Starting phenix.real_space_refine on Sun Mar 17 06:51:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/03_2024/8hwh_35058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/03_2024/8hwh_35058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/03_2024/8hwh_35058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/03_2024/8hwh_35058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/03_2024/8hwh_35058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/03_2024/8hwh_35058.pdb" } resolution = 3.6 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= 0.074 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 93 5.16 5 C 10815 2.51 5 N 2867 2.21 5 O 3167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A ASP 534": "OD1" <-> "OD2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 411": "OD1" <-> "OD2" Residue "B PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B ASP 473": "OD1" <-> "OD2" Residue "B PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B ASP 560": "OD1" <-> "OD2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B GLU 579": "OE1" <-> "OE2" Residue "B ASP 603": "OD1" <-> "OD2" Residue "B ASP 656": "OD1" <-> "OD2" Residue "B TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 695": "OD1" <-> "OD2" Residue "C ASP 346": "OD1" <-> "OD2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 402": "OD1" <-> "OD2" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 411": "OD1" <-> "OD2" Residue "C PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 424": "OD1" <-> "OD2" Residue "C TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 431": "OD1" <-> "OD2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 448": "OD1" <-> "OD2" Residue "C ASP 473": "OD1" <-> "OD2" Residue "C TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 522": "OD1" <-> "OD2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C ASP 537": "OD1" <-> "OD2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 579": "OE1" <-> "OE2" Residue "C PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 656": "OD1" <-> "OD2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 432": "OD1" <-> "OD2" Residue "D ASP 454": "OD1" <-> "OD2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D ASP 467": "OD1" <-> "OD2" Residue "D GLU 480": "OE1" <-> "OE2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "D ASP 534": "OD1" <-> "OD2" Residue "D PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 572": "OD1" <-> "OD2" Residue "D GLU 579": "OE1" <-> "OE2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 611": "OD1" <-> "OD2" Residue "D GLU 691": "OE1" <-> "OE2" Residue "D PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 346": "OD1" <-> "OD2" Residue "E ASP 402": "OD1" <-> "OD2" Residue "E GLU 405": "OE1" <-> "OE2" Residue "E ASP 431": "OD1" <-> "OD2" Residue "E GLU 459": "OE1" <-> "OE2" Residue "E ASP 467": "OD1" <-> "OD2" Residue "E GLU 480": "OE1" <-> "OE2" Residue "E ASP 522": "OD1" <-> "OD2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 579": "OE1" <-> "OE2" Residue "E PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 346": "OD1" <-> "OD2" Residue "F PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 424": "OD1" <-> "OD2" Residue "F ASP 431": "OD1" <-> "OD2" Residue "F PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 457": "OE1" <-> "OE2" Residue "F ASP 467": "OD1" <-> "OD2" Residue "F PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 611": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16948 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2858 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 17, 'TRANS': 335} Chain breaks: 1 Chain: "B" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2887 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 1 Chain: "C" Number of atoms: 2920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2920 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain breaks: 1 Chain: "D" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2940 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 17, 'TRANS': 345} Chain breaks: 1 Chain: "E" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2662 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Chain: "F" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2561 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 14, 'TRANS': 301} Chain breaks: 3 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 8.52, per 1000 atoms: 0.50 Number of scatterers: 16948 At special positions: 0 Unit cell: (109.5, 131.4, 132.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 6 15.00 O 3167 8.00 N 2867 7.00 C 10815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.03 Conformation dependent library (CDL) restraints added in 2.8 seconds 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3966 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 23 sheets defined 43.