Starting phenix.real_space_refine on Wed Feb 21 11:19:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/02_2024/7wrf_32725_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/02_2024/7wrf_32725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/02_2024/7wrf_32725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/02_2024/7wrf_32725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/02_2024/7wrf_32725_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/02_2024/7wrf_32725_updated.pdb" } resolution = 3.04 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 Na 1 4.78 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 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 "B ARG 119": "NH1" <-> "NH2" 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 "C ARG 119": "NH1" <-> "NH2" 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 "D ARG 119": "NH1" <-> "NH2" 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" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30469 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CA': 1, ' NA': 1, 'KX7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 16.10, per 1000 atoms: 0.53 Number of scatterers: 30469 At special positions: 0 Unit cell: (151.086, 151.086, 156.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 140 16.00 Na 1 11.00 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=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.02 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.02 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.02 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: 11.24 Conformation dependent library (CDL) restraints added in 5.2 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: 180 helices and 4 sheets defined 63.3% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.04 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: 3.781A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 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: 4.102A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.787A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 4.230A 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 460 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: 3.901A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 603 removed outlier: 4.300A pdb=" N LYS A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 635 removed outlier: 3.773A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 removed outlier: 4.217A 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 removed outlier: 3.603A pdb=" N VAL A 705 " --> pdb=" O ILE A 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 705' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'A' and resid 766 through 789 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: 4.187A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 862 removed outlier: 4.080A pdb=" N GLN A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 4.475A 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: 3.821A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 911 removed outlier: 4.039A pdb=" N MET A 911 " --> pdb=" O PRO A 907 " (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: 3.620A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1029 removed outlier: 4.963A pdb=" N VAL A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.859A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.790A 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: 3.782A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 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: 4.102A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.786A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 4.230A 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 460 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: 3.902A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 603 removed outlier: 4.300A pdb=" N LYS B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 635 removed outlier: 3.774A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 removed outlier: 4.218A 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 removed outlier: 3.603A pdb=" N VAL B 705 " --> pdb=" O ILE B 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 702 through 705' Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'B' and resid 766 through 789 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: 4.186A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 862 removed outlier: 4.080A pdb=" N GLN B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 4.475A 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: 3.821A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 911 removed outlier: 4.038A pdb=" N MET B 911 " --> pdb=" O PRO B 907 " (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: 3.620A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1029 removed outlier: 4.964A pdb=" N VAL B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1070 removed outlier: 3.859A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.790A 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: 3.782A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 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: 4.103A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 403 through 419 removed outlier: 3.786A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 4.229A 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 460 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: 3.902A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 603 removed outlier: 4.300A pdb=" N LYS C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 635 removed outlier: 3.774A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 645 removed outlier: 4.217A 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 removed outlier: 3.604A pdb=" N VAL C 705 " --> pdb=" O ILE C 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 702 through 705' Processing helix chain 'C' and resid 724 through 731 Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'C' and resid 766 through 789 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: 4.186A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR C 848 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 862 removed outlier: 4.081A pdb=" N GLN C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) removed outlier: 4.474A 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: 3.821A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 911 removed outlier: 4.038A pdb=" N MET C 911 " --> pdb=" O PRO C 907 " (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: 3.620A pdb=" N LEU C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1029 removed outlier: 4.963A pdb=" N VAL C1017 " --> pdb=" O PRO C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1070 removed outlier: 3.859A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.790A 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: 3.781A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 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: 4.102A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 403 through 419 removed outlier: 3.786A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) removed outlier: 4.229A 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 460 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: 