Starting phenix.real_space_refine on Mon Mar 18 19:40:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/03_2024/8apl_15574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/03_2024/8apl_15574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/03_2024/8apl_15574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/03_2024/8apl_15574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/03_2024/8apl_15574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/03_2024/8apl_15574.pdb" } resolution = 4.1 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 14082 2.51 5 N 3648 2.21 5 O 4050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21888 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Chain: "B" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Chain: "C" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Chain: "D" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Chain: "E" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Chain: "F" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Time building chain proxies: 10.89, per 1000 atoms: 0.50 Number of scatterers: 21888 At special positions: 0 Unit cell: (129.47, 122.21, 107.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4050 8.00 N 3648 7.00 C 14082 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: 7.82 Conformation dependent library (CDL) restraints added in 3.8 seconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 42 sheets defined 47.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 489 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 548 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 654 through 661 removed outlier: 3.837A pdb=" N LYS A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 689 through 692 Processing helix chain 'A' and resid 693 through 706 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 736 through 747 removed outlier: 3.971A pdb=" N LYS A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 778 through 782 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 570 through 577 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 654 through 661 removed outlier: 3.838A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 689 through 692 Processing helix chain 'B' and resid 693 through 706 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 716 through 721 Processing helix chain 'B' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS B 745 " --> pdb=" O GLN B 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 778 through 782 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 614 through 620 Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.837A pdb=" N LYS C 658 " --> pdb=" O GLY C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 689 through 692 Processing helix chain 'C' and resid 693 through 706 Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 716 through 721 Processing helix chain 'C' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 764 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.976A pdb=" N ASN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.684A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 435 Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 475 through 489 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 541 through 548 Processing helix chain 'D' and resid 570 through 577 Processing helix chain 'D' and resid 614 through 620 Processing helix chain 'D' and resid 654 through 661 removed outlier: 3.838A pdb=" N LYS D 658 " --> pdb=" O GLY D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 689 through 692 Processing helix chain 'D' and resid 693 through 706 Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 716 through 721 Processing helix chain 'D' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS D 745 " --> pdb=" O GLN D 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR D 746 " --> pdb=" O LYS D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 764 Processing helix chain 'D' and resid 778 through 782 Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) 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 384 removed outlier: 3.683A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 430 through 435 Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 541 through 548 Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 614 through 620 Processing helix chain 'E' and resid 654 through 661 removed outlier: 3.838A pdb=" N LYS E 658 " --> pdb=" O GLY E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'E' and resid 689 through 692 Processing helix chain 'E' and resid 693 through 706 Processing helix chain 'E' and resid 713 through 715 No H-bonds generated for 'chain 'E' and resid 713 through 715' Processing helix chain 'E' and resid 716 through 721 Processing helix chain 'E' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS E 745 " --> pdb=" O GLN E 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR E 746 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 764 Processing helix chain 'E' and resid 778 through 782 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.535A 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 384 removed outlier: 3.683A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 430 through 435 Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 475 through 489 Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 541 through 548 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 614 through 620 Processing helix chain 'F' and resid 654 through 661 removed outlier: 3.837A pdb=" N LYS F 658 " --> pdb=" O GLY F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 689 through 692 Processing helix chain 'F' and resid 693 through 706 Processing helix chain 'F' and resid 713 through 715 No H-bonds generated for 'chain 'F' and resid 713 through 715' Processing helix chain 'F' and resid 716 through 721 Processing helix chain 'F' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS F 745 " --> pdb=" O GLN F 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR F 746 " --> pdb=" O LYS F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 764 Processing helix chain 'F' and resid 778 through 782 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 527 removed outlier: 5.926A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 499 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 582 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 631 Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA8, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB1, first strand: chain 'B' and resid 524 through 527 removed outlier: 5.926A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 499 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 581 through 582 Processing sheet with id=AB3, first strand: chain 'B' and resid 628 through 631 Processing sheet with id=AB4, first strand: chain 'B' and resid 707 through 708 Processing sheet with id=AB5, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AB6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB8, first