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.716A pdb=" N LEU A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.768A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 571 through 576 removed outlier: 4.000A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 571 through 576' Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.891A pdb=" N MET A 618 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.673A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 660' Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.701A pdb=" N LYS A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 removed outlier: 3.904A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.595A pdb=" N LEU B 375 " --> pdb=" O ARG B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.619A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.587A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.954A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.583A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 661' Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.829A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 679 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 692 Processing helix chain 'B' and resid 693 through 700 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.691A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.939A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.535A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.939A pdb=" N THR C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 removed outlier: 3.509A pdb=" N ASP C 432 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.506A pdb=" N LYS C 450 " --> pdb=" O ASP C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.884A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.592A pdb=" N THR C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.561A pdb=" N ASN C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 removed outlier: 4.010A pdb=" N PHE C 668 " --> pdb=" O TYR C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 700 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.539A pdb=" N ILE D 329 " --> pdb=" O LYS D 325 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.741A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.600A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 472 through 475 Processing helix chain 'D' and resid 476 through 488 removed outlier: 3.519A pdb=" N TYR D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.603A pdb=" N ALA D 519 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.660A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 577 " --> pdb=" O ASN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 removed outlier: 4.015A pdb=" N MET D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 614 through 619' Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.952A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN D 661 " --> pdb=" O GLY D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 661' Processing helix chain 'D' and resid 665 through 680 Processing helix chain 'D' and resid 693 through 700 Processing helix chain 'E' and resid 324 through 335 Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.578A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 400 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.575A pdb=" N ASP E 432 " --> pdb=" O SER E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 removed outlier: 4.008A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 488 Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 528 through 533 removed outlier: 3.846A pdb=" N ILE E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 548 removed outlier: 4.187A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN E 546 " --> pdb=" O PRO E 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS E 548 " --> pdb=" O ILE E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 614 through 619 removed outlier: 3.859A pdb=" N MET E 618 " --> pdb=" O ASP E 614 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 614 through 619' Processing helix chain 'E' and resid 657 through 661 removed outlier: 4.569A pdb=" N ASN E 661 " --> pdb=" O GLY E 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 657 through 661' Processing helix chain 'E' and resid 665 through 680 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.571A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 387 through 400 Processing helix chain 'F' and resid 429 through 434 Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.838A pdb=" N LYS F 450 " --> pdb=" O ASP F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 removed outlier: 3.882A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.745A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 520 Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.722A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 546 removed outlier: 4.045A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 578 removed outlier: 3.871A pdb=" N THR F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.626A pdb=" N MET F 618 " --> pdb=" O ASP F 614 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 614 through 619' Processing helix chain 'F' and resid 