Starting phenix.real_space_refine on Sun Apr 14 05:03:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wre_32724/04_2024/7wre_32724_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wre_32724/04_2024/7wre_32724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wre_32724/04_2024/7wre_32724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wre_32724/04_2024/7wre_32724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wre_32724/04_2024/7wre_32724_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wre_32724/04_2024/7wre_32724_updated.pdb" } resolution = 2.52 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 C 19820 2.51 5 N 5052 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 119": "NH1" <-> "NH2" Residue "A PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 784": "NH1" <-> "NH2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 851": "NH1" <-> "NH2" Residue "A ARG 885": "NH1" <-> "NH2" Residue "A PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 784": "NH1" <-> "NH2" Residue "B ARG 816": "NH1" <-> "NH2" Residue "B ARG 842": "NH1" <-> "NH2" Residue "B ARG 851": "NH1" <-> "NH2" Residue "B ARG 885": "NH1" <-> "NH2" Residue "B PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 784": "NH1" <-> "NH2" Residue "C ARG 816": "NH1" <-> "NH2" Residue "C ARG 842": "NH1" <-> "NH2" Residue "C ARG 851": "NH1" <-> "NH2" Residue "C ARG 885": "NH1" <-> "NH2" Residue "C PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 784": "NH1" <-> "NH2" Residue "D ARG 816": "NH1" <-> "NH2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 851": "NH1" <-> "NH2" Residue "D ARG 885": "NH1" <-> "NH2" Residue "D PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30468 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "B" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "C" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "D" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.98, per 1000 atoms: 0.49 Number of scatterers: 30468 At special positions: 0 Unit cell: (153.114, 153.114, 156.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 O 5452 8.00 N 5052 7.00 C 19820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.38 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.38 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.38 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.38 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: 11.57 Conformation dependent library (CDL) restraints added in 5.4 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 4 sheets defined 62.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.42 Creating SS restraints... Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.926A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.914A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.564A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 576 through 583 removed outlier: 3.989A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 603 removed outlier: 4.132A pdb=" N LYS A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 635 removed outlier: 3.522A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 removed outlier: 4.595A pdb=" N VAL A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 662 Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'A' and resid 766 through 787 Processing helix chain 'A' and resid 792 through 795 Processing helix chain 'A' and resid 797 through 816 Processing helix chain 'A' and resid 822 through 849 removed outlier: 4.298A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 removed outlier: 4.238A pdb=" N GLN A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 889 Processing helix chain 'A' and resid 896 through 903 removed outlier: 3.654A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 912 removed outlier: 4.181A pdb=" N MET A 911 " --> pdb=" O PRO A 907 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A 912 " --> pdb=" O TYR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 953 through 968 Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 970 through 1005 removed outlier: 3.667A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.977A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1103 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 159 through 175 Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.926A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.914A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.563A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 503 through 515 Processing helix chain 'B' and resid 519 through 531 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 576 through 583 removed outlier: 3.988A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 603 removed outlier: 4.133A pdb=" N LYS B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 635 removed outlier: 3.521A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 removed outlier: 4.594A pdb=" N VAL B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 666 through 669 No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 702 through 705 Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'B' and resid 766 through 787 Processing helix chain 'B' and resid 792 through 795 Processing helix chain 'B' and resid 797 through 816 Processing helix chain 'B' and resid 822 through 849 removed outlier: 4.297A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 862 removed outlier: 4.238A pdb=" N GLN B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG B 862 " --> pdb=" O ILE B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 889 Processing helix chain 'B' and resid 896 through 903 removed outlier: 3.654A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 912 removed outlier: 4.181A pdb=" N MET B 911 " --> pdb=" O PRO B 907 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE B 912 " --> pdb=" O TYR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 928 No H-bonds generated for 'chain 'B' and resid 926 through 928' Processing helix chain 'B' and resid 953 through 968 Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 970 through 1005 removed outlier: 3.667A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1027 Processing helix chain 'B' and resid 1047 through 1070 removed outlier: 3.977A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1103 Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'C' and resid 159 through 175 Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.927A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 371 through 384 removed outlier: 3.914A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 419 removed outlier: 3.563A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 503 through 515 Processing helix chain 'C' and resid 519 through 531 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 576 through 583 removed outlier: 3.988A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 603 removed outlier: 4.134A pdb=" N LYS C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 635 removed outlier: 3.522A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 645 removed outlier: 4.594A pdb=" N VAL C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 662 Processing helix chain 'C' and resid 666 through 669 No H-bonds generated for 'chain 'C' and resid 666 through 669' Processing helix chain 'C' and resid 672 through 683 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 702 through 705 Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'C' and resid 766 through 787 Processing helix chain 'C' and resid 792 through 795 Processing helix chain 'C' and resid 797 through 816 Processing helix chain 'C' and resid 822 through 849 removed outlier: 4.297A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 848 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 862 removed outlier: 4.239A pdb=" N GLN C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG C 862 " --> pdb=" O ILE C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 889 Processing helix chain 'C' and resid 896 through 903 removed outlier: 3.655A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 912 removed outlier: 4.181A pdb=" N MET C 911 " --> pdb=" O PRO C 907 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE C 912 " --> pdb=" O TYR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 928 No H-bonds generated for 'chain 'C' and resid 926 through 928' Processing helix chain 'C' and resid 953 through 968 Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 970 through 1005 removed outlier: 3.668A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1027 Processing helix chain 'C' and resid 1047 through 1070 removed outlier: 3.978A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1103 Processing helix chain 'D' and resid 126 through 135 Processing helix chain 'D' and resid 159 through 175 Processing helix chain 'D' and resid 188 through 203 removed outlier: 3.926A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 371 through 384 removed outlier: 3.914A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 419 removed outlier: 3.564A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 435 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 484 through 487 No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 519 through 531 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 576 through 583 removed outlier: 3.989A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 603 removed outlier: 4.133A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 635 removed outlier: 3.522A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 645 removed outlier: 4.595A pdb=" N VAL D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 662 Processing helix chain 'D' and resid 666 through 669 No H-bonds generated for 'chain 'D' and resid 666 through 669' Processing helix chain 'D' and resid 672 through 683 Processing helix chain 'D' and resid 692 through 700 Processing helix chain 'D' and resid 702 through 705 Processing helix chain 'D' and resid 724 through 730 Processing helix chain 'D' and resid 734 through 758 Processing helix chain 'D' and resid 766 through 787 Processing helix chain 'D' and resid 792 