3.902A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 603 removed outlier: 4.301A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 635 removed outlier: 3.774A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 645 removed outlier: 4.217A 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 removed outlier: 3.603A pdb=" N VAL D 705 " --> pdb=" O ILE D 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 702 through 705' Processing helix chain 'D' and resid 724 through 731 Processing helix chain 'D' and resid 734 through 758 Processing helix chain 'D' and resid 766 through 789 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: 4.186A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR D 848 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 862 removed outlier: 4.081A pdb=" N GLN D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) removed outlier: 4.475A 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 900 Processing helix chain 'D' and resid 905 through 911 removed outlier: 4.038A pdb=" N MET D 911 " --> pdb=" O PRO D 907 " (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: 3.620A pdb=" N LEU D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1029 removed outlier: 4.963A pdb=" N VAL D1017 " --> pdb=" O PRO D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1070 removed outlier: 3.859A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.790A 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 119 through 121 removed outlier: 8.022A pdb=" N LEU A 120 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU A 262 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 119 through 121 removed outlier: 8.022A pdb=" N LEU B 120 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU B 262 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 119 through 121 removed outlier: 8.022A pdb=" N LEU C 120 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 262 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 119 through 121 removed outlier: 8.022A pdb=" N LEU D 120 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU D 262 " --> pdb=" O LEU D 120 " (cutoff:3.500A) 1606 hydrogen bonds defined for protein. 4638 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: 10.64 Time building geometry restraints manager: 11.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4884 1.31 - 1.44: 8856 1.44 - 1.57: 17236 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 1.402 -0.194 2.00e-02 2.50e+03 9.36e+01 bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" N21 KX7 A1203 " pdb=" O23 KX7 A1203 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" C05 KX7 D1202 " pdb=" N07 KX7 D1202 " ideal model delta sigma weight residual 1.355 1.495 -0.140 2.00e-02 2.50e+03 4.89e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.42: 218 103.42 - 111.09: 10911 111.09 - 118.75: 13705 118.75 - 126.42: 16845 126.42 - 134.09: 573 Bond angle restraints: 42252 Sorted by residual: angle pdb=" N VAL B 791 " pdb=" CA VAL B 791 " pdb=" C VAL B 791 " ideal model delta sigma weight residual 112.96 108.21 4.75 1.00e+00 1.00e+00 2.26e+01 angle pdb=" N VAL A 791 " pdb=" CA VAL A 791 " pdb=" C VAL A 791 " ideal model delta sigma weight residual 112.96 108.25 4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" N VAL C 791 " pdb=" CA VAL C 791 " pdb=" C VAL C 791 " ideal model delta sigma weight residual 112.96 108.26 4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" N VAL D 791 " pdb=" CA VAL D 791 " pdb=" C VAL D 791 " ideal model delta sigma weight residual 112.96 108.28 4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" C ILE A 701 " pdb=" N ILE A 702 " pdb=" CA ILE A 702 " ideal model delta sigma weight residual 120.33 123.78 -3.45 8.00e-01 1.56e+00 1.86e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 17104 14.57 - 29.14: 884 29.14 - 43.71: 272 43.71 - 58.28: 16 58.28 - 72.85: 28 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA PRO B1012 " pdb=" C PRO B1012 " pdb=" N PHE B1013 " pdb=" CA PHE B1013 " ideal model delta harmonic sigma weight residual -180.00 -150.09 -29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA PRO D1012 " pdb=" C PRO D1012 " pdb=" N PHE D1013 " pdb=" CA PHE D1013 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA PRO A1012 " pdb=" C PRO A1012 " pdb=" N PHE A1013 " pdb=" CA PHE A1013 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2875 0.045 - 0.090: 1358 0.090 - 0.134: 352 0.134 - 0.179: 99 0.179 - 0.224: 24 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CG LEU A 521 " pdb=" CB LEU A 521 " pdb=" CD1 LEU A 521 " pdb=" CD2 LEU A 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 521 " pdb=" CB LEU B 521 " pdb=" CD1 LEU B 521 " pdb=" CD2 LEU B 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU D 521 " pdb=" CB LEU D 521 " pdb=" CD1 LEU D 521 " pdb=" CD2 LEU D 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 141 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO D 142 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 141 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 142 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 141 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 142 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " 0.034 5.00e-02 4.00e+02 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 8681 2.82 - 3.34: 28214 3.34 - 3.86: 49069 3.86 - 4.38: 56670 4.38 - 4.90: 96872 Nonbonded interactions: 239506 Sorted by model distance: nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.294 2.440 nonbonded pdb=" O VAL C1065 " pdb=" OG1 THR C1069 " model vdw 2.295 2.440 nonbonded pdb=" O VAL B1065 " pdb=" OG1 THR B1069 " model vdw 2.295 2.440 nonbonded pdb=" O VAL D1065 " pdb=" OG1 THR D1069 " model vdw 2.295 2.440 nonbonded pdb=" O VAL D 728 " pdb=" OG1 THR D 732 " model vdw 2.324 2.440 ... (remaining 239501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 1104 or resid 1201)) selection = (chain 'B' and (resid 102 through 1104 or resid 1201)) selection = (chain 'C' and (resid 102 through 1104 or resid 1201)) selection = (chain 'D' and (resid 102 through 1104 or resid 1201)) } 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: 0.940 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: 5.360 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 77.710 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.008 0.194 31188 Z= 0.514 Angle : 0.987 9.705 42252 Z= 0.543 Chirality : 0.056 0.224 4708 Planarity : 0.007 0.062 5280 Dihedral : 10.460 72.845 11212 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.12 % Allowed : 1.80 % Favored : 98.08 % 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: -3.74 (0.11), residues: 3656 helix: -2.03 (0.08), residues: 2412 sheet: -1.90 (0.32), residues: 208 loop : -3.28 (0.15), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 377 HIS 0.007 0.002 HIS A 138 PHE 0.031 0.003 PHE B 304 TYR 0.038 0.003 TYR A 772 ARG 0.009 0.001 ARG C1008 *********************** 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 831 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 827 time to evaluate : 3.459 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 162 ARG cc_start: 0.8176 (ttt180) cc_final: 0.7920 (ttp-110) REVERT: A 280 GLN cc_start: 0.8309 (tt0) cc_final: 0.8104 (tm-30) REVERT: A 569 ILE cc_start: 0.9136 (tp) cc_final: 0.8904 (tp) REVERT: A 702 ILE cc_start: 0.8413 (mt) cc_final: 0.8151 (tt) REVERT: A 787 TYR