656 through 661 removed outlier: 4.027A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN F 661 " --> pdb=" O GLY F 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 656 through 661' Processing helix chain 'F' and resid 665 through 680 Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AA3, first strand: chain 'A' and resid 601 through 602 removed outlier: 6.646A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.967A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 582 through 583 Processing sheet with id=AA6, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AA7, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.812A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.729A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AB2, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.861A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 525 through 526 removed outlier: 6.940A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB5, first strand: chain 'D' and resid 349 through 350 Processing sheet with id=AB6, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.581A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.430A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AB9, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC1, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AC2, first strand: chain 'E' and resid 525 through 527 removed outlier: 6.447A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR E 499 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 340 through 341 Processing sheet with id=AC4, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AC5, first strand: chain 'F' and resid 525 through 527 removed outlier: 3.597A pdb=" N VAL F 553 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE F 601 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR F 499 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR F 604 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE F 501 " --> pdb=" O THR F 604 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1533 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: 4.49 Time building geometry restraints manager: 6.53 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: 3535 1.33 - 1.45: 3800 1.45 - 1.57: 9819 1.57 - 1.69: 12 1.69 - 1.82: 135 Bond restraints: 17301 Sorted by residual: bond pdb=" N ILE D 531 " pdb=" CA ILE D 531 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.21e+00 bond pdb=" CB PRO D 362 " pdb=" CG PRO D 362 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.93e+00 bond pdb=" N MET A 462 " pdb=" CA MET A 462 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.23e+00 bond pdb=" N ASP A 522 " pdb=" CA ASP A 522 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.17e+00 bond pdb=" N LEU D 532 " pdb=" CA LEU D 532 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.26e+00 ... (remaining 17296 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.53: 365 105.53 - 112.68: 8992 112.68 - 119.82: 5943 119.82 - 126.97: 7905 126.97 - 134.11: 168 Bond angle restraints: 23373 Sorted by residual: angle pdb=" CA PRO D 362 " pdb=" N PRO D 362 " pdb=" CD PRO D 362 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 angle pdb=" N GLY A 418 " pdb=" CA GLY A 418 " pdb=" C GLY A 418 " ideal model delta sigma weight residual 110.96 116.61 -5.65 1.19e+00 7.06e-01 2.25e+01 angle pdb=" N LYS E 434 " pdb=" CA LYS E 434 " pdb=" C LYS E 434 " ideal model delta sigma weight residual 114.75 109.35 5.40 1.26e+00 6.30e-01 1.83e+01 angle pdb=" C SER B 556 " pdb=" N GLU B 557 " pdb=" CA GLU B 557 " ideal model delta sigma weight residual 122.08 127.99 -5.91 1.47e+00 4.63e-01 1.62e+01 angle pdb=" CA MET E 462 " pdb=" CB MET E 462 " pdb=" CG MET E 462 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 ... (remaining 23368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.90: 10084 32.90 - 65.79: 441 65.79 - 98.69: 26 98.69 - 131.59: 0 131.59 - 164.48: 2 Dihedral angle restraints: 10553 sinusoidal: 4452 harmonic: 6101 Sorted by residual: dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 55.52 164.48 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT S 2 " pdb=" C3' DT S 2 " pdb=" O3' DT S 2 " pdb=" P DT S 3 " ideal model delta sinusoidal sigma weight residual 220.00 81.23 138.77 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA HIS D 680 " pdb=" C HIS D 680 " pdb=" N ILE D 681 " pdb=" CA ILE D 681 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 10550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2156 0.056 - 0.112: 431 0.112 - 0.168: 39 0.168 - 0.224: 4 0.224 - 0.280: 1 Chirality restraints: 2631 Sorted by residual: chirality pdb=" CA LEU D 532 " pdb=" N LEU D 532 " pdb=" C LEU D 532 " pdb=" CB LEU D 532 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE F 600 " pdb=" CA ILE F 600 " pdb=" CG1 ILE F 600 " pdb=" CG2 ILE F 600 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 2628 not shown) Planarity restraints: 2953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 385 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO C 386 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 386 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 386 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 479 " -0.161 9.50e-02 1.11e+02 7.27e-02 4.19e+00 pdb=" NE ARG B 479 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 479 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 479 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 479 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 558 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO E 559 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 559 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 559 " 0.027 5.00e-02 4.00e+02 ... (remaining 2950 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1308 2.74 - 3.28: 17034 3.28 - 3.82: 27009 3.82 - 4.36: 32189 4.36 - 4.90: 55076 Nonbonded interactions: 132616 Sorted by model distance: nonbonded pdb=" O GLU D 504 " pdb=" OG1 THR D 507 " model vdw 2.198 2.440 nonbonded pdb=" NH1 ARG D 389 " pdb=" OD2 ASP E 398 " model vdw 2.201 2.520 nonbonded pdb=" OG SER B 455 " pdb=" OE1 GLU B 457 " model vdw 2.231 2.440 nonbonded pdb=" OD1 ASP A 411 " pdb=" NZ LYS A 412 " model vdw 2.231 2.520 nonbonded pdb=" NH1 ARG A 389 " pdb=" OD2 ASP B 398 " model vdw 2.237 2.520 ... (remaining 132611 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 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 656 through 689)) selection = (chain 'B' and (resid 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 652 or resid 657 through 689)) selection = (chain 'C' and (resid 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 656 through 689)) selection = (chain 'D' and (resid 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 656 through 689)) selection = (chain 'E' and (resid 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 656 through 689)) selection = (chain 'F' and (resid 323 through 628 or resid 656 through 689)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.510 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 41.790 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.003 0.132 17301 Z= 0.195 Angle : 0.708 10.467 23373 Z= 0.405 Chirality : 0.044 0.280 2631 Planarity : 0.004 0.073 2953 Dihedral : 17.523 164.482 6587 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 0.42 % Allowed : 30.03 % Favored : 69.55 % 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: -1.34 (0.19), residues: 2049 helix: 0.57 (0.21), residues: 689 sheet: -1.64 (0.33), residues: 256 loop : -1.69 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 675 HIS 0.005 0.001 HIS C 629 PHE 0.021 0.001 PHE C 357 TYR 0.014 0.001 TYR B 482 ARG 0.017 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 2.055 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: A 489 CYS cc_start: 0.8859 (m) cc_final: 0.7812 (t) REVERT: D 660 GLN cc_start: 0.8906 (mp10) cc_final: 0.8625 (mp10) outliers start: 8 outliers final: 2 residues processed: 184 average time/residue: 0.2868 time to fit residues: 80.3257 Evaluate side-chains 161 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 4.9990 chunk 155 optimal weight: 0.0870 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN B 475 ASN B 478 ASN C 529 GLN D 680 HIS E 358 ASN F 529 GLN F 548 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17301 Z= 0.386 Angle : 0.665 7.249 23373 Z= 0.344 Chirality : 0.045 0.162 2631 Planarity : 0.004 0.052 2953 Dihedral : 8.580 161.503 2307 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.50 % Allowed : 26.89 % Favored : 67.61 % 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: -1.57 (0.18), residues: 2049 helix: 0.23 (0.19), residues: 724 sheet: -1.71 (0.33), residues: 255 loop : -1.80 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 675 HIS 0.007 0.001 HIS A 597 PHE 0.020 0.002 PHE B 543 TYR 0.019 0.002 TYR F 482 ARG 0.006 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 170 time to evaluate : 2.175 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: A 489 CYS cc_start: 0.9062 (m) cc_final: 0.8115 (t) REVERT: B 382 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: C 474 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7467 (pp20) REVERT: C 554 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7968 (t80) REVERT: D 504 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: D 543 PHE cc_start: 0.7834 (p90) cc_final: 0.7380 (p90) REVERT: D 611 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7682 (p0) REVERT: D 658 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7636 (pttp) REVERT: E 547 MET cc_start: 0.8365 (tmm) cc_final: 0.8107 (ppp) REVERT: F 462 MET cc_start: 0.7288 (ptp) cc_final: 0.7073 (ptp) REVERT: F 547 MET cc_start: 0.7320 (tmm) cc_final: 0.6858 (tmm) outliers start: 105 outliers final: 69 residues processed: 258 average time/residue: 0.2686 time to fit residues: 106.9923 Evaluate side-chains 229 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 154 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 611 ASP Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 