Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 17:42:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/07_2023/8apl_15574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/07_2023/8apl_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_15574/07_2023/8apl_15574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/07_2023/8apl_15574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/07_2023/8apl_15574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/07_2023/8apl_15574.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 10.55, per 1000 atoms: 0.48 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: 8.69 Conformation dependent library (CDL) restraints added in 3.1 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: 1.80 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: 7.37 Time building geometry restraints manager: 9.24 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: 1.600 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: 5.470 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 54.440 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.170 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.497 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 outliers start: 48 outliers final: 13 residues processed: 727 average time/residue: 0.3788 time to fit residues: 407.7807 Evaluate side-chains 401 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 388 time to evaluate : 2.319 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1879 time to fit residues: 7.8859 ------------------------------------------------------------------------------- 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: 0.2980 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: 4.9990 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 763 HIS A 775 GLN B 324 ASN B 353 ASN 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 353 ASN D 763 HIS D 775 GLN E 324 ASN E 353 ASN E 763 HIS E 775 GLN F 324 ASN F 353 ASN F 463 ASN F 775 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 22356 Z= 0.264 Angle : 0.617 8.121 30180 Z= 0.313 Chirality : 0.043 0.314 3390 Planarity : 0.005 0.074 3816 Dihedral : 4.124 17.318 2922 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.00 % 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: 0.61 (0.15), residues: 1110 sheet: -1.05 (0.29), residues: 288 loop : -0.94 (0.17), residues: 1272 *********************** 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 477 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 2.703 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 outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.3638 time to fit residues: 262.8551 Evaluate side-chains 320 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7559 ------------------------------------------------------------------------------- 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: 3.9990 chunk 74 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 240 optimal weight: 0.9980 chunk 259 optimal weight: 0.2980 chunk 213 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 81 optimal weight: 0.0980 chunk 192 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3598 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= 0.177 Angle : 0.548 6.106 30180 Z= 0.282 Chirality : 0.042 0.166 3390 Planarity : 0.004 0.055 3816 Dihedral : 4.094 17.331 2922 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.08 % 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: -0.46 (0.16), residues: 2670 helix: 0.66 (0.15), residues: 1116 sheet: -1.79 (0.28), residues: 342 loop : -0.66 (0.18), residues: 1212 *********************** 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 481 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 479 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 481 average time/residue: 0.3410 time to fit residues: 255.6323 Evaluate side-chains 335 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4200 ------------------------------------------------------------------------------- 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: 9.9990 chunk 180 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 241 optimal weight: 0.0000 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 228 optimal weight: 0.0870 chunk 68 optimal weight: 8.9990 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 763 HIS C 463 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 763 HIS F 593 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 22356 Z= 0.156 Angle : 0.537 7.446 30180 Z= 0.275 Chirality : 0.041 0.200 3390 Planarity : 0.004 0.044 3816 Dihedral : 4.020 15.710 2922 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.08 % 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: -0.39 (0.16), residues: 2670 helix: 0.66 (0.16), residues: 1122 sheet: -1.67 (0.28), residues: 342 loop : -0.59 (0.18), residues: 1206 *********************** 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 472 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 470 time to evaluate : 2.635 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 outliers start: 2 outliers final: 0 residues processed: 472 average time/residue: 0.3280 time to fit residues: 241.4067 Evaluate side-chains 336 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7592 ------------------------------------------------------------------------------- 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: 3.9990 chunk 144 optimal weight: 0.0070 chunk 3 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 217 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- 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 353 ASN D 593 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 22356 Z= 0.235 Angle : 0.598 8.996 30180 Z= 0.304 Chirality : 0.042 0.226 3390 Planarity : 0.004 0.039 3816 Dihedral : 4.188 18.104 2922 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.12 % 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: -0.56 (0.16), residues: 2670 helix: 0.45 (0.15), residues: 1128 sheet: -1.63 (0.29), residues: 342 loop : -0.66 (0.18), residues: 1200 *********************** 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 429 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 426 time to evaluate : 2.569 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 outliers start: 3 outliers final: 0 residues processed: 428 average time/residue: 0.3367 time to fit residues: 225.5060 Evaluate side-chains 308 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.450 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4134 ------------------------------------------------------------------------------- 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: 0.9990 chunk 229 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 417 ASN ** B 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS C 374 GLN ** C 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN D 629 HIS ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 629 HIS E 763 HIS F 593 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 22356 Z= 0.256 Angle : 0.618 9.751 30180 Z= 0.309 Chirality : 0.042 0.182 3390 Planarity : 0.004 0.037 3816 Dihedral : 4.326 18.067 2922 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.08 % 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: -0.65 (0.16), residues: 2670 helix: 0.35 (0.15), residues: 1128 sheet: -1.52 (0.29), residues: 342 loop : -0.73 (0.17), residues: 1200 *********************** 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 420 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 418 time to evaluate : 2.528 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 outliers start: 2 outliers final: 0 residues processed: 420 average time/residue: 0.3470 time to fit residues: 229.2064 Evaluate side-chains 307 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6877 ------------------------------------------------------------------------------- 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: 7.9990 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 186 optimal weight: 0.4980 chunk 144 optimal weight: 0.0970 chunk 215 optimal weight: 9.9990 chunk 142 optimal weight: 0.7980 chunk 254 optimal weight: 0.0870 chunk 159 optimal weight: 7.9990 chunk 155 optimal weight: 0.0020 chunk 117 optimal weight: 0.8980 overall best weight: 0.2964 ------------------------------------------------------------------------------- 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 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 629 HIS E 763 HIS F 352 ASN ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 593 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 22356 Z= 0.148 Angle : 0.546 8.639 30180 Z= 0.278 Chirality : 0.041 0.164 3390 Planarity : 0.003 0.038 3816 Dihedral : 4.147 18.806 2922 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.04 % 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: -0.42 (0.16), residues: 2670 helix: 0.58 (0.15), residues: 1128 sheet: -1.29 (0.30), residues: 336 loop : -0.69 (0.18), residues: 1206 *********************** 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 455 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 454 time to evaluate : 2.543 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 outliers start: 1 outliers final: 0 residues processed: 455 average time/residue: 0.3378 time to fit residues: 238.6389 Evaluate side-chains 332 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5780 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 0.0670 chunk 161 optimal weight: 0.9990 chunk 173 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 417 ASN B 763 HIS C 353 ASN D 629 HIS ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 629 HIS F 593 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 22356 Z= 0.188 Angle : 0.568 8.841 30180 Z= 0.289 Chirality : 0.042 0.266 3390 Planarity : 0.004 0.037 3816 Dihedral : 4.214 18.708 2922 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.04 % 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: -0.42 (0.16), residues: 2670 helix: 0.52 (0.15), residues: 1128 sheet: -1.20 (0.30), residues: 336 loop : -0.65 (0.18), residues: 1206 *********************** 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 429 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 428 time to evaluate : 2.480 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 outliers start: 1 outliers final: 0 residues processed: 429 average time/residue: 0.3361 time to fit residues: 224.5187 Evaluate side-chains 326 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5515 ------------------------------------------------------------------------------- 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: 0.5980 chunk 237 optimal weight: 8.9990 chunk 142 optimal weight: 0.0770 chunk 103 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 224 optimal weight: 0.6980 chunk 236 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN D 629 HIS ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 629 HIS ** 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: 0.7503 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 22356 Z= 0.155 Angle : 0.548 8.497 30180 Z= 0.280 Chirality : 0.043 0.324 3390 Planarity : 0.004 0.043 3816 Dihedral : 4.187 19.270 2922 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.04 % 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: -0.36 (0.16), residues: 2670 helix: 0.53 (0.16), residues: 1128 sheet: -1.13 (0.30), residues: 336 loop : -0.60 (0.18), residues: 1206 *********************** 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 431 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 430 time to evaluate : 2.537 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 outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.3309 time to fit residues: 223.4269 Evaluate side-chains 324 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4198 ------------------------------------------------------------------------------- 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: 7.9990 chunk 153 optimal weight: 0.0170 chunk 118 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 263 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN D 629 HIS E 629 HIS ** 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: 0.7571 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 22356 Z= 0.256 Angle : 0.640 12.369 30180 Z= 0.321 Chirality : 0.043 0.270 3390 Planarity : 0.004 0.091 3816 Dihedral : 4.437 19.059 2922 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.04 % 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: -0.53 (0.16), residues: 2670 helix: 0.38 (0.15), residues: 1128 sheet: -1.28 (0.30), residues: 336 loop : -0.66 (0.18), residues: 1206 ********************** 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 404 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 403 time to evaluate : 2.782 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 outliers start: 1 outliers final: 0 residues processed: 404 average time/residue: 0.3347 time to fit residues: 213.2591 Evaluate side-chains 305 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6500 ------------------------------------------------------------------------------- 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: 0.8980 chunk 64 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 0.0170 chunk 184 optimal weight: 3.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN C 353 ASN C 593 ASN D 629 HIS E 629 HIS F 548 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.144001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.100984 restraints weight = 63863.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.103263 restraints weight = 39148.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.104738 restraints weight = 28848.108| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 22356 Z= 0.238 Angle : 0.622 9.860 30180 Z= 0.313 Chirality : 0.044 0.253 3390 Planarity : 0.004 0.061 3816 Dihedral : 4.502 18.958 2922 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.12 % 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: -0.63 (0.16), residues: 2670 helix: 0.33 (0.15), residues: 1128 sheet: -1.37 (0.29), residues: 336 loop : -0.73 (0.18), residues: 1206 =============================================================================== Job complete usr+sys time: 4890.48 seconds wall clock time: 90 minutes 5.44 seconds (5405.44 seconds total)