strand: chain 'C' and resid 524 through 527 removed outlier: 5.927A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS C 555 " --> pdb=" O ASP C 603 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 499 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 581 through 582 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 631 Processing sheet with id=AC2, first strand: chain 'C' and resid 707 through 708 Processing sheet with id=AC3, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AC4, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC5, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AC6, first strand: chain 'D' and resid 524 through 527 removed outlier: 5.927A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 499 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 581 through 582 Processing sheet with id=AC8, first strand: chain 'D' and resid 628 through 631 Processing sheet with id=AC9, first strand: chain 'D' and resid 707 through 708 Processing sheet with id=AD1, first strand: chain 'D' and resid 726 through 728 Processing sheet with id=AD2, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD3, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AD4, first strand: chain 'E' and resid 524 through 527 removed outlier: 5.927A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 499 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 581 through 582 Processing sheet with id=AD6, first strand: chain 'E' and resid 628 through 631 Processing sheet with id=AD7, first strand: chain 'E' and resid 707 through 708 Processing sheet with id=AD8, first strand: chain 'E' and resid 726 through 728 Processing sheet with id=AD9, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AE1, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AE2, first strand: chain 'F' and resid 524 through 527 removed outlier: 5.926A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR F 499 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 581 through 582 Processing sheet with id=AE4, first strand: chain 'F' and resid 628 through 631 Processing sheet with id=AE5, first strand: chain 'F' and resid 707 through 708 Processing sheet with id=AE6, first strand: chain 'F' and resid 726 through 728 894 hydrogen bonds defined for protein. 2538 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: 7.79 Time building geometry restraints manager: 8.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6942 1.34 - 1.46: 4818 1.46 - 1.58: 10434 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 22356 Sorted by residual: bond pdb=" C ILE F 714 " pdb=" N PRO F 715 " ideal model delta sigma weight residual 1.336 1.344 -0.008 1.08e-02 8.57e+03 5.21e-01 bond pdb=" C ILE D 714 " pdb=" N PRO D 715 " ideal model delta sigma weight residual 1.336 1.343 -0.008 1.08e-02 8.57e+03 4.85e-01 bond pdb=" N GLY C 503 " pdb=" CA GLY C 503 " ideal model delta sigma weight residual 1.455 1.448 0.007 1.05e-02 9.07e+03 4.70e-01 bond pdb=" C ILE C 714 " pdb=" N PRO C 715 " ideal model delta sigma weight residual 1.336 1.343 -0.007 1.08e-02 8.57e+03 4.35e-01 bond pdb=" N GLY D 503 " pdb=" CA GLY D 503 " ideal model delta sigma weight residual 1.455 1.448 0.007 1.05e-02 9.07e+03 4.34e-01 ... (remaining 22351 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 578 107.13 - 113.84: 12654 113.84 - 120.56: 8728 120.56 - 127.27: 8052 127.27 - 133.99: 168 Bond angle restraints: 30180 Sorted by residual: angle pdb=" C THR F 408 " pdb=" N TYR F 409 " pdb=" CA TYR F 409 " ideal model delta sigma weight residual 120.39 127.34 -6.95 1.39e+00 5.18e-01 2.50e+01 angle pdb=" C THR C 408 " pdb=" N TYR C 409 " pdb=" CA TYR C 409 " ideal model delta sigma weight residual 120.39 127.34 -6.95 1.39e+00 5.18e-01 2.50e+01 angle pdb=" C THR D 408 " pdb=" N TYR D 409 " pdb=" CA TYR D 409 " ideal model delta sigma weight residual 120.39 127.32 -6.93 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C THR B 408 " pdb=" N TYR B 409 " pdb=" CA TYR B 409 " ideal model delta sigma weight residual 120.39 127.32 -6.93 1.39e+00 5.18e-01 2.48e+01 angle pdb=" C THR E 408 " pdb=" N TYR E 409 " pdb=" CA TYR E 409 " ideal model delta sigma weight residual 120.39 127.31 -6.92 1.39e+00 5.18e-01 2.48e+01 ... (remaining 30175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.34: 12774 13.34 - 26.67: 636 26.67 - 40.01: 132 40.01 - 53.35: 30 53.35 - 66.68: 24 Dihedral angle restraints: 13596 sinusoidal: 5652 harmonic: 7944 Sorted by residual: dihedral pdb=" N LEU D 334 " pdb=" CA LEU D 334 " pdb=" CB LEU D 334 " pdb=" CG LEU D 334 " ideal model delta sinusoidal sigma weight residual -60.00 -118.89 58.89 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU F 334 " pdb=" CA LEU F 334 " pdb=" CB LEU F 334 " pdb=" CG LEU F 334 " ideal model delta sinusoidal sigma weight residual -60.00 -118.87 58.87 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU C 334 " pdb=" CA LEU C 334 " pdb=" CB LEU C 334 " pdb=" CG LEU C 334 " ideal model delta sinusoidal sigma weight residual -60.00 -118.86 58.86 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 13593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2030 0.027 - 0.055: 907 0.055 - 0.082: 263 0.082 - 0.110: 144 0.110 - 0.137: 46 Chirality restraints: 3390 Sorted by residual: chirality pdb=" CA ILE A 693 " pdb=" N ILE A 693 " pdb=" C ILE A 693 " pdb=" CB ILE A 693 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE E 693 " pdb=" N ILE E 693 " pdb=" C ILE E 693 " pdb=" CB ILE E 693 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE B 693 " pdb=" N ILE B 693 " pdb=" C ILE B 693 " pdb=" CB ILE B 693 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 3387 not shown) Planarity restraints: 3816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 409 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 410 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 410 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 410 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 409 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO F 410 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 410 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 410 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 409 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO D 410 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 410 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 410 " -0.023 5.00e-02 4.00e+02 ... (remaining 3813 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2241 2.75 - 3.29: 22063 3.29 - 3.83: 37655 3.83 - 4.36: 45804 4.36 - 4.90: 75976 Nonbonded interactions: 183739 Sorted by model distance: nonbonded pdb=" OG1 THR E 406 " pdb=" O THR E 437 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR F 406 " pdb=" O THR F 437 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR B 406 " pdb=" O THR B 437 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR A 406 " pdb=" O THR A 437 