662 ASN C 529 GLN F 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17301 Z= 0.315 Angle : 0.598 6.920 23373 Z= 0.312 Chirality : 0.043 0.176 2631 Planarity : 0.004 0.046 2953 Dihedral : 8.551 163.115 2307 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.29 % Allowed : 27.73 % Favored : 66.98 % 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: -1.41 (0.18), residues: 2049 helix: 0.40 (0.19), residues: 721 sheet: -1.69 (0.34), residues: 244 loop : -1.72 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 675 HIS 0.005 0.001 HIS A 597 PHE 0.021 0.001 PHE B 543 TYR 0.018 0.001 TYR F 482 ARG 0.005 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 167 time to evaluate : 2.022 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: A 489 CYS cc_start: 0.9048 (m) cc_final: 0.8096 (t) REVERT: A 547 MET cc_start: 0.8052 (ppp) cc_final: 0.7590 (ppp) REVERT: B 374 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: B 382 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: C 474 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7404 (pp20) REVERT: C 554 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7784 (t80) REVERT: D 504 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: D 543 PHE cc_start: 0.7941 (p90) cc_final: 0.7359 (p90) REVERT: D 684 MET cc_start: 0.8613 (tmm) cc_final: 0.8392 (tmm) REVERT: E 547 MET cc_start: 0.8457 (tmm) cc_final: 0.8179 (ppp) REVERT: E 548 HIS cc_start: 0.6653 (OUTLIER) cc_final: 0.4705 (t70) REVERT: F 462 MET cc_start: 0.7177 (ptp) cc_final: 0.6734 (ptp) REVERT: F 486 LEU cc_start: 0.9527 (mt) cc_final: 0.9279 (mp) REVERT: F 547 MET cc_start: 0.7631 (tmm) cc_final: 0.7186 (tmm) REVERT: F 656 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7853 (m-30) outliers start: 101 outliers final: 60 residues processed: 254 average time/residue: 0.2509 time to fit residues: 100.1946 Evaluate side-chains 219 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 152 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 611 ASP Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 546 ASN B 594 ASN C 529 GLN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17301 Z= 0.222 Angle : 0.553 8.433 23373 Z= 0.287 Chirality : 0.042 0.244 2631 Planarity : 0.004 0.041 2953 Dihedral : 8.454 162.704 2307 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.77 % Allowed : 28.67 % Favored : 66.56 % 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: -1.24 (0.18), residues: 2049 helix: 0.62 (0.19), residues: 723 sheet: -1.61 (0.34), residues: 244 loop : -1.68 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP F 675 HIS 0.003 0.001 HIS A 548 PHE 0.017 0.001 PHE A 543 TYR 0.016 0.001 TYR F 482 ARG 0.006 0.000 ARG D 627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 173 time to evaluate : 2.021 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: A 489 CYS cc_start: 0.9021 (m) cc_final: 0.8076 (t) REVERT: A 547 MET cc_start: 0.7969 (ppp) cc_final: 0.7553 (ppp) REVERT: B 382 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: B 447 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8241 (t70) REVERT: B 514 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8301 (ttm110) REVERT: C 554 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7676 (t80) REVERT: D 504 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: D 543 PHE cc_start: 0.7898 (p90) cc_final: 0.7538 (p90) REVERT: D 658 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7649 (pttp) REVERT: E 417 ASN cc_start: 0.7140 (OUTLIER) cc_final: 0.6770 (p0) REVERT: F 469 GLN cc_start: 0.7122 (mm-40) cc_final: 0.6859 (tp-100) REVERT: F 486 LEU cc_start: 0.9497 (mt) cc_final: 0.9245 (mm) REVERT: F 501 PHE cc_start: 0.7690 (m-80) cc_final: 0.7327 (m-10) REVERT: F 656 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7860 (m-30) outliers start: 91 outliers final: 66 residues processed: 252 average time/residue: 0.2498 time to fit residues: 99.8044 Evaluate side-chains 232 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 158 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 611 ASP Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 GLN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17301 Z= 0.175 Angle : 0.522 7.427 23373 Z= 0.272 Chirality : 0.042 0.220 2631 Planarity : 0.003 0.039 2953 Dihedral : 8.344 162.843 2307 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.87 % Allowed : 29.25 % Favored : 65.88 % 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: -1.05 (0.18), residues: 2049 helix: 0.83 (0.20), residues: 723 sheet: -1.34 (0.34), residues: 247 loop : -1.64 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP F 675 HIS 0.003 0.001 HIS A 548 PHE 0.017 0.001 PHE A 543 TYR 0.019 0.001 TYR F 482 ARG 0.005 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 173 time to evaluate : 1.908 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: A 489 CYS cc_start: 0.8992 (m) cc_final: 0.8108 (t) REVERT: A 547 MET cc_start: 0.7885 (ppp) cc_final: 0.7471 (ppp) REVERT: B 374 