cc_start: 0.7393 (t80) cc_final: 0.7115 (t80) REVERT: A 868 PHE cc_start: 0.8203 (m-10) cc_final: 0.7609 (t80) REVERT: A 1023 MET cc_start: 0.7034 (mmm) cc_final: 0.5995 (mtp) REVERT: B 162 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7887 (ttp-110) REVERT: B 191 TYR cc_start: 0.7537 (t80) cc_final: 0.7230 (t80) REVERT: B 627 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7843 (mt-10) REVERT: B 691 LYS cc_start: 0.7529 (mtpt) cc_final: 0.7271 (mtpt) REVERT: B 702 ILE cc_start: 0.8410 (mt) cc_final: 0.8163 (tt) REVERT: B 787 TYR cc_start: 0.7387 (t80) cc_final: 0.7103 (t80) REVERT: B 868 PHE cc_start: 0.8192 (m-10) cc_final: 0.7598 (t80) REVERT: B 1023 MET cc_start: 0.6992 (mmm) cc_final: 0.5939 (mtp) REVERT: C 191 TYR cc_start: 0.7627 (t80) cc_final: 0.7354 (t80) REVERT: C 280 GLN cc_start: 0.8276 (tt0) cc_final: 0.8063 (tm-30) REVERT: C 569 ILE cc_start: 0.9143 (tp) cc_final: 0.8922 (tp) REVERT: C 627 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7856 (mt-10) REVERT: C 702 ILE cc_start: 0.8404 (mt) cc_final: 0.8160 (tt) REVERT: C 787 TYR cc_start: 0.7411 (t80) cc_final: 0.7152 (t80) REVERT: C 868 PHE cc_start: 0.8177 (m-10) cc_final: 0.7611 (t80) REVERT: C 1023 MET cc_start: 0.6850 (mmm) cc_final: 0.5838 (mtp) REVERT: C 1047 ASN cc_start: 0.7790 (m-40) cc_final: 0.7583 (m110) REVERT: D 191 TYR cc_start: 0.7609 (t80) cc_final: 0.7317 (t80) REVERT: D 280 GLN cc_start: 0.8337 (tt0) cc_final: 0.8136 (tm-30) REVERT: D 569 ILE cc_start: 0.9109 (tp) cc_final: 0.8898 (tp) REVERT: D 702 ILE cc_start: 0.8403 (mt) cc_final: 0.8141 (tt) REVERT: D 787 TYR cc_start: 0.7408 (t80) cc_final: 0.7140 (t80) REVERT: D 868 PHE cc_start: 0.8181 (m-10) cc_final: 0.7622 (t80) REVERT: D 1023 MET cc_start: 0.6889 (mmm) cc_final: 0.5892 (mtp) outliers start: 4 outliers final: 0 residues processed: 827 average time/residue: 0.4815 time to fit residues: 598.7203 Evaluate side-chains 427 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 0.0070 chunk 150 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 337 optimal weight: 0.8980 overall best weight: 2.7804 ------------------------------------------------------------------------------- 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 572 ASN A 675 GLN A 987 GLN B 256 ASN B 257 HIS B 259 HIS B 572 ASN B 675 GLN B 741 ASN C 257 HIS C 259 HIS C 294 ASN C 572 ASN C 675 GLN C 741 ASN ** C 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 HIS D 259 HIS D 572 ASN D 675 GLN D 973 ASN D 987 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31188 Z= 0.280 Angle : 0.637 7.644 42252 Z= 0.334 Chirality : 0.041 0.149 4708 Planarity : 0.004 0.051 5280 Dihedral : 5.986 51.037 4024 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.49 % Allowed : 8.14 % Favored : 89.36 % 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: -1.70 (0.13), residues: 3656 helix: -0.19 (0.10), residues: 2408 sheet: -1.91 (0.32), residues: 192 loop : -3.07 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 898 HIS 0.004 0.001 HIS A 138 PHE 0.027 0.002 PHE A 752 TYR 0.015 0.002 TYR C 772 ARG 0.003 0.000 ARG B 278 *********************** 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 549 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 466 time to evaluate : 3.129 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: A 280 GLN cc_start: 0.8302 (tt0) cc_final: 0.8054 (tp40) REVERT: A 396 MET cc_start: 0.6800 (mmp) cc_final: 0.5935 (mmp) REVERT: A 491 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7364 (tp30) REVERT: A 702 ILE cc_start: 0.8448 (mt) cc_final: 0.8219 (tt) REVERT: A 787 TYR cc_start: 0.7431 (t80) cc_final: 0.7150 (t80) REVERT: A 868 PHE cc_start: 0.8167 (m-10) cc_final: 0.7530 (t80) REVERT: A 1005 TYR cc_start: 0.6595 (m-10) cc_final: 0.5294 (m-80) REVERT: A 1023 MET cc_start: 0.7163 (mmm) cc_final: 0.6064 (mtp) REVERT: A 1047 ASN cc_start: 0.7866 (m-40) cc_final: 0.7544 (m110) REVERT: B 491 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7311 (tp30) REVERT: B 702 ILE cc_start: 0.8442 (mt) cc_final: 0.8239 (tt) REVERT: B 741 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8350 (m-40) REVERT: B 787 TYR cc_start: 0.7428 (t80) cc_final: 0.7136 (t80) REVERT: B 801 MET cc_start: 0.7612 (ptm) cc_final: 0.7370 (ptt) REVERT: B 868 PHE cc_start: 0.8133 (m-10) cc_final: 0.7509 (t80) REVERT: B 1005 TYR cc_start: 0.6528 (m-10) cc_final: 0.5265 (m-80) REVERT: B 1023 MET cc_start: 0.7049 (mmm) cc_final: 0.5957 (mtp) REVERT: C 191 TYR cc_start: 0.7955 (t80) cc_final: 0.7694 (t80) REVERT: C 280 GLN cc_start: 0.8301 (tt0) cc_final: 0.7988 (tp40) REVERT: C 491 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7343 (tp30) REVERT: C 702 ILE cc_start: 0.8439 (mt) cc_final: 0.8238 (tt) REVERT: C 741 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8361 (m-40) REVERT: C 787 TYR cc_start: 0.7432 (t80) cc_final: 0.7140 (t80) REVERT: C 864 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8268 (mp) REVERT: C 868 PHE cc_start: 0.8119 (m-10) cc_final: 0.7522 (t80) REVERT: C 1023 MET cc_start: 0.7035 (mmm) cc_final: 0.5947 (mtp) REVERT: D 191 TYR cc_start: 0.7976 (t80) cc_final: 0.7568 (t80) REVERT: D 280 GLN cc_start: 0.8318 (tt0) cc_final: 0.8036 (tp40) REVERT: D 491 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7405 (tp30) REVERT: D 702 ILE cc_start: 0.8442 (mt) cc_final: 0.8214 (tt) REVERT: D 787 TYR cc_start: 0.7421 (t80) cc_final: 0.7150 (t80) REVERT: D 868 PHE cc_start: 0.8123 (m-10) cc_final: 0.7520 (t80) REVERT: D 1023 MET cc_start: 0.7146 (mmm) cc_final: 0.6051 (mtp) REVERT: D 1047 ASN cc_start: 0.7959 (m-40) cc_final: 0.7626 (m110) outliers start: 83 outliers final: 48 residues processed: 517 average time/residue: 0.4336 time to fit residues: 349.0190 Evaluate side-chains 444 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 393 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 391 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 741 ASN Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 391 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 741 ASN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1045 PHE 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: 8.9990 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 338 optimal weight: 4.9990 chunk 365 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 335 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 271 optimal weight: 7.