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR D 406 " pdb=" O THR D 437 " model vdw 2.213 2.440 ... (remaining 183734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.840 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 58.030 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.110 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 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 : 0.002 0.017 22356 Z= 0.104 Angle : 0.477 9.262 30180 Z= 0.273 Chirality : 0.038 0.137 3390 Planarity : 0.003 0.042 3816 Dihedral : 9.134 66.684 8448 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.93 % Allowed : 4.11 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.14 (0.17), residues: 2670 helix: 1.14 (0.17), residues: 1098 sheet: -0.76 (0.29), residues: 318 loop : -0.55 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 350 HIS 0.002 0.001 HIS E 763 PHE 0.006 0.001 PHE C 444 TYR 0.013 0.001 TYR F 409 ARG 0.002 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 691 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ASN cc_start: 0.8030 (m-40) cc_final: 0.7728 (m110) REVERT: A 363 LEU cc_start: 0.9105 (mt) cc_final: 0.8870 (mt) REVERT: A 390 LYS cc_start: 0.9034 (tttt) cc_final: 0.8758 (tppt) REVERT: A 428 TYR cc_start: 0.8444 (m-80) cc_final: 0.7985 (m-10) REVERT: A 437 THR cc_start: 0.9184 (p) cc_final: 0.7854 (p) REVERT: A 486 LEU cc_start: 0.9096 (mt) cc_final: 0.8821 (mm) REVERT: A 516 LEU cc_start: 0.9461 (tp) cc_final: 0.9053 (tp) REVERT: A 544 ILE cc_start: 0.9159 (mm) cc_final: 0.8911 (mt) REVERT: A 671 LEU cc_start: 0.9109 (tp) cc_final: 0.8476 (tp) REVERT: A 675 TRP cc_start: 0.8161 (m-10) cc_final: 0.7954 (m-10) REVERT: A 759 PHE cc_start: 0.6243 (t80) cc_final: 0.5615 (t80) REVERT: B 353 ASN cc_start: 0.8113 (m-40) cc_final: 0.7811 (m110) REVERT: B 369 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9015 (tm) REVERT: B 387 ARG cc_start: 0.7334 (ttt180) cc_final: 0.6823 (tmm-80) REVERT: B 390 LYS cc_start: 0.9076 (tttt) cc_final: 0.8743 (tppt) REVERT: B 437 THR cc_start: 0.9122 (p) cc_final: 0.7598 (p) REVERT: B 463 ASN cc_start: 0.8099 (m-40) cc_final: 0.7766 (t0) REVERT: B 486 LEU cc_start: 0.8975 (mt) cc_final: 0.8736 (mm) REVERT: B 516 LEU cc_start: 0.9463 (tp) cc_final: 0.9140 (tp) REVERT: B 538 LYS cc_start: 0.6665 (tptp) cc_final: 0.6458 (mtmm) REVERT: B 544 ILE cc_start: 0.9101 (mm) cc_final: 0.8812 (mt) REVERT: B 671 LEU cc_start: 0.9203 (tp) cc_final: 0.7919 (tp) REVERT: B 675 TRP cc_start: 0.8202 (m-10) cc_final: 0.7836 (m-10) REVERT: B 759 PHE cc_start: 0.6143 (t80) cc_final: 0.5515 (t80) REVERT: C 406 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8042 (t) REVERT: C 428 TYR cc_start: 0.8372 (m-80) cc_final: 0.7961 (m-10) REVERT: C 437 THR cc_start: 0.8963 (p) cc_final: 0.7463 (p) REVERT: C 516 LEU cc_start: 0.9461 (tp) cc_final: 0.9055 (tp) REVERT: C 544 ILE cc_start: 0.9111 (mm) cc_final: 0.8909 (mt) REVERT: C 759 PHE cc_start: 0.5787 (t80) cc_final: 0.5335 (t80) REVERT: D 353 ASN cc_start: 0.8111 (m-40) cc_final: 0.7773 (m110) REVERT: D 428 TYR cc_start: 0.8469 (m-80) cc_final: 0.8015 (m-10) REVERT: D 437 THR cc_start: 0.9191 (p) cc_final: 0.7861 (p) REVERT: D 516 LEU cc_start: 0.9420 (tp) cc_final: 0.8940 (tp) REVERT: D 538 LYS cc_start: 0.6946 (tptp) cc_final: 0.6720 (mttt) REVERT: D 544 ILE cc_start: 0.9157 (mm) cc_final: 0.8915 (mt) REVERT: D 671 LEU cc_start: 0.9111 (tp) cc_final: 0.8431 (tp) REVERT: D 759 PHE cc_start: 0.6341 (t80) cc_final: 0.5780 (t80) REVERT: E 353 ASN cc_start: 0.8278 (m-40) cc_final: 0.7958 (m110) REVERT: E 365 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8863 (p) REVERT: E 369 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9094 (tm) REVERT: E 437 THR cc_start: 0.9113 (p) cc_final: 0.7498 (p) REVERT: E 486 LEU cc_start: 0.8976 (mt) cc_final: 0.8724 (mm) REVERT: E 516 LEU cc_start: 0.9441 (tp) cc_final: 0.9056 (tp) REVERT: E 533 THR cc_start: 0.7736 (p) cc_final: 0.7535 (p) REVERT: E 544 ILE cc_start: 0.9075 (mm) cc_final: 0.8764 (mt) REVERT: E 555 CYS cc_start: 0.8245 (m) cc_final: 0.7888 (m) REVERT: E 629 HIS cc_start: 0.9300 (t70) cc_final: 0.9032 (t70) REVERT: E 630 PHE cc_start: 0.7971 (m-80) cc_final: 0.7007 (m-80) REVERT: E 671 LEU cc_start: 0.9204 (tp) cc_final: 0.8049 (tp) REVERT: E 675 TRP cc_start: 0.8146 (m-10) cc_final: 0.7823 (m-10) REVERT: E 759 PHE cc_start: 0.6372 (t80) cc_final: 0.5890 (t80) REVERT: F 333 ILE cc_start: 0.9596 (mt) cc_final: 0.9385 (mm) REVERT: F 353 ASN cc_start: 0.8165 (m-40) cc_final: 0.7761 (m110) REVERT: F 384 LEU cc_start: 0.9441 (mt) cc_final: 0.9141 (mt) REVERT: F 437 THR cc_start: 0.8952 (p) cc_final: 0.7672 (p) REVERT: F 516 LEU cc_start: 0.9481 (tp) cc_final: 0.9010 (tp) REVERT: F 534 ASP cc_start: 0.8095 (m-30) cc_final: 0.7795 (m-30) REVERT: F 538 LYS cc_start: 0.6837 (tptp) cc_final: 0.6572 (mtmt) REVERT: F 544 ILE cc_start: 0.9074 (mm) cc_final: 0.8833 (mt) REVERT: F 555 CYS cc_start: 0.8044 (m) cc_final: 0.7707 (m) REVERT: F 577 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8711 (mp) REVERT: F 759 PHE cc_start: 0.6410 (t80) cc_final: 0.6165 (t80) outliers start: 48 outliers final: 13 residues processed: 727 average time/residue: 0.3671 time to fit residues: 394.3929 Evaluate side-chains 427 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 409 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.4980 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 763 HIS A 775 GLN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS B 775 GLN C 324 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN D 324 ASN D 763 HIS D 775 GLN E 324 ASN E 763 HIS E 775 GLN F 324 ASN F 463 ASN F 775 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22356 Z= 0.220 Angle : 0.577 8.161 30180 Z= 0.296 Chirality : 0.042 0.297 3390 Planarity : 0.005 0.074 3816 Dihedral : 3.959 16.773 2922 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.41 (0.16), residues: 2670 helix: 0.63 (0.16), residues: 1116 sheet: -1.03 (0.29), residues: 288 loop : -0.83 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 675 HIS 0.003 0.001 HIS A 763 PHE 0.031 0.002 PHE D 502 TYR 0.017 0.002 TYR C 606 ARG 0.005 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.9328 (pt) cc_final: 0.8758 (pt) REVERT: A 390 LYS cc_start: 0.9028 (tttt) cc_final: 0.8652 (tppt) REVERT: A 393 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 467 ASP cc_start: 0.8693 (t0) cc_final: 0.8434 (t0) REVERT: A 491 CYS cc_start: 0.8485 (t) cc_final: 0.8059 (p) REVERT: A 501 PHE cc_start: 0.8866 (m-10) cc_final: 0.8596 (m-80) REVERT: A 625 ARG cc_start: 0.8224 (tpt170) cc_final: 0.7954 (tpt170) REVERT: A 671 LEU cc_start: 0.9134 (tp) cc_final: 0.8190 (tp) REVERT: A 675 TRP cc_start: 0.8276 (m-10) cc_final: 0.8033 (m-10) REVERT: B 384 LEU cc_start: 0.9403 (mt) cc_final: 0.9059 (mt) REVERT: B 387 ARG cc_start: 0.7440 (ttt180) cc_final: 0.6976 (ttt180) REVERT: B 390 LYS cc_start: 0.9058 (tttt) cc_final: 0.8833 (tppt) REVERT: B 491 CYS cc_start: 0.8338 (t) cc_final: 