0.001 ARG A 333 ********************** 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 1017 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 951 time to evaluate : 2.867 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: 0.7333 (ptmm) cc_final: 0.6836 (ttpt) REVERT: A 512 GLU cc_start: 0.5984 (tp30) cc_final: 0.5350 (tp30) REVERT: A 525 ARG cc_start: 0.6804 (tpp80) cc_final: 0.6071 (tpp80) REVERT: A 534 GLU cc_start: 0.5878 (tp30) cc_final: 0.5609 (tp30) REVERT: B 346 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7686 (m) REVERT: B 392 LYS cc_start: 0.7800 (ptmt) cc_final: 0.7444 (ptmt) REVERT: B 428 LYS cc_start: 0.7305 (tttt) cc_final: 0.6981 (tptt) REVERT: B 445 ARG cc_start: 0.8125 (ptm160) cc_final: 0.7800 (ptm-80) REVERT: B 450 LYS cc_start: 0.6373 (mtpt) cc_final: 0.5996 (mtpt) REVERT: B 458 ASP cc_start: 0.6427 (p0) cc_final: 0.6021 (p0) REVERT: C 363 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6661 (mm-40) REVERT: C 411 LYS cc_start: 0.7016 (mtpp) cc_final: 0.6812 (mtpp) REVERT: C 437 MET cc_start: 0.7577 (mmt) cc_final: 0.7278 (mmt) REVERT: C 522 HIS cc_start: 0.7431 (t70) cc_final: 0.7105 (t-90) REVERT: C 547 ILE cc_start: 0.7979 (mt) cc_final: 0.7707 (mm) REVERT: D 352 SER cc_start: 0.7823 (m) cc_final: 0.7264 (p) REVERT: D 389 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6301 (mm-30) REVERT: D 518 ILE cc_start: 0.8207 (tt) cc_final: 0.7774 (tp) REVERT: D 533 ASN cc_start: 0.6516 (m-40) cc_final: 0.6227 (m-40) REVERT: D 601 VAL cc_start: 0.8274 (t) cc_final: 0.8019 (t) REVERT: E 332 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7657 (ttm-80) REVERT: E 340 ASP cc_start: 0.8162 (t0) cc_final: 0.7345 (t0) REVERT: E 367 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.5116 (p90) REVERT: E 428 LYS cc_start: 0.7563 (mmtm) cc_final: 0.7102 (mptt) REVERT: E 433 VAL cc_start: 0.8189 (p) cc_final: 0.7956 (p) REVERT: E 434 LEU cc_start: 0.7800 (mm) cc_final: 0.7511 (mt) REVERT: E 471 GLU cc_start: 0.6719 (mp0) cc_final: 0.6438 (mp0) REVERT: F 317 ILE cc_start: 0.7904 (tp) cc_final: 0.7463 (mm) REVERT: F 425 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6902 (mm110) REVERT: F 427 ASP cc_start: 0.6418 (p0) cc_final: 0.5885 (p0) REVERT: F 516 ARG cc_start: 0.6475 (ttp-170) cc_final: 0.6132 (ttp-170) REVERT: F 531 ARG cc_start: 0.7469 (mtt90) cc_final: 0.7132 (mtt-85) REVERT: F 564 ARG cc_start: 0.6689 (ttm170) cc_final: 0.6361 (ttm170) REVERT: F 603 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7143 (mm110) REVERT: G 347 PHE cc_start: 0.7482 (m-80) cc_final: 0.7073 (m-80) REVERT: G 385 GLN cc_start: 0.7310 (mt0) cc_final: 0.7080 (mt0) REVERT: G 418 ASN cc_start: 0.6013 (t0) cc_final: 0.5778 (t0) REVERT: G 427 ASP cc_start: 0.6814 (t0) cc_final: 0.6522 (t0) REVERT: G 440 LEU cc_start: 0.8556 (tp) cc_final: 0.8274 (tp) REVERT: G 445 ARG cc_start: 0.6992 (ptt-90) cc_final: 0.6182 (ptt-90) REVERT: G 531 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7318 (mtt90) REVERT: G 590 ARG cc_start: 0.6052 (mtt180) cc_final: 0.5597 (mtt180) REVERT: H 334 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7478 (mtpp) REVERT: H 378 ARG cc_start: 0.7085 (ttt180) cc_final: 0.6835 (ttt180) REVERT: H 408 GLN cc_start: 0.6417 (pt0) cc_final: 0.6074 (pt0) REVERT: H 414 LYS cc_start: 0.6988 (tmmt) cc_final: 0.6410 (ptmm) REVERT: H 461 PHE cc_start: 0.7848 (m-80) cc_final: 0.7380 (m-80) REVERT: H 545 GLU cc_start: 0.7139 (mp0) cc_final: 0.5853 (mt-10) REVERT: H 552 LYS cc_start: 0.7547 (tmtt) cc_final: 0.7231 (tptp) outliers start: 66 outliers final: 56 residues processed: 976 average time/residue: 0.4567 time to fit residues: 644.9538 Evaluate side-chains 1000 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 942 time to evaluate : 2.794 ------------------------------------------------------------------------------- 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 331 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 539 LEU 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 527 GLU Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain E residue 318 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 418 ASN Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 463 MET 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 436 ILE Chi-restraints excluded: chain F residue 465 SER Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 310 GLU Chi-restraints excluded: chain H residue 312 ARG Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 592 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 253 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS D 418 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 594 HIS D 603 GLN F 548 GLN ** F 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.163900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132281 restraints weight = 46532.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136367 restraints weight = 21944.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139057 restraints weight = 13197.963| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26184 Z= 0.231 Angle : 0.659 14.254 35244 Z= 0.341 Chirality : 0.044 0.357 3860 Planarity : 0.004 0.049 4540 Dihedral : 8.657 89.882 3706 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 2.78 % Allowed : 25.28 % Favored : 71.93 % Cbeta Deviations : 0.00 % 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: 0.28 (0.15), residues: 3096 helix: 0.52 (0.14), residues: 1489 sheet: -0.13 (0.23), residues: 522 loop : 0.14 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 338 HIS 0.015 0.001 HIS A 475 PHE 0.043 0.002 PHE I 556 TYR 0.022 0.002 TYR G 367 ARG 0.011 0.001 ARG G 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9313.81 seconds wall clock time: 165 minutes 50.94 seconds (9950.94 seconds total)