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 741 ASN A 785 GLN B 609 ASN B 785 GLN C 609 ASN C 785 GLN D 609 ASN D 741 ASN D 785 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31188 Z= 0.272 Angle : 0.605 7.686 42252 Z= 0.313 Chirality : 0.040 0.156 4708 Planarity : 0.004 0.050 5280 Dihedral : 5.742 52.023 4024 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.85 % Allowed : 10.70 % Favored : 86.45 % 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: -0.83 (0.14), residues: 3656 helix: 0.54 (0.10), residues: 2448 sheet: -1.85 (0.32), residues: 192 loop : -2.98 (0.16), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 898 HIS 0.003 0.001 HIS C 138 PHE 0.019 0.002 PHE D 752 TYR 0.017 0.002 TYR B 191 ARG 0.007 0.000 ARG D1046 *********************** 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 506 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 411 time to evaluate : 3.533 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 191 TYR cc_start: 0.7921 (t80) cc_final: 0.7617 (t80) REVERT: A 280 GLN cc_start: 0.8319 (tt0) cc_final: 0.8053 (tp40) REVERT: A 491 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7351 (tp30) REVERT: A 521 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7129 (tp) REVERT: A 702 ILE cc_start: 0.8472 (mt) cc_final: 0.8223 (tt) REVERT: A 787 TYR cc_start: 0.7426 (t80) cc_final: 0.7116 (t80) REVERT: A 868 PHE cc_start: 0.8137 (m-10) cc_final: 0.7514 (t80) REVERT: A 914 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7936 (mm-40) REVERT: A 1005 TYR cc_start: 0.6785 (m-10) cc_final: 0.5372 (m-80) REVERT: A 1023 MET cc_start: 0.7179 (mmm) cc_final: 0.6111 (mtp) REVERT: A 1047 ASN cc_start: 0.7697 (m-40) cc_final: 0.7399 (m-40) REVERT: B 191 TYR cc_start: 0.7908 (t80) cc_final: 0.7630 (t80) REVERT: B 194 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7812 (pt0) REVERT: B 396 MET cc_start: 0.7009 (mmp) cc_final: 0.6145 (mmp) REVERT: B 491 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7343 (tp30) REVERT: B 521 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7076 (tp) REVERT: B 702 ILE cc_start: 0.8462 (mt) cc_final: 0.8227 (tt) REVERT: B 787 TYR cc_start: 0.7419 (t80) cc_final: 0.7106 (t80) REVERT: B 868 PHE cc_start: 0.8102 (m-10) cc_final: 0.7501 (t80) REVERT: B 914 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7960 (mm-40) REVERT: B 1005 TYR cc_start: 0.6710 (m-10) cc_final: 0.5364 (m-80) REVERT: B 1023 MET cc_start: 0.7183 (mmm) cc_final: 0.6090 (mtp) REVERT: C 280 GLN cc_start: 0.8329 (tt0) cc_final: 0.8059 (tp40) REVERT: C 396 MET cc_start: 0.6921 (mmp) cc_final: 0.6130 (mmp) REVERT: C 491 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7377 (tp30) REVERT: C 521 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7092 (tp) REVERT: C 702 ILE cc_start: 0.8461 (mt) cc_final: 0.8235 (tt) REVERT: C 787 TYR cc_start: 0.7447 (t80) cc_final: 0.7148 (t80) REVERT: C 864 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8262 (mp) REVERT: C 868 PHE cc_start: 0.8110 (m-10) cc_final: 0.7530 (t80) REVERT: C 1005 TYR cc_start: 0.6713 (m-10) cc_final: 0.5300 (m-80) REVERT: C 1023 MET cc_start: 0.7077 (mmm) cc_final: 0.5975 (mtp) REVERT: D 280 GLN cc_start: 0.8339 (tt0) cc_final: 0.8051 (tp40) REVERT: D 396 MET cc_start: 0.6969 (mmp) cc_final: 0.6308 (mmp) REVERT: D 491 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7413 (tp30) REVERT: D 702 ILE cc_start: 0.8471 (mt) cc_final: 0.8222 (tt) REVERT: D 787 TYR cc_start: 0.7445 (t80) cc_final: 0.7138 (t80) REVERT: D 868 PHE cc_start: 0.8115 (m-10) cc_final: 0.7526 (t80) REVERT: D 914 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7907 (mm-40) REVERT: D 1005 TYR cc_start: 0.6838 (m-10) cc_final: 0.5403 (m-80) REVERT: D 1023 MET cc_start: 0.7147 (mmm) cc_final: 0.6059 (mtp) REVERT: D 1047 ASN cc_start: 0.7721 (m-40) cc_final: 0.7425 (m-40) outliers start: 95 outliers final: 57 residues processed: 473 average time/residue: 0.4135 time to fit residues: 312.3545 Evaluate side-chains 442 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 381 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU 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 353 MET Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1010 ASN Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 7.9990 chunk 254 optimal weight: 0.9980 chunk 175 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 359 optimal weight: 0.5980 chunk 177 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 438 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN C 438 GLN C 483 ASN D 256 ASN D 438 GLN D 483 ASN D 973 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31188 Z= 0.168 Angle : 0.540 7.902 42252 Z= 0.279 Chirality : 0.038 0.147 4708 Planarity : 0.003 0.044 5280 Dihedral : 5.380 51.037 4024 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.61 % Allowed : 12.05 % Favored : 85.34 % 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: -0.13 (0.14), residues: 3656 helix: 1.06 (0.11), residues: 2436 sheet: -1.49 (0.33), residues: 192 loop : -2.64 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 898 HIS 0.003 0.001 HIS B 138 PHE 0.013 0.001 PHE C1013 TYR 0.020 0.001 TYR C 191 ARG 0.005 0.000 ARG D1046 *********************** 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 499 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 412 time to evaluate : 3.391 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 280 GLN cc_start: 0.8282 (tt0) cc_final: 0.8009 (tp40) REVERT: A 396 MET cc_start: 0.7015 (mmp) cc_final: 0.6219 (mmp) REVERT: A 491 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7327 (tp30) REVERT: A 521 LEU cc_start: 0.7304 (mp) cc_final: 0.7096 (tp) REVERT: A 702 ILE cc_start: 0.8475 (mt) cc_final: 0.8167 (tt) REVERT: A 727 TYR cc_start: 0.6432 (t80) cc_final: 0.5925 (t80) REVERT: A 863 MET cc_start: 0.8561 (mmt) cc_final: 0.8137 (mmt) REVERT: A 864 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 868 PHE cc_start: 0.8057 (m-10) cc_final: 0.7445 (t80) REVERT: A 1005 TYR cc_start: 0.6773 (m-10) cc_final: 0.5388 (m-80) REVERT: A 1021 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.7023 (t80) REVERT: A 1023 MET cc_start: 0.7114 (mmm) cc_final: 0.6047 (mtp) REVERT: B 491 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7332 (tp30) REVERT: B 521 LEU cc_start: 0.7307 (mp) cc_final: 0.7040 (tp) REVERT: B 702 ILE cc_start: 0.8505 (mt) cc_final: 0.8254 (tt) REVERT: B 787 TYR cc_start: 0.7341 (t80) cc_final: 0.7135 (t80) REVERT: B 868 PHE cc_start: 0.8002 (m-10) cc_final: 0.7450 (t80) REVERT: B 1021 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6932 (t80) REVERT: B 1023 MET cc_start: 0.7090 (mmm) cc_final: 0.6033 (mtp) REVERT: C 280 GLN cc_start: 0.8300 (tt0) cc_final: 0.8017 (tp40) REVERT: C 491 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7418 (tp30) REVERT: C 521 LEU cc_start: 0.7288 (mp) cc_final: 0.7087 (tp) REVERT: C 702 ILE cc_start: 0.8506 (mt) cc_final: 0.8260 (tt) REVERT: C 787 TYR cc_start: 0.7336 (t80) cc_final: 0.7030 (t80) REVERT: C 864 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8212 (mp) REVERT: C 868 PHE cc_start: 0.8046 (m-10) cc_final: 0.7464 (t80) REVERT: C 1005 TYR cc_start: 0.6668 (m-80) cc_final: 0.5281 (m-80) REVERT: C 1023 MET cc_start: 0.7076 (mmm) cc_final: 0.6002 (mtp) REVERT: D 280 GLN cc_start: 0.8313 (tt0) cc_final: 0.8038 (tp40) REVERT: D 294 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7602 (p0) REVERT: D 491 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7421 (tp30) REVERT: D 702 ILE cc_start: 0.8517 (mt) cc_final: 0.8250 (tt) REVERT: D 863 MET cc_start: 0.8558 (mmt) cc_final: 0.8162 (mmt) REVERT: D 868 PHE cc_start: 0.8047 (m-10) cc_final: 0.7460 (t80) REVERT: D 1021 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6987 (t80) REVERT: D 1023 MET cc_start: 0.7109 (mmm) cc_final: 0.6028 (mtp) outliers start: 87 outliers final: 45 residues processed: 469 average time/residue: 0.4103 time to fit residues: 306.6088 Evaluate side-chains 428 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 377 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1010 ASN Chi-restraints excluded: chain B residue 1021 PHE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 806 LEU 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 1010 ASN Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 148 optimal weight: 0.0870 chunk 306 