0.8080 (p) REVERT: B 501 PHE cc_start: 0.8932 (m-10) cc_final: 0.8613 (m-10) REVERT: B 514 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7745 (ptp90) REVERT: B 531 ILE cc_start: 0.8071 (mt) cc_final: 0.7778 (mm) REVERT: B 538 LYS cc_start: 0.6686 (tptp) cc_final: 0.6430 (mtmm) REVERT: B 544 ILE cc_start: 0.8977 (mm) cc_final: 0.8775 (mt) REVERT: B 671 LEU cc_start: 0.9188 (tp) cc_final: 0.7792 (tp) REVERT: B 675 TRP cc_start: 0.8282 (m-10) cc_final: 0.7869 (m-10) REVERT: B 759 PHE cc_start: 0.6059 (t80) cc_final: 0.5784 (t80) REVERT: C 359 SER cc_start: 0.8926 (p) cc_final: 0.8719 (p) REVERT: C 371 ILE cc_start: 0.9418 (pt) cc_final: 0.8680 (tp) REVERT: C 428 TYR cc_start: 0.8163 (m-80) cc_final: 0.7960 (m-10) REVERT: C 463 ASN cc_start: 0.8555 (m-40) cc_final: 0.8197 (m-40) REVERT: C 467 ASP cc_start: 0.8734 (t0) cc_final: 0.8524 (t0) REVERT: C 486 LEU cc_start: 0.9098 (mm) cc_final: 0.8867 (mm) REVERT: C 514 ARG cc_start: 0.8202 (mtm180) cc_final: 0.7680 (ptp90) REVERT: C 567 LYS cc_start: 0.7651 (mttt) cc_final: 0.7321 (mtpt) REVERT: C 618 MET cc_start: 0.7988 (tmm) cc_final: 0.7699 (tmm) REVERT: C 671 LEU cc_start: 0.9281 (tp) cc_final: 0.9068 (tp) REVERT: C 759 PHE cc_start: 0.5658 (t80) cc_final: 0.5386 (t80) REVERT: D 351 ILE cc_start: 0.9302 (pt) cc_final: 0.8821 (pt) REVERT: D 384 LEU cc_start: 0.9298 (mt) cc_final: 0.9069 (mt) REVERT: D 491 CYS cc_start: 0.8507 (t) cc_final: 0.8118 (p) REVERT: D 501 PHE cc_start: 0.9109 (m-10) cc_final: 0.8800 (m-80) REVERT: D 538 LYS cc_start: 0.6851 (tptp) cc_final: 0.6640 (mttt) REVERT: D 618 MET cc_start: 0.7855 (tmm) cc_final: 0.7602 (tmm) REVERT: D 671 LEU cc_start: 0.9118 (tp) cc_final: 0.7720 (tp) REVERT: D 675 TRP cc_start: 0.8359 (m-10) cc_final: 0.8019 (m-10) REVERT: D 759 PHE cc_start: 0.6086 (t80) cc_final: 0.5865 (t80) REVERT: E 384 LEU cc_start: 0.9340 (mt) cc_final: 0.9069 (mt) REVERT: E 398 ASP cc_start: 0.8443 (m-30) cc_final: 0.8203 (m-30) REVERT: E 491 CYS cc_start: 0.8402 (t) cc_final: 0.8201 (p) REVERT: E 531 ILE cc_start: 0.7954 (mt) cc_final: 0.7537 (tt) REVERT: E 618 MET cc_start: 0.7757 (tmm) cc_final: 0.7484 (tmm) REVERT: E 671 LEU cc_start: 0.9198 (tp) cc_final: 0.7787 (tp) REVERT: E 675 TRP cc_start: 0.8141 (m-10) cc_final: 0.7805 (m-10) REVERT: F 359 SER cc_start: 0.8981 (p) cc_final: 0.8771 (p) REVERT: F 371 ILE cc_start: 0.9430 (pt) cc_final: 0.9179 (pt) REVERT: F 384 LEU cc_start: 0.9420 (mt) cc_final: 0.9007 (mt) REVERT: F 467 ASP cc_start: 0.8637 (t0) cc_final: 0.8334 (t0) REVERT: F 500 PHE cc_start: 0.8467 (m-10) cc_final: 0.8233 (m-80) REVERT: F 501 PHE cc_start: 0.9091 (m-10) cc_final: 0.8874 (m-10) REVERT: F 517 LYS cc_start: 0.9339 (tptm) cc_final: 0.9083 (tptt) REVERT: F 538 LYS cc_start: 0.6481 (tptp) cc_final: 0.6279 (mtmt) REVERT: F 572 ASP cc_start: 0.8913 (m-30) cc_final: 0.8654 (p0) REVERT: F 603 ASP cc_start: 0.5930 (m-30) cc_final: 0.5560 (m-30) REVERT: F 675 TRP cc_start: 0.8384 (m-10) cc_final: 0.8038 (m-10) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.3576 time to fit residues: 278.4302 Evaluate side-chains 376 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 chunk 213 optimal weight: 30.0000 chunk 238 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 192 optimal weight: 0.6980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 417 ASN B 763 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 HIS F 593 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22356 Z= 0.251 Angle : 0.590 7.820 30180 Z= 0.303 Chirality : 0.041 0.198 3390 Planarity : 0.004 0.055 3816 Dihedral : 4.180 17.300 2922 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.55 (0.16), residues: 2670 helix: 0.55 (0.15), residues: 1122 sheet: -1.83 (0.27), residues: 342 loop : -0.68 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 675 HIS 0.004 0.001 HIS A 629 PHE 0.027 0.002 PHE E 554 TYR 0.020 0.001 TYR A 482 ARG 0.004 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 463 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 491 CYS cc_start: 0.8587 (t) cc_final: 0.7965 (p) REVERT: A 501 PHE cc_start: 0.8924 (m-10) cc_final: 0.8599 (m-80) REVERT: A 531 ILE cc_start: 0.8096 (mm) cc_final: 0.7764 (mm) REVERT: A 671 LEU cc_start: 0.9128 (tp) cc_final: 0.7774 (tp) REVERT: B 384 LEU cc_start: 0.9361 (mt) cc_final: 0.9081 (mt) REVERT: B 390 LYS cc_start: 0.9071 (tttt) cc_final: 0.8844 (tppt) REVERT: B 486 LEU cc_start: 0.9048 (mm) cc_final: 0.8801 (mm) REVERT: B 491 CYS cc_start: 0.8347 (t) cc_final: 0.7987 (p) REVERT: B 499 THR cc_start: 0.7379 (t) cc_final: 0.7163 (t) REVERT: B 531 ILE cc_start: 0.8112 (mt) cc_final: 0.7837 (mm) REVERT: B 544 ILE cc_start: 0.8928 (mm) cc_final: 0.8696 (mt) REVERT: B 671 LEU cc_start: 0.9220 (tp) cc_final: 0.7938 (tp) REVERT: B 675 TRP cc_start: 0.8290 (m-10) cc_final: 0.7989 (m-10) REVERT: B 759 PHE cc_start: 0.6108 (t80) cc_final: 0.5865 (t80) REVERT: C 349 VAL cc_start: 0.9513 (t) cc_final: 0.9174 (p) REVERT: C 486 LEU cc_start: 0.9292 (mm) cc_final: 0.9082 (mm) REVERT: C 495 LYS cc_start: 0.7597 (pptt) cc_final: 0.7244 (pptt) REVERT: C 531 ILE cc_start: 0.8198 (mm) cc_final: 0.7893 (mm) REVERT: C 567 LYS cc_start: 0.7581 (mttt) cc_final: 0.7196 (mtpt) REVERT: C 759 PHE cc_start: 0.5735 (t80) cc_final: 0.5498 (t80) REVERT: D 486 LEU cc_start: 0.9304 (mm) cc_final: 0.9011 (mm) REVERT: D 491 CYS cc_start: 0.8693 (t) cc_final: 0.8068 (p) REVERT: D 501 PHE cc_start: 0.9197 (m-10) cc_final: 0.8888 (m-10) REVERT: D 531 ILE cc_start: 0.8113 (mm) cc_final: 0.7567 (tt) REVERT: D 671 LEU cc_start: 0.9103 (tp) cc_final: 0.7694 (tp) REVERT: D 675 TRP cc_start: 0.8323 (m-10) cc_final: 0.7950 (m-10) REVERT: D 759 PHE cc_start: 0.6093 (t80) cc_final: 0.5829 (t80) REVERT: E 387 ARG cc_start: 0.7354 (ttt180) cc_final: 0.7066 (ttt180) REVERT: E 438 CYS cc_start: 0.8733 (m) cc_final: 0.8308 (p) REVERT: E 458 MET cc_start: 0.7997 (ttm) cc_final: 0.7664 (ttp) REVERT: E 486 LEU cc_start: 0.9193 (mm) cc_final: 0.8757 (mm) REVERT: E 491 CYS cc_start: 0.8453 (t) cc_final: 0.8076 (p) REVERT: E 501 PHE cc_start: 0.9102 (m-10) cc_final: 0.8830 (m-80) REVERT: E 625 ARG cc_start: 0.8168 (tpt170) cc_final: 0.7870 (tpt170) REVERT: E 629 HIS cc_start: 0.8875 (t-90) cc_final: 0.8578 (t-90) REVERT: E 671 LEU cc_start: 0.9137 (tp) cc_final: 0.7764 (tp) REVERT: E 675 TRP cc_start: 0.8276 (m-10) cc_final: 0.7917 (m-10) REVERT: F 384 LEU cc_start: 0.9489 (mt) cc_final: 0.9195 (mt) REVERT: F 495 LYS cc_start: 0.7591 (pptt) cc_final: 0.7277 (pptt) REVERT: F 499 THR cc_start: 0.7207 (t) cc_final: 0.6710 (t) REVERT: F 500 PHE cc_start: 0.8540 (m-10) cc_final: 0.8207 (m-80) REVERT: F 501 PHE cc_start: 0.9135 (m-10) cc_final: 0.8891 (m-10) REVERT: F 572 ASP cc_start: 0.8865 (m-30) cc_final: 0.8549 (p0) REVERT: F 603 ASP cc_start: 0.5977 (m-30) cc_final: 0.5303 (m-30) REVERT: F 675 TRP cc_start: 0.8326 (m-10) cc_final: 0.7981 (m-10) outliers start: 2 outliers final: 0 residues processed: 465 average time/residue: 0.3312 time to fit residues: 237.0325 Evaluate