through 795 Processing helix chain 'D' and resid 797 through 816 Processing helix chain 'D' and resid 822 through 849 removed outlier: 4.298A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 848 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 862 removed outlier: 4.238A pdb=" N GLN D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG D 862 " --> pdb=" O ILE D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 864 through 889 Processing helix chain 'D' and resid 896 through 903 removed outlier: 3.654A pdb=" N SER D 902 " --> pdb=" O TRP D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 912 removed outlier: 4.181A pdb=" N MET D 911 " --> pdb=" O PRO D 907 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE D 912 " --> pdb=" O TYR D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 953 through 968 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 970 through 1005 removed outlier: 3.667A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1027 Processing helix chain 'D' and resid 1047 through 1070 removed outlier: 3.977A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1103 Processing sheet with id= A, first strand: chain 'A' and resid 118 through 121 removed outlier: 4.105A pdb=" N VAL A 210 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN A 143 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU A 180 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 145 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 118 through 121 removed outlier: 4.105A pdb=" N VAL B 210 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B 143 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU B 180 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 145 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 118 through 121 removed outlier: 4.105A pdb=" N VAL C 210 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN C 143 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU C 180 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 145 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 118 through 121 removed outlier: 4.105A pdb=" N VAL D 210 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN D 143 " --> pdb=" O TRP D 178 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU D 180 " --> pdb=" O ASN D 143 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL D 145 " --> pdb=" O LEU D 180 " (cutoff:3.500A) 1592 hydrogen bonds defined for protein. 4728 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: 10.40 Time building geometry restraints manager: 12.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4892 1.31 - 1.44: 8876 1.44 - 1.57: 17208 1.57 - 1.70: 0 1.70 - 1.83: 212 Bond restraints: 31188 Sorted by residual: bond pdb=" N21 KX7 D1202 " pdb=" O23 KX7 D1202 " ideal model delta sigma weight residual 1.208 1.399 -0.191 2.00e-02 2.50e+03 9.17e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.399 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" N21 KX7 A1202 " pdb=" O23 KX7 A1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C05 KX7 D1202 " pdb=" N07 KX7 D1202 " ideal model delta sigma weight residual 1.355 1.486 -0.131 2.00e-02 2.50e+03 4.29e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 96.72 - 104.24: 296 104.24 - 111.76: 13647 111.76 - 119.27: 12152 119.27 - 126.79: 15675 126.79 - 134.31: 482 Bond angle restraints: 42252 Sorted by residual: angle pdb=" N SER C 917 " pdb=" CA SER C 917 " pdb=" C SER C 917 " ideal model delta sigma weight residual 111.36 121.66 -10.30 1.09e+00 8.42e-01 8.93e+01 angle pdb=" N SER A 917 " pdb=" CA SER A 917 " pdb=" C SER A 917 " ideal model delta sigma weight residual 111.36 121.63 -10.27 1.09e+00 8.42e-01 8.88e+01 angle pdb=" N SER D 917 " pdb=" CA SER D 917 " pdb=" C SER D 917 " ideal model delta sigma weight residual 111.36 121.50 -10.14 1.09e+00 8.42e-01 8.65e+01 angle pdb=" N SER B 917 " pdb=" CA SER B 917 " pdb=" C SER B 917 " ideal model delta sigma weight residual 111.36 121.35 -9.99 1.09e+00 8.42e-01 8.41e+01 angle pdb=" N ASP A 920 " pdb=" CA ASP A 920 " pdb=" C ASP A 920 " ideal model delta sigma weight residual 111.36 120.96 -9.60 1.09e+00 8.42e-01 7.76e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 16879 14.80 - 29.60: 1111 29.60 - 44.40: 262 44.40 - 59.20: 20 59.20 - 74.01: 32 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA LYS D 573 " pdb=" C LYS D 573 " pdb=" N LYS D 574 " pdb=" CA LYS D 574 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS A 573 " pdb=" C LYS A 573 " pdb=" N LYS A 574 " pdb=" CA LYS A 574 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS C 573 " pdb=" C LYS C 573 " pdb=" N LYS C 574 " pdb=" CA LYS C 574 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3237 0.065 - 0.130: 1186 0.130 - 0.195: 237 0.195 - 0.260: 31 0.260 - 0.325: 17 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA SER A 917 " pdb=" N SER A 917 " pdb=" C SER A 917 " pdb=" CB SER A 917 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA SER C 917 " pdb=" N SER C 917 " pdb=" C SER C 917 " pdb=" CB SER C 917 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA SER D 917 " pdb=" N SER D 917 " pdb=" C SER D 917 " pdb=" CB SER D 917 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 752 " 0.002 2.00e-02 2.50e+03 2.36e-02 9.75e+00 pdb=" CG PHE B 752 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 752 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 752 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE B 752 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 752 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE B 752 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 752 " -0.002 2.00e-02 2.50e+03 2.34e-02 9.56e+00 pdb=" CG PHE A 752 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 752 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 752 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE A 752 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 752 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 752 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 752 " 0.002 2.00e-02 2.50e+03 2.33e-02 9.52e+00 pdb=" CG PHE C 752 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 752 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 752 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE C 752 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 752 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE C 752 " -0.006 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4620 2.75 - 3.29: 29150 3.29 - 3.82: 49670 3.82 - 4.36: 59320 4.36 - 4.90: 99225 Nonbonded interactions: 241985 Sorted by model distance: nonbonded pdb=" OD1 ASP A 920 " pdb=" NH2 ARG B 901 " model vdw 2.212 2.520 nonbonded pdb=" OD1 ASP C 920 " pdb=" NH2 ARG D 901 " model vdw 2.213 2.520 nonbonded pdb=" NH2 ARG A 901 " pdb=" OD1 ASP D 920 " model vdw 2.224 2.520 nonbonded pdb=" OD1 ASP B 920 " pdb=" NH2 ARG C 901 " model vdw 2.251 2.520 nonbonded pdb=" OG SER D 205 " pdb=" OE1 GLU D 206 " model vdw 2.259 2.440 ... (remaining 241980 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' } 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 individual isotropic 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: 1.150 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: 0.030 Extract box with map and model: 5.180 Check model and map are aligned: 0.440 Set scattering table: 0.320 Process input model: 76.660 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.190 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.013 0.191 31188 Z= 0.817 Angle : 1.179 10.819 42252 Z= 0.658 Chirality : 0.068 0.325 4708 Planarity : 0.007 0.066 5280 Dihedral : 10.862 74.005 11212 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.15 % Favored : 93.52 % Rotamer: Outliers : 0.24 % Allowed : 3.25 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.11), residues: 3656 helix: -1.98 (0.08), residues: 2400 sheet: -2.21 (0.32), residues: 192 loop : -3.18 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 651 HIS 0.016 0.004 HIS A 765 PHE 0.043 0.004 PHE C 832 TYR 0.051 0.004 TYR A 772 ARG 0.010 0.001 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 659 time to evaluate : 3.505 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: A 189 MET cc_start: 0.8251 (mpp) cc_final: 0.7924 (mtt) REVERT: A 198 ASP cc_start: 0.8432 (m-30) cc_final: 0.7986 (m-30) REVERT: B 189 MET cc_start: 0.8248 (mpp) cc_final: 0.7927 (mtt) REVERT: C 189 MET cc_start: 0.8260 (mpp) cc_final: 0.7931 (mtt) REVERT: D 189 MET cc_start: 0.8253 (mpp) cc_final: 0.7920 (mtt) REVERT: D 198 ASP cc_start: 0.8428 (m-30) cc_final: 0.7978 (m-30) outliers start: 8 outliers final: 4 residues processed: 667 average time/residue: 1.6502 time to fit residues: 1270.4665 Evaluate side-chains 391 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 387 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 144 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 337 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS A 259 HIS A 270 HIS A 294 ASN A 667 HIS A 675 GLN A 741 ASN B 257 HIS B 259 HIS B 270 HIS B 294 ASN B 667 HIS B 675 GLN C 257 HIS C 259 HIS C 270 HIS C 294 ASN C 667 HIS C 675 GLN D 257 HIS D 259 HIS D 270 HIS D 294 ASN D 572 ASN D 667 HIS D 675 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31188 Z= 0.303 Angle : 0.686 8.203 42252 Z= 0.361 Chirality : 0.042 0.148 4708 Planarity : 0.005 0.050 5280 Dihedral : 6.140 53.823 4032 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.94 % Allowed : 11.78 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3656 helix: -0.26 (0.10), residues: 2440 sheet: -2.10 (0.33), residues: 204 loop : -2.67 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 453 HIS 0.006 0.001 HIS C 138 PHE 0.020 0.002 PHE D 735 TYR 0.018 0.002 TYR B 787 ARG 0.008 0.001 ARG A1079 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 431 time to evaluate : 3.678 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 189 MET cc_start: 0.8119 (mpp) cc_final: 0.7893 (mtm) REVERT: A 191 TYR cc_start: 0.8254 (t80) cc_final: 0.7867 (t80) REVERT: A 282 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: A 518 ASP