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 30.0000 chunk 322 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 483 ASN D 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31188 Z= 0.257 Angle : 0.581 7.242 42252 Z= 0.299 Chirality : 0.040 0.149 4708 Planarity : 0.004 0.043 5280 Dihedral : 5.239 48.600 4024 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.97 % Allowed : 12.77 % Favored : 84.25 % 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: 0.10 (0.14), residues: 3656 helix: 1.25 (0.11), residues: 2424 sheet: -1.36 (0.34), residues: 192 loop : -2.56 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 898 HIS 0.003 0.001 HIS C 765 PHE 0.016 0.001 PHE A 752 TYR 0.027 0.002 TYR C 191 ARG 0.003 0.000 ARG D 901 *********************** 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 483 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 384 time to evaluate : 3.511 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: A 280 GLN cc_start: 0.8338 (tt0) cc_final: 0.8082 (tp40) REVERT: A 304 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.6586 (m-80) REVERT: A 353 MET cc_start: 0.6251 (mpp) cc_final: 0.5975 (pmm) REVERT: A 521 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7189 (tp) REVERT: A 702 ILE cc_start: 0.8451 (mt) cc_final: 0.8215 (tt) REVERT: A 868 PHE cc_start: 0.8115 (m-10) cc_final: 0.7501 (t80) REVERT: A 1021 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.7049 (t80) REVERT: A 1023 MET cc_start: 0.7153 (mmm) cc_final: 0.6075 (mtp) REVERT: B 396 MET cc_start: 0.7171 (mmp) cc_final: 0.6296 (mmp) REVERT: B 521 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7135 (tp) REVERT: B 627 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7609 (mp0) REVERT: B 702 ILE cc_start: 0.8514 (mt) cc_final: 0.8262 (tt) REVERT: B 787 TYR cc_start: 0.7377 (t80) cc_final: 0.7036 (t80) REVERT: B 868 PHE cc_start: 0.8062 (m-10) cc_final: 0.7505 (t80) REVERT: B 1021 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6929 (t80) REVERT: B 1023 MET cc_start: 0.7095 (mmm) cc_final: 0.6004 (mtp) REVERT: C 280 GLN cc_start: 0.8338 (tt0) cc_final: 0.8055 (tp40) REVERT: C 353 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6305 (ptp) REVERT: C 396 MET cc_start: 0.7046 (mmp) cc_final: 0.6323 (mmp) REVERT: C 702 ILE cc_start: 0.8503 (mt) cc_final: 0.8259 (tt) REVERT: C 787 TYR cc_start: 0.7403 (t80) cc_final: 0.7072 (t80) REVERT: C 864 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8239 (mp) REVERT: C 868 PHE cc_start: 0.8081 (m-10) cc_final: 0.7520 (t80) REVERT: C 1023 MET cc_start: 0.7091 (mmm) cc_final: 0.5992 (mtp) REVERT: D 280 GLN cc_start: 0.8344 (tt0) cc_final: 0.8074 (tp40) REVERT: D 353 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6387 (ptp) REVERT: D 396 MET cc_start: 0.7160 (mmp) cc_final: 0.6630 (mmp) REVERT: D 702 ILE cc_start: 0.8514 (mt) cc_final: 0.8180 (tt) REVERT: D 727 TYR cc_start: 0.6460 (t80) cc_final: 0.5937 (t80) REVERT: D 868 PHE cc_start: 0.8094 (m-10) cc_final: 0.7517 (t80) REVERT: D 1021 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.7026 (t80) REVERT: D 1023 MET cc_start: 0.7149 (mmm) cc_final: 0.6067 (mtp) outliers start: 99 outliers final: 60 residues processed: 441 average time/residue: 0.4099 time to fit residues: 289.3533 Evaluate side-chains 429 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 360 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1010 ASN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1010 ASN Chi-restraints excluded: chain B residue 1021 PHE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1010 ASN Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1010 ASN Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.6980 chunk 323 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 359 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 188 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.8013 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31188 Z= 0.159 Angle : 0.536 10.814 42252 Z= 0.272 Chirality : 0.038 0.153 4708 Planarity : 0.003 0.044 5280 Dihedral : 5.047 46.886 4024 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.46 % Allowed : 14.21 % Favored : 83.32 % 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: 0.39 (0.14), residues: 3656 helix: 1.48 (0.11), residues: 2432 sheet: -1.20 (0.34), residues: 192 loop : -2.50 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 898 HIS 0.003 0.001 HIS C 138 PHE 0.019 0.001 PHE C 776 TYR 0.025 0.001 TYR D 191 ARG 0.003 0.000 ARG A 364 *********************** 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 478 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 396 time to evaluate : 3.196 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: A 280 GLN cc_start: 0.8305 (tt0) cc_final: 0.8039 (tp40) REVERT: A 353 MET cc_start: 0.6214 (mpp) cc_final: 0.5931 (pmm) REVERT: A 396 MET cc_start: 0.7021 (mmp) cc_final: 0.6121 (mmp) REVERT: A 702 ILE cc_start: 0.8461 (mt) cc_final: 0.8030 (tt) REVERT: A 704 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7447 (tt) REVERT: A 727 TYR cc_start: 0.6337 (t80) cc_final: 0.5633 (t80) REVERT: A 863 MET cc_start: 0.8580 (mmt) cc_final: 0.8180 (mmt) REVERT: A 868 PHE cc_start: 0.8018 (m-10) cc_final: 0.7433 (t80) REVERT: A 1021 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7071 (t80) REVERT: A 1023 MET cc_start: 0.6942 (mmm) cc_final: 0.6061 (mtp) REVERT: A 1059 MET cc_start: 0.7478 (mpp) cc_final: 0.7177 (mmm) REVERT: B 304 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: B 353 MET cc_start: 0.6818 (mpp) cc_final: 0.6237 (pmm) REVERT: B 627 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 646 TYR cc_start: 0.5498 (t80) cc_final: 0.5279 (t80) REVERT: B 702 ILE cc_start: 0.8488 (mt) cc_final: 0.8232 (tt) REVERT: B 787 TYR cc_start: 0.7342 (t80) cc_final: 0.7000 (t80) REVERT: B 863 MET cc_start: 0.8587 (mmt) cc_final: 0.8081 (mmt) REVERT: B 868 PHE cc_start: 0.7987 (m-10) cc_final: 0.7444 (t80) REVERT: B 1021 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6937 (t80) REVERT: B 1023 MET cc_start: 0.7102 (mmm) cc_final: 0.6042 (mtp) REVERT: B 1059 MET cc_start: 0.7441 (mpp) cc_final: 0.7038 (mmm) REVERT: C 280 GLN cc_start: 0.8298 (tt0) cc_final: 0.8032 (tp40) REVERT: C 396 MET cc_start: 0.7187 (mmp) cc_final: 0.6648 (mmp) REVERT: C 627 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7563 (mp0) REVERT: C 646 TYR cc_start: 0.5508 (t80) cc_final: 0.5239 (t80) REVERT: C 702 ILE cc_start: 0.8490 (mt) cc_final: 0.8245 (tt) REVERT: C 787 TYR cc_start: 0.7336 (t80) cc_final: 0.7002 (t80) REVERT: C 863 MET cc_start: 0.8588 (mmt) cc_final: 0.8139 (mmt) REVERT: C 864 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8234 (mp) REVERT: C 868 PHE cc_start: 0.8018 (m-10) cc_final: 0.7458 (t80) REVERT: C 1021 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6916 (t80) REVERT: C 1023 MET cc_start: 0.7101 (mmm) cc_final: 0.6028 (mtp) REVERT: C 1059 MET cc_start: 0.7458 (mpp) cc_final: 0.7088 (mmm) REVERT: D 280 GLN cc_start: 0.8339 (tt0) cc_final: 0.8081 (tp40) REVERT: D 304 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: D 702 ILE cc_start: 0.8500 (mt) cc_final: 0.8037 (tt) REVERT: D 727 TYR cc_start: 0.6342 (t80) cc_final: 0.5642 (t80) REVERT: D 863 MET cc_start: 0.8586 (mmt) cc_final: 0.8177 (mmt) REVERT: D 868 PHE cc_start: 0.8011 (m-10) cc_final: 0.7447 (t80) REVERT: D 1021 