side-chains 337 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 228 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 763 HIS C 353 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 629 HIS E 763 HIS F 593 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22356 Z= 0.235 Angle : 0.582 8.656 30180 Z= 0.293 Chirality : 0.042 0.149 3390 Planarity : 0.004 0.045 3816 Dihedral : 4.240 20.708 2922 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.04 % Allowed : 2.70 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.57 (0.16), residues: 2670 helix: 0.51 (0.15), residues: 1122 sheet: -1.77 (0.28), residues: 342 loop : -0.67 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 675 HIS 0.006 0.001 HIS D 548 PHE 0.026 0.002 PHE F 554 TYR 0.020 0.001 TYR F 699 ARG 0.004 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8497 (tm-30) REVERT: A 438 CYS cc_start: 0.8883 (m) cc_final: 0.8655 (p) REVERT: A 486 LEU cc_start: 0.9306 (mm) cc_final: 0.9068 (mm) REVERT: A 501 PHE cc_start: 0.8984 (m-10) cc_final: 0.8535 (m-80) REVERT: A 531 ILE cc_start: 0.8079 (mm) cc_final: 0.7808 (mt) REVERT: A 671 LEU cc_start: 0.9143 (tp) cc_final: 0.7776 (tp) REVERT: A 675 TRP cc_start: 0.8378 (m-10) cc_final: 0.7990 (m-10) REVERT: A 759 PHE cc_start: 0.6347 (t80) cc_final: 0.6061 (t80) REVERT: B 384 LEU cc_start: 0.9377 (mt) cc_final: 0.9079 (mt) REVERT: B 390 LYS cc_start: 0.9047 (tttt) cc_final: 0.8846 (tppt) REVERT: B 411 ASP cc_start: 0.8362 (p0) cc_final: 0.7432 (t0) REVERT: B 486 LEU cc_start: 0.9093 (mm) cc_final: 0.8833 (mm) REVERT: B 491 CYS cc_start: 0.8307 (t) cc_final: 0.7981 (p) REVERT: B 499 THR cc_start: 0.7400 (t) cc_final: 0.7185 (t) REVERT: B 514 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7880 (mtm110) REVERT: B 671 LEU cc_start: 0.9183 (tp) cc_final: 0.7880 (tp) REVERT: B 675 TRP cc_start: 0.8290 (m-10) cc_final: 0.8059 (m-10) REVERT: C 349 VAL cc_start: 0.9486 (t) cc_final: 0.9171 (p) REVERT: C 359 SER cc_start: 0.8936 (p) cc_final: 0.8712 (p) REVERT: C 384 LEU cc_start: 0.9399 (mt) cc_final: 0.9194 (mt) REVERT: C 387 ARG cc_start: 0.6861 (ptm160) cc_final: 0.6496 (ttt180) REVERT: C 495 LYS cc_start: 0.7232 (pptt) cc_final: 0.6817 (pptt) REVERT: C 499 THR cc_start: 0.7340 (t) cc_final: 0.6904 (t) REVERT: C 567 LYS cc_start: 0.7512 (mttt) cc_final: 0.7118 (mtpt) REVERT: C 618 MET cc_start: 0.7601 (tmm) cc_final: 0.7344 (tmm) REVERT: C 759 PHE cc_start: 0.5761 (t80) cc_final: 0.5551 (t80) REVERT: D 398 ASP cc_start: 0.8590 (m-30) cc_final: 0.8333 (m-30) REVERT: D 486 LEU cc_start: 0.9352 (mm) cc_final: 0.9051 (mm) REVERT: D 499 THR cc_start: 0.7120 (t) cc_final: 0.6833 (t) REVERT: D 602 ILE cc_start: 0.8032 (mt) cc_final: 0.7795 (tt) REVERT: D 671 LEU cc_start: 0.9250 (tp) cc_final: 0.7935 (tp) REVERT: D 675 TRP cc_start: 0.8345 (m-10) cc_final: 0.7979 (m-10) REVERT: E 371 ILE cc_start: 0.9460 (pt) cc_final: 0.9205 (pt) REVERT: E 384 LEU cc_start: 0.9303 (mt) cc_final: 0.9062 (mt) REVERT: E 438 CYS cc_start: 0.8774 (m) cc_final: 0.8335 (p) REVERT: E 458 MET cc_start: 0.7922 (ttm) cc_final: 0.7668 (ttp) REVERT: E 486 LEU cc_start: 0.9057 (mm) cc_final: 0.8785 (mm) REVERT: E 491 CYS cc_start: 0.8461 (t) cc_final: 0.8173 (p) REVERT: E 499 THR cc_start: 0.7386 (t) cc_final: 0.7046 (t) REVERT: E 500 PHE cc_start: 0.8248 (m-10) cc_final: 0.7955 (m-80) REVERT: E 625 ARG cc_start: 0.8105 (tpt170) cc_final: 0.7885 (tpt170) REVERT: E 629 HIS cc_start: 0.8689 (t70) cc_final: 0.8407 (t-90) REVERT: E 759 PHE cc_start: 0.6255 (t80) cc_final: 0.5889 (t80) REVERT: F 384 LEU cc_start: 0.9417 (mt) cc_final: 0.9042 (mt) REVERT: F 495 LYS cc_start: 0.7668 (pptt) cc_final: 0.7250 (pptt) REVERT: F 499 THR cc_start: 0.7239 (t) cc_final: 0.6770 (t) REVERT: F 500 PHE cc_start: 0.8527 (m-10) cc_final: 0.8102 (m-80) REVERT: F 572 ASP cc_start: 0.8849 (m-30) cc_final: 0.8543 (p0) REVERT: F 629 HIS cc_start: 0.8555 (t-90) cc_final: 0.8173 (t-90) REVERT: F 675 TRP cc_start: 0.8365 (m-10) cc_final: 0.8026 (m-10) REVERT: F 759 PHE cc_start: 0.6480 (t80) cc_final: 0.6217 (t80) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.3341 time to fit residues: 231.8860 Evaluate side-chains 343 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS D 629 HIS E 763 HIS F 353 ASN ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 593 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22356 Z= 0.179 Angle : 0.545 8.104 30180 Z= 0.277 Chirality : 0.041 0.164 3390 Planarity : 0.004 0.040 3816 Dihedral : 4.145 17.534 2922 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.04 % Allowed : 1.81 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.45 (0.16), residues: 2670 helix: 0.59 (0.15), residues: 1122 sheet: -1.66 (0.28), residues: 342 loop : -0.62 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 675 HIS 0.012 0.001 HIS B 548 PHE 0.024 0.002 PHE D 554 TYR 0.019 0.001 TYR C 699 ARG 0.006 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 482 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8673 (t80) cc_final: 0.8282 (t80) REVERT: A 343 GLU cc_start: 0.7365 (pm20) cc_final: 0.7081 (mp0) REVERT: A 393 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8455 (tm-30) REVERT: A 438 CYS cc_start: 0.8858 (m) cc_final: 0.8647 (p) REVERT: A 486 LEU cc_start: 0.9266 (mm) cc_final: 0.9014 (mm) REVERT: A 500 PHE cc_start: 0.8291 (m-10) cc_final: 0.8025 (m-80) REVERT: A 501 PHE cc_start: 0.8953 (m-10) cc_final: 0.8656 (m-10) REVERT: A 531 ILE cc_start: 0.8072 (mm) cc_final: 0.7859 (mm) REVERT: A 671 LEU cc_start: 0.9122 (tp) cc_final: 0.7713 (tp) REVERT: A 675 TRP cc_start: 0.8329 (m-10) cc_final: 0.7931 (m-10) REVERT: A 759 PHE cc_start: 0.6408 (t80) cc_final: 0.6084 (t80) REVERT: B 384 LEU cc_start: 0.9350 (mt) cc_final: 0.9094 (mt) REVERT: B 411 ASP cc_start: 0.8404 (p0) cc_final: 0.7482 (t0) REVERT: B 486 LEU cc_start: 0.9238 (mm) cc_final: 0.9005 (mm) REVERT: B 491 CYS cc_start: 0.8124 (t) cc_final: 0.7843 (p) REVERT: B 501 PHE cc_start: 0.9054 (m-10) cc_final: 0.8848 (m-10) REVERT: B 671 LEU cc_start: 0.9182 (tp) cc_final: 0.7898 (tp) REVERT: B 675 TRP cc_start: 0.8210 (m-10) cc_final: 0.7887 (m-10) REVERT: B 759 PHE cc_start: 0.6065 (t80) cc_final: 0.5786 (t80) REVERT: C 349 VAL cc_start: 0.9456 (t) cc_final: 0.9089 (p) REVERT: C 384 LEU cc_start: 0.9323 (mt) cc_final: 0.9099 (mt) REVERT: C 387 ARG cc_start: 0.6767 (ptm160) cc_final: 0.6444 (ttt180) REVERT: C 458 MET cc_start: 0.7561 (ttm) cc_final: 0.7235 (ttm) REVERT: C 495 LYS cc_start: 0.7330 (pptt) cc_final: 0.6920 (pptt) REVERT: C 499 THR cc_start: 0.7030 (t) cc_final: 0.6825 (t) REVERT: C 516 LEU cc_start: 0.9207 (tp) cc_final: 0.8991 (tp) REVERT: C 531 ILE cc_start: 0.8259 (mm) cc_final: 0.8050 (mm) REVERT: C 567 LYS cc_start: 0.7503 (mttt) cc_final: 0.7067 (mtpt) REVERT: C 759 PHE cc_start: 0.5958 (t80) cc_final: 0.5641 (t80) REVERT: D 398 ASP cc_start: 0.8571 (m-30) cc_final: 0.8291 (m-30) REVERT: D 486 LEU cc_start: 0.9379 (mm) cc_final: 0.9118 (mm) REVERT: D 553 VAL cc_start: 0.8584 (t) cc_final: 