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: B 382 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: B 447 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8207 (t70) REVERT: B 514 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8263 (ttm110) REVERT: C 426 MET cc_start: 0.6417 (mtm) cc_final: 0.6165 (ptm) REVERT: D 543 PHE cc_start: 0.7879 (p90) cc_final: 0.7656 (p90) REVERT: D 658 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7770 (pttp) REVERT: D 660 GLN cc_start: 0.9138 (mp10) cc_final: 0.8903 (mp10) REVERT: E 417 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6641 (p0) REVERT: E 597 HIS cc_start: 0.8121 (m170) cc_final: 0.7441 (m-70) REVERT: E 612 ARG cc_start: 0.7563 (mtm110) cc_final: 0.6923 (tmm-80) REVERT: F 469 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6858 (tp-100) REVERT: F 486 LEU cc_start: 0.9492 (mt) cc_final: 0.9232 (mp) REVERT: F 547 MET cc_start: 0.7786 (tmm) cc_final: 0.7576 (tmm) REVERT: F 656 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7873 (m-30) outliers start: 93 outliers final: 67 residues processed: 253 average time/residue: 0.2605 time to fit residues: 101.3334 Evaluate side-chains 234 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 160 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 ASN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 662 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17301 Z= 0.195 Angle : 0.540 8.775 23373 Z= 0.278 Chirality : 0.042 0.221 2631 Planarity : 0.003 0.039 2953 Dihedral : 8.337 163.119 2307 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 6.08 % Allowed : 28.25 % Favored : 65.67 % 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: -0.99 (0.19), residues: 2049 helix: 0.87 (0.20), residues: 723 sheet: -1.29 (0.34), residues: 247 loop : -1.60 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP F 675 HIS 0.003 0.001 HIS D 347 PHE 0.019 0.001 PHE A 543 TYR 0.015 0.001 TYR F 482 ARG 0.004 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 169 time to evaluate : 2.177 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: A 489 CYS cc_start: 0.9023 (m) cc_final: 0.8413 (t) REVERT: A 547 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7431 (ppp) REVERT: B 374 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: B 382 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: B 514 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8274 (ttm110) REVERT: C 554 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7586 (t80) REVERT: D 504 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8073 (tp30) REVERT: D 543 PHE cc_start: 0.8041 (p90) cc_final: 0.7807 (p90) REVERT: D 658 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7727 (pttp) REVERT: D 660 GLN cc_start: 0.9157 (mp10) cc_final: 0.8915 (mp10) REVERT: E 417 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6807 (p0) REVERT: E 597 HIS cc_start: 0.8061 (m170) cc_final: 0.7343 (m-70) REVERT: E 612 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7000 (tmm-80) REVERT: F 469 GLN cc_start: 0.7097 (mm-40) cc_final: 0.6798 (tp-100) REVERT: F 501 PHE cc_start: 0.7470 (m-80) cc_final: 0.7118 (m-10) REVERT: F 514 ARG cc_start: 0.8507 (mtm180) cc_final: 0.8277 (mtm110) REVERT: F 547 MET cc_start: 0.7854 (tmm) cc_final: 0.7638 (tmm) REVERT: F 656 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7920 (m-30) outliers start: 116 outliers final: 87 residues processed: 269 average time/residue: 0.2490 time to fit residues: 104.6382 Evaluate side-chains 256 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 160 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 20.0000 chunk 22 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 166 optimal weight: 0.0170 chunk 110 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 GLN C 605 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17301 Z= 0.163 Angle : 0.537 10.197 23373 Z= 0.276 Chirality : 0.042 0.252 2631 Planarity : 0.003 0.036 2953 Dihedral : 8.277 162.996 2307 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.82 % Allowed : 29.72 % Favored : 65.46 % 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: -0.93 (0.19), residues: 2049 helix: 0.86 (0.20), residues: 730 sheet: -1.25 (0.34), residues: 249 loop : -1.55 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP F 675 HIS 0.006 0.001 HIS E 680 PHE 0.014 0.001 PHE A 543 TYR 0.016 0.001 TYR F 664 ARG 0.008 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 172 time to evaluate : 1.564 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: A 489 CYS cc_start: 0.8992 (m) cc_final: 0.8403 (t) REVERT: A 547 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7487 (ppp) REVERT: B 374 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: B 382 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: B 489 CYS cc_start: 0.8481 (m) cc_final: 0.8164 (t) REVERT: B 514 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8241 (ttm110) REVERT: C 592 ILE cc_start: 0.8723 (mm) cc_final: 0.8518 (tp) REVERT: D 504 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: D 543 PHE cc_start: 0.8010 (p90) cc_final: 0.7773 (p90) REVERT: D 658 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7767 (pttp) REVERT: E 360 GLU cc_start: 0.7282 (pm20) cc_final: 0.7047 (pm20) REVERT: E 417 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6752 (p0) REVERT: E 597 HIS cc_start: 0.8033 (m170) cc_final: 0.7289 (m-70) REVERT: E 612 ARG cc_start: 0.7575 (mtm110) cc_final: 0.6998 (tmm-80) REVERT: F 390 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7708 (mptt) REVERT: F 469 GLN cc_start: 0.7117 (mm-40) cc_final: 0.6830 (tp-100) REVERT: F 501 PHE cc_start: 0.7458 (m-80) cc_final: 0.7123 (m-10) REVERT: F 514 ARG cc_start: 0.8485 (mtm180) cc_final: 0.8269 (mtm180) REVERT: F 547 MET cc_start: 0.7855 (tmm) cc_final: 0.7638 (tmm) REVERT: F 656 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7877 (m-30) outliers start: 92 outliers final: 66 residues processed: 248 average time/residue: 0.2490 time to fit residues: 96.9744 Evaluate side-chains 238 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 163 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 390 LYS Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 485 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 0.0980 chunk 155 optimal weight: 40.0000 chunk 179 optimal weight: 0.5980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17301 Z= 0.193 Angle : 0.556 9.398 23373 Z= 0.286 Chirality : 0.042 0.221 2631 Planarity : 0.003 0.038 2953 Dihedral : 8.302 163.300 2307 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.29 % Allowed : 29.25 % Favored : 65.46 % 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: -0.94 (0.19), residues: 2049 helix: 0.78 (0.20), residues: 739 sheet: -1.20 (0.34), residues: 243 loop : -1.53 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP F 675 HIS 0.006 0.001 HIS E 680 PHE 0.013 0.001 PHE E 561 TYR 0.055 0.001 TYR F 482 ARG 0.006 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 169 time to evaluate : 2.120 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: A 489 CYS cc_start: 0.9005 (m) cc_final: 0.8398 (t) REVERT: A 547 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7411 (ppp) REVERT: B 374 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: B 382 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: B 481 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8904 (tt) REVERT: B 514 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8258 (ttm110) REVERT: B 689 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.7142 (p) REVERT: C 426 MET cc_start: 0.6566 (mtm) cc_final: 0.6356 (ttp) REVERT: C 435 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8246 (ptpp) REVERT: D 504 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8094 (tp30) REVERT: D 543 PHE cc_start: 0.8014 (p90) cc_final: 0.7798 (p90) REVERT: D 658 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7568 (pttp) REVERT: E 360 GLU cc_start: 0.7409 (pm20) cc_final: 0.7191 (pm20) REVERT: E 417 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6765 (p0) REVERT: E 597 HIS cc_start: 0.8027 (m170) cc_final: 0.7288 (m-70) REVERT: E 612 ARG cc_start: 0.7559 (mtm110) cc_final: 0.6997 (tmm-80) REVERT: F 390 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7806 (mptt) REVERT: F 469 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6856 (tp-100) REVERT: F 501 PHE cc_start: 0.7592 (m-80) cc_final: 0.7155 (m-10) REVERT: F 514 ARG cc_start: 0.8512 (mtm180) cc_final: 0.8231 (mtm180) REVERT: F 547 MET cc_start: 0.7866 (tmm) cc_final: 0.7638 (tmm) REVERT: F 656 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7868 (m-30) outliers start: 101 outliers final: 83 residues processed: 254 average time/residue: 0.2523 time to fit residues: 100.5983 Evaluate side-chains 259 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 164 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 390 LYS Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.0870 chunk 172 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17301 Z= 0.211 Angle : 0.567 10.002 23373 Z= 0.290 Chirality : 0.042 0.216 2631 Planarity : 0.004 0.039 2953 Dihedral : 8.337 163.580 2307 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.14 % Allowed : 29.14 % Favored : 65.72 % 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: -0.94 (0.19), residues: 2049 helix: 0.78 (0.20), residues: 740 sheet: -1.18 (0.34), residues: 243 loop : -1.54 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP F 675 HIS 0.011 0.001 HIS E 548 PHE 0.011 0.001 PHE A 543 TYR 0.018 0.001 TYR F 482 ARG 0.010 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 165 time to evaluate : 2.088 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: A 489 CYS cc_start: 0.8995 (m) cc_final: 0.8511 (t) REVERT: A 547 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7326 (ppp) REVERT: B 374 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: B 382 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: B 481 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8871 (tt) REVERT: B 514 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8295 (ttm110) REVERT: C 435 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8167 (ptpp) REVERT: C 534 ASP cc_start: 0.8312 (p0) cc_final: 0.8045 (p0) REVERT: D 504 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8057 (tp30) REVERT: D 543 PHE cc_start: 0.8029 (p90) cc_final: 0.7758 (p90) REVERT: D 658 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7713 (pttp) REVERT: E 360 GLU cc_start: 0.7439 (pm20) cc_final: 0.7237 (pm20) REVERT: E 417 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6674 (p0) REVERT: E 597 HIS cc_start: 0.7954 (m170) cc_final: 0.7243 (m-70) REVERT: E 612 ARG cc_start: 0.7469 (mtm110) cc_final: 0.6954 (tmm-80) REVERT: F 390 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7851 (mptt) REVERT: F 469 GLN cc_start: 0.6913 (mm-40) cc_final: 0.6665 (tp-100) REVERT: F 514 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8240 (ptp-110) REVERT: F 532 LEU cc_start: 0.7999 (tp) cc_final: 0.7465 (pp) REVERT: F 547 MET cc_start: 0.7913 (tmm) cc_final: 0.7694 (tmm) outliers start: 98 outliers final: 78 residues processed: 251 average time/residue: 0.2668 time to fit residues: 104.2178 Evaluate side-chains 245 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 157 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 390 LYS Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 7.9990 chunk 118 optimal weight: 0.0670 chunk 92 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17301 Z= 0.156 Angle : 0.557 11.242 23373 Z= 0.283 Chirality : 0.042 0.223 2631 Planarity : 0.003 0.039 2953 Dihedral : 8.142 163.259 2303 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.67 % Allowed : 30.71 % Favored : 65.62 % 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: -0.77 (0.19), residues: 2049 helix: 0.92 (0.20), residues: 735 sheet: -1.10 (0.35), residues: 244 loop : -1.42 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP F 675 HIS 0.008 0.001 HIS E 548 PHE 0.015 0.001 PHE D 696 TYR 0.014 0.001 TYR C 482 ARG 0.009 0.000 ARG B 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 170 time to evaluate : 1.989 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: A 489 CYS cc_start: 0.8951 (m) cc_final: 0.8462 (t) REVERT: A 547 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7409 (ppp) REVERT: B 374 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: B 377 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8211 (tptm) REVERT: B 382 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: B 481 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8865 (tt) REVERT: B 489 CYS cc_start: 0.8453 (m) cc_final: 0.8169 (t) REVERT: B 514 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8192 (ttm110) REVERT: B 689 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7130 (p) REVERT: C 534 ASP cc_start: 0.8246 (p0) cc_final: 0.7920 (p0) REVERT: D 504 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: D 543 PHE cc_start: 0.8038 (p90) cc_final: 0.7734 (p90) REVERT: D 658 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7601 (pttp) REVERT: E 360 GLU cc_start: 0.7375 (pm20) cc_final: 0.7140 (pm20) REVERT: E 417 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6659 (p0) REVERT: E 597 HIS cc_start: 0.7873 (m170) cc_final: 0.7161 (m-70) REVERT: E 612 ARG cc_start: 0.7405 (mtm110) cc_final: 0.6908 (tmm-80) REVERT: F 390 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7675 (mptt) REVERT: F 469 GLN cc_start: 0.6821 (mm-40) cc_final: 0.6567 (tp-100) REVERT: F 532 LEU cc_start: 0.7980 (tp) cc_final: 0.7448 (pp) REVERT: F 547 MET cc_start: 0.7957 (tmm) cc_final: 0.7531 (tmm) outliers start: 70 outliers final: 54 residues processed: 232 average time/residue: 0.2549 time to fit residues: 92.6768 Evaluate side-chains 223 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 159 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 390 LYS Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 162 optimal weight: 0.0030 chunk 68 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.141072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094229 restraints weight = 36963.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097572 restraints weight = 21017.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099745 restraints weight = 14822.627| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17301 Z= 0.330 Angle : 0.647 11.085 23373 Z= 0.329 Chirality : 0.044 0.208 2631 Planarity : 0.004 0.042 2953 Dihedral : 8.312 164.458 2303 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.45 % Allowed : 29.98 % Favored : 65.57 % 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: -1.03 (0.18), residues: 2049 helix: 0.57 (0.20), residues: 744 sheet: -1.16 (0.34), residues: 243 loop : -1.51 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.003 TRP F 675 HIS 0.011 0.001 HIS E 548 PHE 0.012 0.001 PHE F 501 TYR 0.025 0.001 TYR F 482 ARG 0.014 0.000 ARG F 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.38 seconds wall clock time: 57 minutes 38.23 seconds (3458.23 seconds total)