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7052 (t80) REVERT: D 1023 MET cc_start: 0.6973 (mmm) cc_final: 0.6099 (mtp) REVERT: D 1059 MET cc_start: 0.7496 (mpp) cc_final: 0.7150 (mmm) outliers start: 82 outliers final: 50 residues processed: 445 average time/residue: 0.4256 time to fit residues: 300.2565 Evaluate side-chains 422 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 364 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1010 ASN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 1010 ASN Chi-restraints excluded: chain B residue 1021 PHE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1010 ASN Chi-restraints excluded: chain C residue 1021 PHE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 1010 ASN Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 chunk 205 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 358 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31188 Z= 0.212 Angle : 0.570 11.513 42252 Z= 0.289 Chirality : 0.039 0.161 4708 Planarity : 0.003 0.042 5280 Dihedral : 5.007 48.116 4024 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.91 % Allowed : 14.51 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3656 helix: 1.54 (0.11), residues: 2432 sheet: -1.06 (0.36), residues: 188 loop : -2.40 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 898 HIS 0.002 0.001 HIS C 138 PHE 0.026 0.001 PHE B 779 TYR 0.027 0.002 TYR A 191 ARG 0.002 0.000 ARG D 901 *********************** 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 468 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 371 time to evaluate : 3.448 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: A 280 GLN cc_start: 0.8317 (tt0) cc_final: 0.8034 (tp40) REVERT: A 304 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.6621 (m-80) REVERT: A 353 MET cc_start: 0.6159 (mpp) cc_final: 0.5853 (pmm) REVERT: A 396 MET cc_start: 0.7063 (mmp) cc_final: 0.6200 (mmp) REVERT: A 627 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7601 (mp0) REVERT: A 689 ASP cc_start: 0.7800 (t0) cc_final: 0.7406 (m-30) REVERT: A 702 ILE cc_start: 0.8472 (mt) cc_final: 0.8032 (tt) REVERT: A 727 TYR cc_start: 0.6336 (t80) cc_final: 0.5632 (t80) REVERT: A 868 PHE cc_start: 0.8033 (m-10) cc_final: 0.7480 (t80) REVERT: A 1021 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7106 (t80) REVERT: A 1023 MET cc_start: 0.6948 (mmm) cc_final: 0.6061 (mtp) REVERT: A 1059 MET cc_start: 0.7517 (mpp) cc_final: 0.7207 (mmm) REVERT: B 304 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: B 353 MET cc_start: 0.6794 (mpp) cc_final: 0.6204 (pmm) REVERT: B 395 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8429 (mmtm) REVERT: B 627 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 702 ILE cc_start: 0.8491 (mt) cc_final: 0.8235 (tt) REVERT: B 787 TYR cc_start: 0.7377 (t80) cc_final: 0.7038 (t80) REVERT: B 868 PHE cc_start: 0.8011 (m-10) cc_final: 0.7487 (t80) REVERT: B 1021 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6957 (t80) REVERT: B 1023 MET cc_start: 0.7115 (mmm) cc_final: 0.6044 (mtp) REVERT: B 1059 MET cc_start: 0.7523 (mpp) cc_final: 0.7173 (mmm) REVERT: C 141 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7690 (p) REVERT: C 280 GLN cc_start: 0.8338 (tt0) cc_final: 0.8081 (tp40) REVERT: C 353 MET cc_start: 0.6587 (mpp) cc_final: 0.5886 (pmm) REVERT: C 356 GLU cc_start: 0.8425 (pt0) cc_final: 0.8149 (tp30) REVERT: C 396 MET cc_start: 0.7206 (mmp) cc_final: 0.6668 (mmp) REVERT: C 627 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7657 (mt-10) REVERT: C 646 TYR cc_start: 0.5456 (t80) cc_final: 0.5242 (t80) REVERT: C 702 ILE cc_start: 0.8479 (mt) cc_final: 0.8102 (tt) REVERT: C 727 TYR cc_start: 0.6269 (t80) cc_final: 0.5601 (t80) REVERT: C 787 TYR cc_start: 0.7355 (t80) cc_final: 0.7031 (t80) REVERT: C 868 PHE cc_start: 0.8055 (m-10) cc_final: 0.7488 (t80) REVERT: C 1021 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6926 (t80) REVERT: C 1023 MET cc_start: 0.7148 (mmm) cc_final: 0.6089 (mtp) REVERT: C 1059 MET cc_start: 0.7493 (mpp) cc_final: 0.7173 (mmm) REVERT: D 280 GLN cc_start: 0.8337 (tt0) cc_final: 0.8066 (tp40) REVERT: D 304 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.6727 (m-80) REVERT: D 356 GLU cc_start: 0.8386 (pt0) cc_final: 0.8157 (tp30) REVERT: D 396 MET cc_start: 0.6979 (mmp) cc_final: 0.6319 (mmp) REVERT: D 702 ILE cc_start: 0.8493 (mt) cc_final: 0.8084 (tt) REVERT: D 727 TYR cc_start: 0.6361 (t80) cc_final: 0.5661 (t80) REVERT: D 868 PHE cc_start: 0.8076 (m-10) cc_final: 0.7480 (t80) REVERT: D 1021 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6986 (t80) REVERT: D 1023 MET cc_start: 0.6929 (mmm) cc_final: 0.6053 (mtp) REVERT: D 1059 MET cc_start: 0.7500 (mpp) cc_final: 0.7230 (mmm) outliers start: 97 outliers final: 65 residues processed: 429 average time/residue: 0.4286 time to fit residues: 292.8156 Evaluate side-chains 433 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 360 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1010 ASN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1010 ASN Chi-restraints excluded: chain B residue 1021 PHE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1010 ASN Chi-restraints excluded: chain C residue 1021 PHE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 1010 ASN Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 177 optimal weight: 0.0170 chunk 33 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- 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: 0.8021 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31188 Z= 0.176 Angle : 0.560 14.652 42252 Z= 0.281 Chirality : 0.038 0.148 4708 Planarity : 0.003 0.044 5280 Dihedral : 4.930 46.974 4024 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.64 % Allowed : 15.32 % Favored : 82.03 % 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: 0.58 (0.14), residues: 3656 helix: 1.61 (0.11), residues: 2436 sheet: -0.99 (0.35), residues: 192 loop : -2.43 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 898 HIS 0.002 0.001 HIS C 138 PHE 0.010 0.001 PHE D 629 TYR 0.025 0.001 TYR A 191 ARG 0.007 0.000 ARG C 688 *********************** 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 464 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 376 time to evaluate : 3.463 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: A 280 GLN cc_start: 0.8317 (tt0) cc_final: 0.8043 (tp40) REVERT: A 353 MET cc_start: 0.6169 (mpp) cc_final: 0.5821 (pmm) REVERT: A 395 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8589 (mmtm) REVERT: A 396 MET cc_start: 0.7280 (mmp) cc_final: 0.6595 (mmp) REVERT: A 627 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7603 (mp0) REVERT: A 689 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: A 702 ILE cc_start: 0.8461 (mt) cc_final: 0.8005 (tt) REVERT: A 727 TYR cc_start: 0.6279 (t80) cc_final: 0.5618 (t80) REVERT: A 868 PHE cc_start: 0.8023 (m-10) cc_final: 0.7447 (t80) REVERT: A 1021 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7077 (t80) REVERT: A 1023 MET cc_start: 0.6990 (mmm) cc_final: 0.6126 (mtp) REVERT: A 1059 MET cc_start: 0.7493 (mpp) cc_final: 0.7250 (mmm) REVERT: B 304 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: B 353 MET cc_start: 0.6823 (mpp) cc_final: 0.6185 (pmm) REVERT: B 356 GLU cc_start: 0.8387 (pt0) cc_final: 0.8089 (tp30) REVERT: B 396 MET cc_start: 0.6827 (mmp) cc_final: 0.5777 (mmp) REVERT: B 627 