0.8235 (t) REVERT: D 597 HIS cc_start: 0.6484 (m170) cc_final: 0.6124 (m170) REVERT: D 601 ILE cc_start: 0.8269 (mt) cc_final: 0.7952 (mp) REVERT: D 671 LEU cc_start: 0.9212 (tp) cc_final: 0.7880 (tp) REVERT: D 675 TRP cc_start: 0.8376 (m-10) cc_final: 0.7997 (m-10) REVERT: E 384 LEU cc_start: 0.9259 (mt) cc_final: 0.8978 (mt) REVERT: E 411 ASP cc_start: 0.8263 (p0) cc_final: 0.7586 (t0) REVERT: E 438 CYS cc_start: 0.8666 (m) cc_final: 0.8353 (p) REVERT: E 458 MET cc_start: 0.7850 (ttm) cc_final: 0.7583 (ttm) REVERT: E 486 LEU cc_start: 0.9104 (mm) cc_final: 0.8858 (mm) REVERT: E 491 CYS cc_start: 0.8441 (t) cc_final: 0.8148 (p) REVERT: E 499 THR cc_start: 0.7447 (t) cc_final: 0.7219 (t) REVERT: E 500 PHE cc_start: 0.8138 (m-10) cc_final: 0.7877 (m-80) REVERT: E 601 ILE cc_start: 0.8410 (mt) cc_final: 0.8168 (mt) REVERT: E 629 HIS cc_start: 0.8645 (t70) cc_final: 0.8252 (t70) REVERT: E 759 PHE cc_start: 0.6335 (t80) cc_final: 0.6133 (t80) REVERT: F 384 LEU cc_start: 0.9417 (mt) cc_final: 0.8994 (mt) REVERT: F 495 LYS cc_start: 0.7604 (pptt) cc_final: 0.7059 (pptt) REVERT: F 499 THR cc_start: 0.7405 (t) cc_final: 0.6915 (t) REVERT: F 500 PHE cc_start: 0.8396 (m-10) cc_final: 0.7883 (m-80) REVERT: F 501 PHE cc_start: 0.9014 (m-10) cc_final: 0.8633 (m-80) REVERT: F 514 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7755 (ptt-90) REVERT: F 567 LYS cc_start: 0.7429 (mttt) cc_final: 0.7066 (mtpt) REVERT: F 572 ASP cc_start: 0.8884 (m-30) cc_final: 0.8546 (p0) REVERT: F 629 HIS cc_start: 0.8538 (t-90) cc_final: 0.8012 (t-90) REVERT: F 675 TRP cc_start: 0.8334 (m-10) cc_final: 0.7984 (m-10) REVERT: F 759 PHE cc_start: 0.6455 (t80) cc_final: 0.6252 (t80) outliers start: 1 outliers final: 0 residues processed: 483 average time/residue: 0.3407 time to fit residues: 250.0073 Evaluate side-chains 363 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 134 optimal weight: 0.1980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 763 HIS D 629 HIS E 763 HIS ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 593 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22356 Z= 0.235 Angle : 0.584 8.934 30180 Z= 0.293 Chirality : 0.042 0.349 3390 Planarity : 0.004 0.035 3816 Dihedral : 4.310 16.825 2922 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.04 % Allowed : 1.25 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.49 (0.16), residues: 2670 helix: 0.54 (0.15), residues: 1122 sheet: -1.49 (0.29), residues: 342 loop : -0.68 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 675 HIS 0.008 0.001 HIS F 548 PHE 0.030 0.002 PHE D 626 TYR 0.018 0.001 TYR E 482 ARG 0.005 0.000 ARG F 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 447 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 343 GLU cc_start: 0.7389 (pm20) cc_final: 0.7131 (mp0) REVERT: A 486 LEU cc_start: 0.9293 (mm) cc_final: 0.9065 (mm) REVERT: A 499 THR cc_start: 0.7762 (t) cc_final: 0.7463 (t) REVERT: A 500 PHE cc_start: 0.8358 (m-10) cc_final: 0.8096 (m-80) REVERT: A 501 PHE cc_start: 0.8967 (m-10) cc_final: 0.8645 (m-80) REVERT: A 671 LEU cc_start: 0.9089 (tp) cc_final: 0.7523 (tp) REVERT: A 675 TRP cc_start: 0.8384 (m-10) cc_final: 0.8023 (m-10) REVERT: A 759 PHE cc_start: 0.6389 (t80) cc_final: 0.6063 (t80) REVERT: B 384 LEU cc_start: 0.9341 (mt) cc_final: 0.8954 (mt) REVERT: B 411 ASP cc_start: 0.8522 (p0) cc_final: 0.7584 (t0) REVERT: B 486 LEU cc_start: 0.9198 (mm) cc_final: 0.8962 (mm) REVERT: B 501 PHE cc_start: 0.9049 (m-10) cc_final: 0.8743 (m-10) REVERT: B 551 ARG cc_start: 0.7890 (mmt90) cc_final: 0.7685 (mmt-90) REVERT: B 671 LEU cc_start: 0.9188 (tp) cc_final: 0.7913 (tp) REVERT: B 675 TRP cc_start: 0.8343 (m-10) cc_final: 0.8096 (m-10) REVERT: C 384 LEU cc_start: 0.9353 (mt) cc_final: 0.9108 (mt) REVERT: C 499 THR cc_start: 0.7451 (t) cc_final: 0.6970 (t) REVERT: C 567 LYS cc_start: 0.7483 (mttt) cc_final: 0.7059 (mtpt) REVERT: C 618 MET cc_start: 0.8065 (tmm) cc_final: 0.7842 (tmm) REVERT: C 629 HIS cc_start: 0.8508 (t70) cc_final: 0.8044 (t70) REVERT: C 759 PHE cc_start: 0.5896 (t80) cc_final: 0.5582 (t80) REVERT: D 398 ASP cc_start: 0.8572 (m-30) cc_final: 0.8314 (m-30) REVERT: D 486 LEU cc_start: 0.9360 (mm) cc_final: 0.9082 (mm) REVERT: D 597 HIS cc_start: 0.6290 (m170) cc_final: 0.6033 (m170) REVERT: D 626 PHE cc_start: 0.6072 (m-80) cc_final: 0.5841 (m-80) REVERT: D 671 LEU cc_start: 0.9141 (tp) cc_final: 0.7696 (tp) REVERT: D 675 TRP cc_start: 0.8418 (m-10) cc_final: 0.8182 (m-10) REVERT: E 384 LEU cc_start: 0.9284 (mt) cc_final: 0.9071 (mt) REVERT: E 486 LEU cc_start: 0.9041 (mm) cc_final: 0.8695 (mm) REVERT: E 491 CYS cc_start: 0.8312 (t) cc_final: 0.7963 (p) REVERT: E 499 THR cc_start: 0.7595 (t) cc_final: 0.7366 (t) REVERT: E 500 PHE cc_start: 0.8068 (m-10) cc_final: 0.7859 (m-80) REVERT: E 629 HIS cc_start: 0.8568 (t70) cc_final: 0.8192 (t70) REVERT: F 384 LEU cc_start: 0.9474 (mt) cc_final: 0.9160 (mt) REVERT: F 499 THR cc_start: 0.7580 (t) cc_final: 0.7190 (t) REVERT: F 500 PHE cc_start: 0.8484 (m-10) cc_final: 0.8048 (m-80) REVERT: F 514 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7803 (ptt-90) REVERT: F 567 LYS cc_start: 0.7420 (mttt) cc_final: 0.7140 (mtpt) REVERT: F 572 ASP cc_start: 0.8798 (m-30) cc_final: 0.8538 (p0) REVERT: F 759 PHE cc_start: 0.6440 (t80) cc_final: 0.6219 (t80) outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.3426 time to fit residues: 233.9177 Evaluate side-chains 345 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 254 optimal weight: 0.3980 chunk 159 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 763 HIS ** C 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 593 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22356 Z= 0.224 Angle : 0.581 9.313 30180 Z= 0.291 Chirality : 0.042 0.296 3390 Planarity : 0.004 0.040 3816 Dihedral : 4.314 19.199 2922 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.08 % Allowed : 1.45 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.41 (0.16), residues: 2670 helix: 0.57 (0.15), residues: 1122 sheet: -0.61 (0.32), residues: 288 loop : -0.90 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 675 HIS 0.009 0.001 HIS F 548 PHE 0.040 0.002 PHE E 554 TYR 0.018 0.001 TYR B 482 ARG 0.006 0.000 ARG F 551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 446 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8731 (t80) cc_final: 0.8350 (t80) REVERT: A 486 LEU cc_start: 0.9301 (mm) cc_final: 0.9040 (mm) REVERT: A 500 PHE cc_start: 0.8300 (m-10) cc_final: 0.8078 (m-80) REVERT: A 618 MET cc_start: 0.7058 (tmm) cc_final: 0.6716 (mtp) REVERT: A 671 LEU cc_start: 0.9122 (tp) cc_final: 0.7574 (tp) REVERT: A 675 TRP cc_start: 0.8413 (m-10) cc_final: 0.8009 (m-10) REVERT: A 759 PHE cc_start: 0.6283 (t80) cc_final: 0.6060 (t80) REVERT: B 384 LEU cc_start: 0.9358 (mt) cc_final: 0.8953 (mt) REVERT: B 411 ASP cc_start: 0.8518 (p0) cc_final: 0.7534 (t0) REVERT: B 486 LEU cc_start: 0.9060 (mm) cc_final: 0.8786 (mm) REVERT: B 501 PHE cc_start: 0.9022 (m-10) cc_final: 0.8785 (m-10) REVERT: B 548 HIS cc_start: 0.8168 (p-80) cc_final: 0.7864 (p-80) REVERT: B 671 LEU cc_start: 0.9162 (tp) cc_final: 0.7876 (tp) REVERT: B 675 TRP cc_start: 0.8351 (m-10) cc_final: 0.8086 (m-10) REVERT: C 384 LEU cc_start: 0.9379 (mt) cc_final: 0.9110 (mt) REVERT: C 438 CYS cc_start: 0.8454 (m) cc_final: 0.8239 (p) REVERT: C 567 LYS cc_start: 0.7412 (mttt) cc_final: 0.6941 (mtpt) REVERT: C 629 HIS cc_start: 0.8578 (t70) cc_final: 0.8088 (t70) REVERT: C 759 PHE cc_start: 0.5895 (t80) cc_final: 0.5582 (t80) REVERT: D 398 ASP cc_start: 0.8432 (m-30) cc_final: 0.8213 (m-30) REVERT: D 486 LEU cc_start: 0.9343 (mm) cc_final: 0.8982 (mm) REVERT: D 597 HIS cc_start: 0.6261 (m170) cc_final: 0.5984 (m170) REVERT: E 384 LEU cc_start: 0.9267 (mt) cc_final: 0.9023 (mt) REVERT: E 393 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8363 (tm-30) REVERT: E 407 ASP cc_start: 0.7886 (m-30) cc_final: 0.7596 (m-30) REVERT: E 411 ASP cc_start: 0.8512 (p0) cc_final: 0.7656 (t0) REVERT: E 486 LEU cc_start: 0.8946 (mm) cc_final: 0.8668 (mm) REVERT: E 491 CYS cc_start: 0.8376 (t) cc_final: 0.8015 (p) REVERT: E 499 THR cc_start: 0.7591 (t) cc_final: 0.7090 (t) REVERT: E 500 PHE cc_start: 0.8073 (m-10) cc_final: 0.7760 (m-80) REVERT: E 501 PHE cc_start: 0.9037 (m-80) cc_final: 0.8830 (m-10) REVERT: E 629 HIS cc_start: 0.8462 (t70) cc_final: 0.8067 (t70) REVERT: E 671 LEU cc_start: 0.9179 (tp) cc_final: 0.7802 (tp) REVERT: E 675 TRP cc_start: 0.8321 (m-10) cc_final: 0.7793 (m-10) REVERT: F 384 LEU cc_start: 0.9488 (mt) cc_final: 0.9032 (mt) REVERT: F 499 THR cc_start: 0.7558 (t) cc_final: 0.7262 (t) REVERT: F 500 PHE cc_start: 0.8497 (m-10) cc_final: 0.8068 (m-80) REVERT: F 567 LYS cc_start: 0.7506 (mttt) cc_final: 0.7217 (mtpt) REVERT: F 572 ASP cc_start: 0.8843 (m-30) cc_final: 0.8539 (p0) REVERT: F 759 PHE cc_start: 0.6440 (t80) cc_final: 0.6213 (t80) outliers start: 2 outliers final: 1 residues processed: 448 average time/residue: 0.3375 time to fit residues: 230.8056 Evaluate side-chains 339 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 0.0060 chunk 49 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 629 HIS B 763 HIS ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22356 Z= 0.184 Angle : 0.564 8.522 30180 Z= 0.283 Chirality : 0.042 0.188 3390 Planarity : 0.004 0.038 3816 Dihedral : 4.251 18.785 2922 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.34 (0.16), residues: 2670 helix: 0.62 (0.15), residues: 1122 sheet: -0.65 (0.32), residues: 288 loop : -0.84 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 675 HIS 0.007 0.001 HIS D 548 PHE 0.036 0.002 PHE B 554 TYR 0.020 0.001 TYR B 482 ARG 0.005 0.000 ARG F 551 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8638 (t80) cc_final: 0.8183 (t80) REVERT: A 486 LEU cc_start: 0.9252 (mm) cc_final: 0.8994 (mm) REVERT: A 500 PHE cc_start: 0.8301 (m-10) cc_final: 0.8088 (m-80) REVERT: A 671 LEU cc_start: 0.9139 (tp) cc_final: 0.8198 (tp) REVERT: A 675 TRP cc_start: 0.8413 (m-10) cc_final: 0.8094 (m-10) REVERT: A 759 PHE cc_start: 0.6313 (t80) cc_final: 0.6098 (t80) REVERT: B 384 LEU cc_start: 0.9331 (mt) cc_final: 0.8995 (mt) REVERT: B 407 ASP cc_start: 0.7888 (m-30) cc_final: 0.7670 (m-30) REVERT: B 411 ASP cc_start: 0.8496 (p0) cc_final: 0.7546 (t0) REVERT: B 501 PHE cc_start: 0.8985 (m-10) cc_final: 0.8652 (m-10) REVERT: B 548 HIS cc_start: 0.8229 (p-80) cc_final: 0.7998 (p-80) REVERT: B 671 LEU cc_start: 0.9192 (tp) cc_final: 0.7911 (tp) REVERT: B 675 TRP cc_start: 0.8319 (m-10) cc_final: 0.8057 (m-10) REVERT: C 349 VAL cc_start: 0.9463 (t) cc_final: 0.9035 (p) REVERT: C 384 LEU cc_start: 0.9340 (mt) cc_final: 0.9042 (mt) REVERT: C 567 LYS cc_start: 0.7444 (mttt) cc_final: 0.6993 (mtpt) REVERT: C 618 MET cc_start: 0.7999 (tmm) cc_final: 0.7712 (tmm) REVERT: C 629 HIS cc_start: 0.8508 (t70) cc_final: 0.7970 (t70) REVERT: C 759 PHE cc_start: 0.5844 (t80) cc_final: 0.5585 (t80) REVERT: D 486 LEU cc_start: 0.9303 (mm) cc_final: 0.8739 (mm) REVERT: D 516 LEU cc_start: 0.9238 (tp) cc_final: 0.9009 (tp) REVERT: D 548 HIS cc_start: 0.8468 (p90) cc_final: 0.8099 (p-80) REVERT: E 384 LEU cc_start: 0.9219 (mt) cc_final: 0.8687 (mt) REVERT: E 393 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8408 (tm-30) REVERT: E 407 ASP cc_start: 0.7897 (m-30) cc_final: 0.7688 (m-30) REVERT: E 411 ASP cc_start: 0.8502 (p0) cc_final: 0.7688 (t0) REVERT: E 491 CYS cc_start: 0.8347 (t) cc_final: 0.7991 (p) REVERT: E 499 THR cc_start: 0.7242 (t) cc_final: 0.7020 (t) REVERT: E 500 PHE cc_start: 0.8164 (m-10) cc_final: 0.7750 (m-80) REVERT: E 501 PHE cc_start: 0.8999 (m-80) cc_final: 0.8798 (m-10) REVERT: E 548 HIS cc_start: 0.8538 (p-80) cc_final: 0.8328 (p-80) REVERT: E 629 HIS cc_start: 0.8535 (t70) cc_final: 0.8184 (t70) REVERT: F 327 PHE cc_start: 0.8564 (t80) cc_final: 0.7986 (t80) REVERT: F 384 LEU cc_start: 0.9418 (mt) cc_final: 0.8873 (mt) REVERT: F 499 THR cc_start: 0.7546 (t) cc_final: 0.7234 (t) REVERT: F 500 PHE cc_start: 0.8525 (m-10) cc_final: 0.8027 (m-80) REVERT: F 567 LYS cc_start: 0.7429 (mttt) cc_final: 0.7144 (mtpt) REVERT: F 572 ASP cc_start: 0.8914 (m-30) cc_final: 0.8577 (p0) REVERT: F 615 ASN cc_start: 0.7796 (t0) cc_final: 0.7433 (t0) REVERT: F 759 PHE cc_start: 0.6430 (t80) cc_final: 0.6206 (t80) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.3270 time to fit residues: 232.5423 Evaluate side-chains 353 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 10.0000 chunk 222 optimal weight: 0.0970 chunk 237 optimal weight: 4.9990 chunk 142 optimal weight: 0.0030 chunk 103 optimal weight: 0.5980 chunk 186 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 224 optimal weight: 0.5980 chunk 236 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN C 593 ASN D 593 ASN D 629 HIS F 629 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22356 Z= 0.151 Angle : 0.538 7.354 30180 Z= 0.273 Chirality : 0.042 0.184 3390 Planarity : 0.004 0.033 3816 Dihedral : 4.148 17.604 2922 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.19 (0.16), residues: 2670 helix: 0.74 (0.16), residues: 1122 sheet: -0.63 (0.32), residues: 288 loop : -0.73 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 350 HIS 0.007 0.001 HIS D 548 PHE 0.023 0.001 PHE B 554 TYR 0.021 0.001 TYR B 482 ARG 0.004 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 478 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8560 (t80) cc_final: 0.8112 (t80) REVERT: A 343 GLU cc_start: 0.7354 (pm20) cc_final: 0.7087 (mp0) REVERT: A 393 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8397 (tm-30) REVERT: A 398 ASP cc_start: 0.8129 (m-30) cc_final: 0.7877 (m-30) REVERT: A 486 LEU cc_start: 0.9307 (mm) cc_final: 0.8930 (mm) REVERT: A 501 PHE cc_start: 0.9070 (m-10) cc_final: 0.8324 (m-80) REVERT: A 514 ARG cc_start: 0.8496 (mtm180) cc_final: 0.8072 (ptt-90) REVERT: A 516 LEU cc_start: 0.9365 (tp) cc_final: 0.9081 (tp) REVERT: A 671 LEU cc_start: 0.9122 (tp) cc_final: 0.8211 (tp) REVERT: A 675 TRP cc_start: 