cc_start: 0.8075 (t0) cc_final: 0.7768 (t0) REVERT: B 189 MET cc_start: 0.8108 (mpp) cc_final: 0.7893 (mtm) REVERT: B 191 TYR cc_start: 0.8251 (t80) cc_final: 0.7868 (t80) REVERT: B 282 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: B 518 ASP cc_start: 0.8037 (t0) cc_final: 0.7736 (t0) REVERT: B 689 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7143 (p0) REVERT: C 189 MET cc_start: 0.8128 (mpp) cc_final: 0.7926 (mtm) REVERT: C 191 TYR cc_start: 0.8256 (t80) cc_final: 0.7872 (t80) REVERT: C 282 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: C 518 ASP cc_start: 0.8042 (t0) cc_final: 0.7735 (t0) REVERT: C 689 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7164 (p0) REVERT: D 189 MET cc_start: 0.8115 (mpp) cc_final: 0.7907 (mtm) REVERT: D 191 TYR cc_start: 0.8247 (t80) cc_final: 0.7840 (t80) REVERT: D 282 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: D 457 ASP cc_start: 0.7156 (t0) cc_final: 0.6833 (t0) REVERT: D 518 ASP cc_start: 0.8040 (t0) cc_final: 0.7733 (t0) REVERT: D 689 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7090 (p0) outliers start: 98 outliers final: 37 residues processed: 500 average time/residue: 1.4090 time to fit residues: 831.0845 Evaluate side-chains 368 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 324 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 991 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 281 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 338 optimal weight: 0.9980 chunk 365 optimal weight: 10.0000 chunk 301 optimal weight: 20.0000 chunk 335 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 271 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 609 ASN A 671 GLN A 761 HIS A 886 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 609 ASN B 761 HIS B 886 GLN B 987 GLN C 204 ASN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 609 ASN C 886 GLN D 204 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 ASN D 761 HIS D 886 GLN D 987 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 31188 Z= 0.462 Angle : 0.715 8.571 42252 Z= 0.375 Chirality : 0.045 0.151 4708 Planarity : 0.005 0.040 5280 Dihedral : 5.964 50.883 4024 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.12 % Allowed : 12.59 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3656 helix: 0.32 (0.10), residues: 2440 sheet: -1.90 (0.34), residues: 188 loop : -2.65 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 453 HIS 0.007 0.002 HIS B 765 PHE 0.024 0.002 PHE D 735 TYR 0.018 0.002 TYR C 646 ARG 0.007 0.001 ARG D 688 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 345 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8260 (p) REVERT: A 162 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7664 (mtm-85) REVERT: A 282 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: A 985 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8181 (mp) REVERT: B 141 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8267 (p) REVERT: B 162 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7663 (mtm-85) REVERT: B 282 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7474 (pp20) REVERT: B 689 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7106 (p0) REVERT: B 985 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8175 (mp) REVERT: C 141 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8279 (p) REVERT: C 162 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7668 (mtm-85) REVERT: C 282 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7477 (pp20) REVERT: C 689 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7135 (p0) REVERT: C 985 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8162 (mp) REVERT: C 1023 MET cc_start: 0.7652 (mmp) cc_final: 0.6419 (ttm) REVERT: D 141 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8262 (p) REVERT: D 162 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7664 (mtm-85) REVERT: D 282 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7466 (pp20) REVERT: D 457 ASP cc_start: 0.7334 (t0) cc_final: 0.7117 (t0) REVERT: D 689 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7106 (p0) REVERT: D 985 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8224 (mp) outliers start: 137 outliers final: 61 residues processed: 448 average time/residue: 1.2732 time to fit residues: 685.0307 Evaluate side-chains 374 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 295 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1095 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain D residue 1095 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.0040 chunk 254 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 339 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 321 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN C 438 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 GLN D 438 GLN D 449 ASN D 671 GLN D 741 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31188 Z= 0.204 Angle : 0.596 10.210 42252 Z= 0.308 Chirality : 0.041 0.150 4708 Planarity : 0.004 0.033 5280 Dihedral : 5.621 51.326 4024 