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 689 ASP cc_start: 0.7775 (t0) cc_final: 0.7335 (m-30) REVERT: B 702 ILE cc_start: 0.8474 (mt) cc_final: 0.8007 (tt) REVERT: B 727 TYR cc_start: 0.6216 (t80) cc_final: 0.5585 (t80) REVERT: B 787 TYR cc_start: 0.7324 (t80) cc_final: 0.6993 (t80) REVERT: B 863 MET cc_start: 0.8614 (mmt) cc_final: 0.8107 (mmt) REVERT: B 868 PHE cc_start: 0.7991 (m-10) cc_final: 0.7457 (t80) REVERT: B 1021 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6981 (t80) REVERT: B 1023 MET cc_start: 0.6904 (mmm) cc_final: 0.6018 (mtp) REVERT: B 1059 MET cc_start: 0.7498 (mpp) cc_final: 0.7210 (mmm) REVERT: C 280 GLN cc_start: 0.8310 (tt0) cc_final: 0.8042 (tp40) REVERT: C 304 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.6573 (m-80) REVERT: C 353 MET cc_start: 0.6677 (mpp) cc_final: 0.5978 (pmm) REVERT: C 356 GLU cc_start: 0.8442 (pt0) cc_final: 0.8164 (tp30) REVERT: C 396 MET cc_start: 0.7267 (mmp) cc_final: 0.6788 (mmp) REVERT: C 627 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 689 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: C 702 ILE cc_start: 0.8457 (mt) cc_final: 0.7991 (tt) REVERT: C 727 TYR cc_start: 0.6236 (t80) cc_final: 0.5612 (t80) REVERT: C 787 TYR cc_start: 0.7319 (t80) cc_final: 0.6993 (t80) REVERT: C 863 MET cc_start: 0.8607 (mmt) cc_final: 0.8144 (mmt) REVERT: C 868 PHE cc_start: 0.8007 (m-10) cc_final: 0.7464 (t80) REVERT: C 1021 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.7052 (t80) REVERT: C 1023 MET cc_start: 0.6934 (mmm) cc_final: 0.6064 (mtp) REVERT: C 1059 MET cc_start: 0.7465 (mpp) cc_final: 0.7209 (mmm) REVERT: D 280 GLN cc_start: 0.8341 (tt0) cc_final: 0.8083 (tp40) REVERT: D 304 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: D 356 GLU cc_start: 0.8414 (pt0) cc_final: 0.8159 (tp30) REVERT: D 396 MET cc_start: 0.7042 (mmp) cc_final: 0.6504 (mmp) REVERT: D 627 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7734 (mt-10) REVERT: D 689 ASP cc_start: 0.7784 (t0) cc_final: 0.7379 (m-30) REVERT: D 702 ILE cc_start: 0.8474 (mt) cc_final: 0.7973 (tt) REVERT: D 727 TYR cc_start: 0.6295 (t80) cc_final: 0.5640 (t80) REVERT: D 863 MET cc_start: 0.8606 (mmt) cc_final: 0.8236 (mmt) REVERT: D 868 PHE cc_start: 0.8018 (m-10) cc_final: 0.7456 (t80) REVERT: D 1021 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7003 (t80) REVERT: D 1023 MET cc_start: 0.6955 (mmm) cc_final: 0.6090 (mtp) REVERT: D 1059 MET cc_start: 0.7498 (mpp) cc_final: 0.7242 (mmm) outliers start: 88 outliers final: 60 residues processed: 431 average time/residue: 0.4150 time to fit residues: 286.3715 Evaluate side-chains 432 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 363 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1010 ASN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1010 ASN Chi-restraints excluded: chain B residue 1021 PHE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL 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 689 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 1010 ASN Chi-restraints excluded: chain C residue 1021 PHE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 1010 ASN Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 1.9990 chunk 343 optimal weight: 7.9990 chunk 313 optimal weight: 1.9990 chunk 334 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 262 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 301 optimal weight: 4.9990 chunk 316 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 635 ASN B1102 ASN C 635 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31188 Z= 0.266 Angle : 0.605 15.036 42252 Z= 0.305 Chirality : 0.040 0.183 4708 Planarity : 0.003 0.040 5280 Dihedral : 5.072 52.472 4024 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.70 % Allowed : 15.41 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3656 helix: 1.50 (0.11), residues: 2424 sheet: -1.12 (0.35), residues: 188 loop : -2.32 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 453 HIS 0.003 0.001 HIS A 235 PHE 0.015 0.001 PHE B 752 TYR 0.022 0.002 TYR D 170 ARG 0.006 0.000 ARG C 688 *********************** 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 451 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 361 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: A 280 GLN cc_start: 0.8306 (tt0) cc_final: 0.8028 (tp40) REVERT: A 304 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 353 MET cc_start: 0.6287 (mpp) cc_final: 0.5897 (pmm) REVERT: A 395 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8503 (mmtm) REVERT: A 627 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7760 (mt-10) REVERT: A 689 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7433 (m-30) REVERT: A 702 ILE cc_start: 0.8501 (mt) cc_final: 0.8272 (tt) REVERT: A 868 PHE cc_start: 0.8072 (m-10) cc_final: 0.7492 (t80) REVERT: A 1021 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7038 (t80) REVERT: A 1023 MET cc_start: 0.6954 (mmm) cc_final: 0.6074 (mtp) REVERT: A 1059 MET cc_start: 0.7490 (mpp) cc_final: 0.7233 (mmm) REVERT: B 304 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: B 353 MET cc_start: 0.6821 (mpp) cc_final: 0.6241 (pmm) REVERT: B 395 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8466 (mmtm) REVERT: B 396 MET cc_start: 0.6901 (mmp) cc_final: 0.5846 (mmp) REVERT: B 627 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7687 (mt-10) REVERT: B 689 ASP cc_start: 0.7781 (t0) cc_final: 0.7421 (m-30) REVERT: B 702 ILE cc_start: 0.8448 (mt) cc_final: 0.8194 (tt) REVERT: B 787 TYR cc_start: 0.7404 (t80) cc_final: 0.7087 (t80) REVERT: B 868 PHE cc_start: 0.8039 (m-10) cc_final: 0.7482 (t80) REVERT: B 1021 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7002 (t80) REVERT: B 1023 MET cc_start: 0.7117 (mmm) cc_final: 0.6030 (mtp) REVERT: B 1059 MET cc_start: 0.7478 (mpp) cc_final: 0.7164 (mmm) REVERT: C 141 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7743 (p) REVERT: C 280 GLN cc_start: 0.8296 (tt0) cc_final: 0.8045 (tp40) REVERT: C 304 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: C 353 MET cc_start: 0.6727 (mpp) cc_final: 0.6134 (pmm) REVERT: C 627 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 689 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: C 702 ILE cc_start: 0.8455 (mt) cc_final: 0.8200 (tt) REVERT: C 787 TYR cc_start: 0.7405 (t80) cc_final: 0.7080 (t80) REVERT: C 868 PHE cc_start: 0.8052 (m-10) cc_final: 0.7509 (t80) REVERT: C 1021 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7026 (t80) REVERT: C 1023 MET cc_start: 0.7149 (mmm) cc_final: 0.6062 (mtp) REVERT: C 1059 MET cc_start: 0.7432 (mpp) cc_final: 0.7170 (mmm) REVERT: D 191 TYR cc_start: 0.8001 (t80) cc_final: 0.7785 (t80) REVERT: D 280 GLN cc_start: 0.8363 (tt0) cc_final: 0.8110 (tp40) REVERT: D 304 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: D 356 GLU cc_start: 0.8391 (pt0) cc_final: 0.8141 (tp30) REVERT: D 627 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7669 (mp0) REVERT: D 689 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: D 702 ILE cc_start: 0.8460 (mt) cc_final: 0.8066 (tt) REVERT: D 727 TYR cc_start: 0.6300 (t80) cc_final: 0.5626 (t80) REVERT: D 868 PHE cc_start: 0.8103 (m-10) cc_final: 0.7524 (t80) REVERT: D 1021 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.7035 (t80) REVERT: D 1023 MET cc_start: 0.6951 (mmm) cc_final: 0.6064 (mtp) REVERT: D 1059 MET cc_start: 0.7538 (mpp) cc_final: 0.7289 (mmm) outliers start: 90 outliers final: 60 residues processed: 413 average time/residue: 0.4366 time to fit residues: 290.4408 Evaluate side-chains 426 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 354 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1010 ASN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 1021 PHE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 402 GLU 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 645 VAL Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1021 PHE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain C residue 1078 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 499 THR 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 797 LEU Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 835 ASP Chi-restraints excluded: chain D residue 1010 ASN Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.6980 chunk 353 optimal weight: 0.9980 chunk 215 optimal weight: 0.0970 chunk 167 optimal weight: 0.7980 chunk 245 optimal weight: 0.2980 chunk 370 optimal weight: 5.9990 chunk 341 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31188 Z= 0.144 Angle : 0.560 13.876 42252 Z= 0.280 Chirality : 0.038 0.137 4708 Planarity : 0.003 0.043 5280 Dihedral : 4.815 43.601 4024 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.92 % Allowed : 16.08 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3656 helix: 1.66 (0.11), residues: 2432 sheet: -0.73 (0.35), residues: 184 loop : -2.35 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 898 HIS 0.003 0.001 HIS D 845 PHE 0.011 0.001 PHE A 463 TYR 0.025 0.001 TYR B 191 ARG 0.007 0.000 ARG C 688 ********************** REFINEMENT MACRO_CYCLE 10 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 445 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 381 time to evaluate : 3.679 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 280 GLN cc_start: 0.8277 (tt0) cc_final: 0.8032 (tp40) REVERT: A 353 MET cc_start: 0.6299 (mpp) cc_final: 0.5857 (pmm) REVERT: A 356 GLU cc_start: 0.8366 (pt0) cc_final: 0.8118 (tp30) REVERT: A 395 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8415 (mmtm) REVERT: A 396 MET cc_start: 0.6893 (mmp) cc_final: 0.5845 (mmp) REVERT: A 605 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7955 (mmtm) REVERT: A 627 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 689 ASP cc_start: 0.7781 (t0) cc_final: 0.7495 (m-30) REVERT: A 702 ILE cc_start: 0.8510 (mt) cc_final: 0.8278 (tt) REVERT: A 868 PHE cc_start: 0.7974 (m-10) cc_final: 0.7368 (t80) REVERT: A 1021 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7038 (t80) REVERT: A 1023 MET cc_start: 0.6998 (mmm) cc_final: 0.6131 (mtp) REVERT: A 1059 MET cc_start: 0.7508 (mpp) cc_final: 0.7229 (mmm) REVERT: B 304 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: B 353 MET cc_start: 0.6793 (mpp) cc_final: 0.6191 (pmm) REVERT: B 356 GLU cc_start: 0.8374 (pt0) cc_final: 0.8109 (tp30) REVERT: B 396 MET cc_start: 0.6833 (mmp) cc_final: 0.5833 (mmp) REVERT: B 627 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7551 (mt-10) REVERT: B 689 ASP cc_start: 0.7841 (t0) cc_final: 0.7499 (m-30) REVERT: B 702 ILE cc_start: 0.8522 (mt) cc_final: 0.8251 (tt) REVERT: B 787 TYR cc_start: 0.7299 (t80) cc_final: 0.6970 (t80) REVERT: B 863 MET cc_start: 0.8595 (mmt) cc_final: 0.8035 (mmt) REVERT: B 868 PHE cc_start: 0.7954 (m-10) cc_final: 0.7404 (t80) REVERT: B 1021 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6998 (t80) REVERT: B 1023 MET cc_start: 0.6941 (mmm) cc_final: 0.6084 (mtp) REVERT: B 1059 MET cc_start: 0.7494 (mpp) cc_final: 0.7183 (mmm) REVERT: C 280 GLN cc_start: 0.8306 (tt0) cc_final: 0.8043 (tp40) REVERT: C 353 MET cc_start: 0.6853 (mpp) cc_final: 0.6200 (pmm) REVERT: C 356 GLU cc_start: 0.8421 (pt0) cc_final: 0.8183 (tp30) REVERT: C 605 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7938 (mmtm) REVERT: C 689 ASP cc_start: 0.7853 (t0) cc_final: 0.7535 (m-30) REVERT: C 702 ILE cc_start: 0.8515 (mt) cc_final: 0.7997 (tt) REVERT: C 727 TYR cc_start: 0.6169 (t80) cc_final: 0.5597 (t80) REVERT: C 787 TYR cc_start: 0.7329 (t80) cc_final: 0.7021 (t80) REVERT: C 863 MET cc_start: 0.8587 (mmt) cc_final: 0.8076 (mmt) REVERT: C 868 PHE cc_start: 0.7957 (m-10) cc_final: 0.7409 (t80) REVERT: C 1021 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6975 (t80) REVERT: C 1023 MET cc_start: 0.6878 (mmm) cc_final: 0.6001 (mtp) REVERT: C 1059 MET cc_start: 0.7463 (mpp) cc_final: 0.7189 (mmm) REVERT: D 280 GLN cc_start: 0.8337 (tt0) cc_final: 0.8083 (tp40) REVERT: D 304 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: D 356 GLU cc_start: 0.8374 (pt0) cc_final: 0.8157 (tp30) REVERT: D 605 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7856 (mmtm) REVERT: D 627 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7597 (mp0) REVERT: D 689 ASP cc_start: 0.7776 (t0) cc_final: 0.7412 (m-30) REVERT: D 702 ILE cc_start: 0.8549 (mt) cc_final: 0.8034 (tt) REVERT: D 727 TYR cc_start: 0.6261 (t80) cc_final: 0.5680 (t80) REVERT: D 863 MET cc_start: 0.8592 (mmt) cc_final: 0.8179 (mmt) REVERT: D 868 PHE cc_start: 0.7977 (m-10) cc_final: 0.7390 (t80) REVERT: D 1021 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7082 (t80) REVERT: D 1023 MET cc_start: 0.6940 (mmm) cc_final: 0.6051 (mtp) REVERT: D 1059 MET cc_start: 0.7515 (mpp) cc_final: 0.7259 (mmm) outliers start: 64 outliers final: 48 residues processed: 421 average time/residue: 0.4087 time to fit residues: 274.8815 Evaluate side-chains 410 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 356 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1010 ASN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1045 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 1021 PHE Chi-restraints excluded: chain B residue 1045 PHE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 402 GLU 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 645 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 1021 PHE Chi-restraints excluded: chain C residue 1045 PHE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 835 ASP Chi-restraints excluded: chain D residue 1010 ASN Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1045 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 272 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 295 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 303 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS B 136 HIS C 136 HIS C 886 GLN D 136 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.156453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104791 restraints weight = 48714.299| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.35 r_work: 0.3172 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 31188 Z= 0.450 Angle : 0.699 13.460 42252 Z= 0.356 Chirality : 0.044 0.210 4708 Planarity : 0.004 0.039 5280 Dihedral : 5.311 56.696 4024 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.34 % Allowed : 15.72 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3656 helix: 1.26 (0.11), residues: 2420 sheet: -1.22 (0.34), residues: 188 loop : -2.37 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 453 HIS 0.005 0.001 HIS D 765 PHE 0.024 0.002 PHE D 776 TYR 0.022 0.002 TYR A 170 ARG 0.006 0.001 ARG B 901 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7602.15 seconds wall clock time: 137 minutes 45.31 seconds (8265.31 seconds total)