0.8326 (m-10) cc_final: 0.7964 (m-10) REVERT: B 384 LEU cc_start: 0.9224 (mt) cc_final: 0.8880 (mt) REVERT: B 393 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 407 ASP cc_start: 0.7901 (m-30) cc_final: 0.7682 (m-30) REVERT: B 411 ASP cc_start: 0.8471 (p0) cc_final: 0.7579 (t0) REVERT: B 458 MET cc_start: 0.8146 (ttt) cc_final: 0.7927 (ttt) REVERT: B 501 PHE cc_start: 0.8970 (m-10) cc_final: 0.8670 (m-10) REVERT: B 554 PHE cc_start: 0.8166 (m-80) cc_final: 0.7706 (m-80) REVERT: B 671 LEU cc_start: 0.9206 (tp) cc_final: 0.7941 (tp) REVERT: B 675 TRP cc_start: 0.8281 (m-10) cc_final: 0.8035 (m-10) REVERT: C 349 VAL cc_start: 0.9438 (t) cc_final: 0.9057 (p) REVERT: C 384 LEU cc_start: 0.9254 (mt) cc_final: 0.9000 (mt) REVERT: C 567 LYS cc_start: 0.7289 (mttt) cc_final: 0.6872 (mtpt) REVERT: C 618 MET cc_start: 0.8094 (tmm) cc_final: 0.7826 (tmm) REVERT: C 629 HIS cc_start: 0.8570 (t70) cc_final: 0.8324 (t70) REVERT: C 759 PHE cc_start: 0.5805 (t80) cc_final: 0.5573 (t80) REVERT: D 486 LEU cc_start: 0.9093 (mm) cc_final: 0.8802 (mm) REVERT: D 531 ILE cc_start: 0.7868 (mm) cc_final: 0.7554 (tt) REVERT: D 548 HIS cc_start: 0.8466 (p90) cc_final: 0.8115 (p-80) REVERT: E 384 LEU cc_start: 0.9112 (mt) cc_final: 0.8652 (mt) REVERT: E 411 ASP cc_start: 0.8468 (p0) cc_final: 0.7720 (t0) REVERT: E 491 CYS cc_start: 0.8458 (t) cc_final: 0.8100 (p) REVERT: E 500 PHE cc_start: 0.8145 (m-10) cc_final: 0.7715 (m-80) REVERT: E 629 HIS cc_start: 0.8512 (t70) cc_final: 0.8037 (t70) REVERT: F 327 PHE cc_start: 0.8321 (t80) cc_final: 0.7932 (t80) REVERT: F 384 LEU cc_start: 0.9342 (mt) cc_final: 0.8733 (mt) REVERT: F 499 THR cc_start: 0.7479 (t) cc_final: 0.7224 (t) REVERT: F 500 PHE cc_start: 0.8501 (m-10) cc_final: 0.7982 (m-80) REVERT: F 567 LYS cc_start: 0.7378 (mttt) cc_final: 0.7069 (mtpt) REVERT: F 572 ASP cc_start: 0.8917 (m-30) cc_final: 0.8628 (p0) REVERT: F 615 ASN cc_start: 0.7677 (t0) cc_final: 0.7420 (t0) REVERT: F 665 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7600 (ttm-80) outliers start: 2 outliers final: 1 residues processed: 480 average time/residue: 0.3336 time to fit residues: 246.3029 Evaluate side-chains 356 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 9.9990 chunk 153 optimal weight: 0.0000 chunk 118 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 242 optimal weight: 0.1980 chunk 209 optimal weight: 0.7980 chunk 21 optimal weight: 0.0570 chunk 161 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 775 GLN C 593 ASN ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 22356 Z= 0.160 Angle : 0.548 10.467 30180 Z= 0.278 Chirality : 0.042 0.299 3390 Planarity : 0.003 0.032 3816 Dihedral : 4.115 17.819 2922 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.04 % Allowed : 0.16 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2670 helix: 0.76 (0.16), residues: 1122 sheet: -0.68 (0.32), residues: 288 loop : -0.62 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 355 HIS 0.008 0.001 HIS A 548 PHE 0.048 0.002 PHE A 500 TYR 0.013 0.001 TYR C 482 ARG 0.007 0.000 ARG C 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 478 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8529 (t80) cc_final: 0.8119 (t80) REVERT: A 343 GLU cc_start: 0.7362 (pm20) cc_final: 0.7092 (mp0) REVERT: A 384 LEU cc_start: 0.9238 (mt) cc_final: 0.8939 (mt) REVERT: A 393 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 398 ASP cc_start: 0.8067 (m-30) cc_final: 0.7823 (m-30) REVERT: A 486 LEU cc_start: 0.9069 (mm) cc_final: 0.8821 (mm) REVERT: A 618 MET cc_start: 0.7230 (tmm) cc_final: 0.6816 (mtp) REVERT: A 671 LEU cc_start: 0.9138 (tp) cc_final: 0.7835 (tp) REVERT: A 675 TRP cc_start: 0.8309 (m-10) cc_final: 0.7798 (m-10) REVERT: A 759 PHE cc_start: 0.6215 (t80) cc_final: 0.5971 (t80) REVERT: B 384 LEU cc_start: 0.9195 (mt) cc_final: 0.8912 (mt) REVERT: B 393 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8356 (tm-30) REVERT: B 407 ASP cc_start: 0.7893 (m-30) cc_final: 0.7691 (m-30) REVERT: B 411 ASP cc_start: 0.8480 (p0) cc_final: 0.7607 (t0) REVERT: B 458 MET cc_start: 0.8103 (ttt) cc_final: 0.7864 (ttm) REVERT: B 484 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8478 (mtmp) REVERT: B 671 LEU cc_start: 0.9209 (tp) cc_final: 0.7949 (tp) REVERT: B 675 TRP cc_start: 0.8270 (m-10) cc_final: 0.7986 (m-10) REVERT: C 349 VAL cc_start: 0.9428 (t) cc_final: 0.9180 (p) REVERT: C 384 LEU cc_start: 0.9191 (mt) cc_final: 0.8915 (mt) REVERT: C 548 HIS cc_start: 0.8158 (p-80) cc_final: 0.7789 (p90) REVERT: C 567 LYS cc_start: 0.7317 (mttt) cc_final: 0.6873 (mtpt) REVERT: C 629 HIS cc_start: 0.8566 (t70) cc_final: 0.8285 (t70) REVERT: D 398 ASP cc_start: 0.8435 (m-30) cc_final: 0.8200 (m-30) REVERT: D 601 ILE cc_start: 0.8413 (mt) cc_final: 0.8065 (mp) REVERT: D 626 PHE cc_start: 0.5919 (m-80) cc_final: 0.5698 (m-80) REVERT: E 384 LEU cc_start: 0.9062 (mt) cc_final: 0.8561 (mt) REVERT: E 407 ASP cc_start: 0.7820 (m-30) cc_final: 0.7583 (m-30) REVERT: E 411 ASP cc_start: 0.8501 (p0) cc_final: 0.7628 (t0) REVERT: E 491 CYS cc_start: 0.8461 (t) cc_final: 0.8101 (p) REVERT: E 500 PHE cc_start: 0.8098 (m-10) cc_final: 0.7684 (m-80) REVERT: E 629 HIS cc_start: 0.8503 (t70) cc_final: 0.8222 (t70) REVERT: F 327 PHE cc_start: 0.8368 (t80) cc_final: 0.7853 (t80) REVERT: F 384 LEU cc_start: 0.9288 (mt) cc_final: 0.8691 (mt) REVERT: F 499 THR cc_start: 0.7470 (t) cc_final: 0.7204 (t) REVERT: F 500 PHE cc_start: 0.8469 (m-10) cc_final: 0.7899 (m-80) REVERT: F 567 LYS cc_start: 0.7431 (mttt) cc_final: 0.7143 (mtpt) REVERT: F 615 ASN cc_start: 0.7632 (t0) cc_final: 0.7423 (t0) REVERT: F 665 ARG cc_start: 0.7929 (ttm170) cc_final: 0.7640 (ttm-80) outliers start: 1 outliers final: 1 residues processed: 479 average time/residue: 0.3382 time to fit residues: 247.8130 Evaluate side-chains 346 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 345 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 775 GLN ** B 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.145628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.101011 restraints weight = 62331.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.103367 restraints weight = 37835.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104883 restraints weight = 27831.273| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22356 Z= 0.263 Angle : 0.613 10.062 30180 Z= 0.307 Chirality : 0.043 0.277 3390 Planarity : 0.004 0.045 3816 Dihedral : 4.332 18.392 2922 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.04 % Allowed : 0.08 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.30 (0.16), residues: 2670 helix: 0.64 (0.15), residues: 1116 sheet: -0.79 (0.32), residues: 288 loop : -0.75 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 675 HIS 0.006 0.001 HIS B 548 PHE 0.032 0.002 PHE D 554 TYR 0.013 0.001 TYR F 482 ARG 0.008 0.001 ARG A 551 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5171.24 seconds wall clock time: 94 minutes 28.25 seconds (5668.25 seconds total)