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.22 % Allowed : 14.69 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3656 helix: 0.90 (0.10), residues: 2460 sheet: -1.86 (0.34), residues: 188 loop : -2.36 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 453 HIS 0.004 0.001 HIS A 138 PHE 0.025 0.001 PHE B 779 TYR 0.022 0.002 TYR A 191 ARG 0.007 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 362 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8148 (p) REVERT: A 282 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7516 (pp20) REVERT: A 353 MET cc_start: 0.7322 (mpp) cc_final: 0.7051 (pmm) REVERT: A 1023 MET cc_start: 0.7581 (mmp) cc_final: 0.6446 (ttm) REVERT: B 141 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 282 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7513 (pp20) REVERT: B 353 MET cc_start: 0.7323 (mpp) cc_final: 0.7054 (pmm) REVERT: B 689 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6990 (p0) REVERT: B 1023 MET cc_start: 0.7605 (mmp) cc_final: 0.6484 (ttm) REVERT: C 141 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8153 (p) REVERT: C 282 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7505 (pp20) REVERT: C 353 MET cc_start: 0.7316 (mpp) cc_final: 0.7054 (pmm) REVERT: C 689 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6983 (p0) REVERT: C 1023 MET cc_start: 0.7646 (mmp) cc_final: 0.6452 (ttm) REVERT: D 141 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8151 (p) REVERT: D 282 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7497 (pp20) REVERT: D 353 MET cc_start: 0.7317 (mpp) cc_final: 0.7064 (pmm) REVERT: D 689 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6968 (p0) REVERT: D 1023 MET cc_start: 0.7623 (mmp) cc_final: 0.6478 (ttm) outliers start: 107 outliers final: 40 residues processed: 443 average time/residue: 1.3099 time to fit residues: 692.4538 Evaluate side-chains 341 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 290 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 148 optimal weight: 0.0040 chunk 306 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 322 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 overall best weight: 4.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN B 449 ASN C 449 ASN C 741 ASN C 761 HIS C 987 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 31188 Z= 0.372 Angle : 0.667 10.742 42252 Z= 0.345 Chirality : 0.044 0.167 4708 Planarity : 0.004 0.046 5280 Dihedral : 5.628 53.976 4024 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.54 % Allowed : 15.50 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3656 helix: 0.98 (0.10), residues: 2464 sheet: -1.99 (0.34), residues: 188 loop : -2.34 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 786 HIS 0.006 0.001 HIS A 138 PHE 0.027 0.002 PHE B1021 TYR 0.014 0.002 TYR D 186 ARG 0.011 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 308 time to evaluate : 3.771 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: A 141 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8239 (p) REVERT: A 282 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7592 (pp20) REVERT: A 985 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 1023 MET cc_start: 0.7656 (mmp) cc_final: 0.6460 (ttm) REVERT: B 141 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 282 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7599 (pp20) REVERT: B 689 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7126 (p0) REVERT: B 985 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 1023 MET cc_start: 0.7641 (mmp) cc_final: 0.6447 (ttm) REVERT: C 141 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8254 (p) REVERT: C 282 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7607 (pp20) REVERT: C 689 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7128 (p0) REVERT: C 985 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8103 (mp) REVERT: D 141 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8257 (p) REVERT: D 282 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: D 689 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7107 (p0) REVERT: D 985 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8164 (mp) REVERT: D 1023 MET cc_start: 0.7657 (mmp) cc_final: 0.6453 (ttm) outliers start: 151 outliers final: 64 residues processed: 438 average time/residue: 1.2580 time to fit residues: 664.5472 Evaluate side-chains 359 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 280 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1015 PHE Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain D residue 1095 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 10.0000 chunk 323 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 211 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 359 optimal weight: 0.9990 chunk 298 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 119 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN B 438 GLN B 973 ASN C 256 ASN C 973 ASN D 973 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31188 Z= 0.172 Angle : 0.580 9.772 42252 Z= 0.302 Chirality : 0.040 0.143 4708 Planarity : 0.004 0.030 5280 Dihedral : 5.234 51.179 4024 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.97 % Allowed : 16.44 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3656 helix: 1.40 (0.11), residues: 2432 sheet: -1.89 (0.33), residues: 188 loop : -2.25 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 786 HIS 0.004 0.000 HIS A 138 PHE 0.031 0.001 PHE C1021 TYR 0.022 0.001 TYR D 191 ARG 0.006 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 344 time to evaluate : 3.703 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 1023 MET cc_start: 0.7476 (mmp) cc_final: 0.6444 (ttp) REVERT: B 141 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8145 (p) REVERT: B 294 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8412 (m-40) REVERT: B 689 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7010 (p0) REVERT: B 1023 MET cc_start: 0.7493 (mmp) cc_final: 0.6465 (ttp) REVERT: C 141 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8169 (p) REVERT: C 294 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8421 (m-40) REVERT: C 689 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7011 (p0) REVERT: C 1023 MET cc_start: 0.7505 (mmp) cc_final: 0.6402 (ttm) REVERT: D 141 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8179 (p) REVERT: D 294 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8417 (m-40) REVERT: D 689 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6972 (p0) REVERT: D 1023 MET cc_start: 0.7483 (mmp) cc_final: 0.6437 (ttp) outliers start: 99 outliers final: 49 residues processed: 423 average time/residue: 1.2013 time to fit residues: 616.1254 Evaluate side-chains 352 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 293 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 1015 PHE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 1015 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 205 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 302 optimal weight: 30.0000 chunk 200 optimal weight: 0.8980 chunk 358 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 973 ASN A 987 GLN D 136 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31188 Z= 0.225 Angle : 0.589 10.449 42252 Z= 0.307 Chirality : 0.041 0.158 4708 Planarity : 0.004 0.057 5280 Dihedral : 5.124 52.977 4024 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.70 % Allowed : 16.59 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3656 helix: 1.49 (0.11), residues: 2456 sheet: -1.85 (0.33), residues: 188 loop : -2.09 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 786 HIS 0.004 0.001 HIS A 138 PHE 0.035 0.001 PHE C1021 TYR 0.011 0.001 TYR A 727 ARG 0.004 0.000 ARG A1081 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 313 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8202 (p) REVERT: A 353 MET cc_start: 0.7103 (mpp) cc_final: 0.6869 (pmm) REVERT: A 985 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 1023 MET cc_start: 0.7497 (mmp) cc_final: 0.6429 (ttp) REVERT: B 141 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8180 (p) REVERT: B 294 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8437 (m-40) REVERT: B 689 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6989 (p0) REVERT: B 985 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8012 (mp) REVERT: B 1023 MET cc_start: 0.7524 (mmp) cc_final: 0.6473 (ttp) REVERT: B 1095 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8711 (tp) REVERT: C 141 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8216 (p) REVERT: C 294 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8408 (m-40) REVERT: C 353 MET cc_start: 0.7107 (mpp) cc_final: 0.6838 (pmm) REVERT: C 689 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7002 (p0) REVERT: C 985 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.8005 (mp) REVERT: C 1023 MET cc_start: 0.7489 (mmp) cc_final: 0.6497 (ttp) REVERT: D 141 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8228 (p) REVERT: D 294 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8430 (m-40) REVERT: D 689 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6987 (p0) REVERT: D 985 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8039 (mp) REVERT: D 1023 MET cc_start: 0.7505 (mmp) cc_final: 0.6423 (ttp) outliers start: 123 outliers final: 59 residues processed: 407 average time/residue: 1.1958 time to fit residues: 591.3547 Evaluate side-chains 371 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 297 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1015 PHE Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1015 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 281 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 HIS C 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31188 Z= 0.183 Angle : 0.584 10.209 42252 Z= 0.303 Chirality : 0.040 0.184 4708 Planarity : 0.003 0.044 5280 Dihedral : 4.982 48.939 4024 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.91 % Allowed : 17.85 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3656 helix: 1.62 (0.11), residues: 2436 sheet: -1.83 (0.33), residues: 188 loop : -2.00 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 786 HIS 0.003 0.001 HIS A 138 PHE 0.037 0.001 PHE B1021 TYR 0.019 0.001 TYR D 186 ARG 0.014 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 321 time to evaluate : 3.527 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: A 141 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 353 MET cc_start: 0.7104 (mpp) cc_final: 0.6819 (pmm) REVERT: A 985 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 1023 MET cc_start: 0.7511 (mmp) cc_final: 0.6510 (ttp) REVERT: B 141 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8171 (p) REVERT: B 294 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (m-40) REVERT: B 689 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6974 (p0) REVERT: B 985 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 1023 MET cc_start: 0.7525 (mmp) cc_final: 0.6508 (ttp) REVERT: C 141 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8189 (p) REVERT: C 294 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8424 (m-40) REVERT: C 353 MET cc_start: 0.7102 (mpp) cc_final: 0.6822 (pmm) REVERT: C 689 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6985 (p0) REVERT: C 985 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.8006 (mp) REVERT: C 1023 MET cc_start: 0.7441 (mmp) cc_final: 0.6461 (ttp) REVERT: D 141 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8194 (p) REVERT: D 294 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8416 (m-40) REVERT: D 689 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6956 (p0) REVERT: D 985 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8029 (mp) REVERT: D 1023 MET cc_start: 0.7534 (mmp) cc_final: 0.6489 (ttp) outliers start: 97 outliers final: 55 residues processed: 397 average time/residue: 1.2108 time to fit residues: 584.1239 Evaluate side-chains 377 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 308 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1015 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 4.9990 chunk 343 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 301 optimal weight: 1.9990 chunk 316 optimal weight: 8.9990 chunk 332 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31188 Z= 0.186 Angle : 0.586 10.601 42252 Z= 0.303 Chirality : 0.040 0.179 4708 Planarity : 0.003 0.049 5280 Dihedral : 4.831 47.818 4024 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.70 % Allowed : 18.48 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3656 helix: 1.70 (0.11), residues: 2436 sheet: -1.78 (0.33), residues: 188 loop : -1.91 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 786 HIS 0.003 0.001 HIS A 138 PHE 0.037 0.001 PHE C1021 TYR 0.017 0.001 TYR A 186 ARG 0.016 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 319 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8185 (p) REVERT: A 353 MET cc_start: 0.7042 (mpp) cc_final: 0.6743 (pmm) REVERT: A 985 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8009 (mp) REVERT: A 1023 MET cc_start: 0.7576 (mmp) cc_final: 0.6570 (ttp) REVERT: A 1078 MET cc_start: 0.7128 (mmt) cc_final: 0.6810 (mmt) REVERT: B 141 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8176 (p) REVERT: B 294 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8444 (m-40) REVERT: B 689 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6958 (p0) REVERT: B 985 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7994 (mp) REVERT: B 1023 MET cc_start: 0.7580 (mmp) cc_final: 0.6578 (ttp) REVERT: C 141 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8193 (p) REVERT: C 294 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8424 (m-40) REVERT: C 353 MET cc_start: 0.7126 (mpp) cc_final: 0.6832 (pmm) REVERT: C 451 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7162 (pmt-80) REVERT: C 452 ARG cc_start: 0.6033 (ptt180) cc_final: 0.5799 (tmm-80) REVERT: C 689 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6973 (p0) REVERT: C 985 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7999 (mp) REVERT: C 1023 MET cc_start: 0.7458 (mmp) cc_final: 0.6481 (ttp) REVERT: D 141 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8197 (p) REVERT: D 294 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8436 (m-40) REVERT: D 457 ASP cc_start: 0.7449 (t70) cc_final: 0.7101 (t0) REVERT: D 689 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6927 (p0) REVERT: D 985 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.8010 (mp) REVERT: D 1023 MET cc_start: 0.7592 (mmp) cc_final: 0.6580 (ttp) outliers start: 90 outliers final: 53 residues processed: 390 average time/residue: 1.2287 time to fit residues: 584.1837 Evaluate side-chains 375 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 307 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 2.9990 chunk 353 optimal weight: 0.0970 chunk 215 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 370 optimal weight: 30.0000 chunk 341 optimal weight: 0.8980 chunk 295 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4261 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: