Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 13 02:56:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/05_2023/7wrf_32725_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/05_2023/7wrf_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_32725/05_2023/7wrf_32725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/05_2023/7wrf_32725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/05_2023/7wrf_32725_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrf_32725/05_2023/7wrf_32725_updated.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 15.00, per 1000 atoms: 0.49 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: 12.68 Conformation dependent library (CDL) restraints added in 4.7 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: 4.28 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: 10.25 Time building geometry restraints manager: 13.61 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.180 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 72.020 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.720 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 827 average time/residue: 0.4759 time to fit residues: 595.8548 Evaluate side-chains 422 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8995 ------------------------------------------------------------------------------- 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: 0.4980 chunk 217 optimal weight: 9.9990 chunk 337 optimal weight: 0.8980 overall best weight: 2.4802 ------------------------------------------------------------------------------- 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 406 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 987 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 31188 Z= 0.261 Angle : 0.628 7.391 42252 Z= 0.328 Chirality : 0.041 0.146 4708 Planarity : 0.004 0.050 5280 Dihedral : 5.930 49.870 4024 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 2.43 % 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: -1.71 (0.13), residues: 3656 helix: -0.19 (0.10), residues: 2436 sheet: -1.90 (0.32), residues: 192 loop : -3.15 (0.15), residues: 1028 *********************** 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 552 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 471 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 48 residues processed: 520 average time/residue: 0.4280 time to fit residues: 351.5612 Evaluate side-chains 436 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 388 time to evaluate : 3.737 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.3016 time to fit residues: 31.8117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 281 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 338 optimal weight: 4.9990 chunk 365 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 335 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 154 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 741 ASN A 785 GLN B 136 HIS B 154 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN B 609 ASN B 785 GLN C 136 HIS C 154 ASN C 406 ASN C 438 GLN C 609 ASN C 785 GLN D 136 HIS D 154 ASN D 294 ASN D 609 ASN D 741 ASN D 785 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.103 31188 Z= 0.501 Angle : 0.742 11.066 42252 Z= 0.380 Chirality : 0.045 0.164 4708 Planarity : 0.005 0.051 5280 Dihedral : 5.971 57.206 4024 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 2.22 % 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: -1.13 (0.13), residues: 3656 helix: 0.29 (0.10), residues: 2432 sheet: -2.07 (0.31), residues: 196 loop : -2.94 (0.16), residues: 1028 *********************** 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 463 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 389 time to evaluate : 3.853 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 outliers start: 74 outliers final: 29 residues processed: 443 average time/residue: 0.4357 time to fit residues: 306.9150 Evaluate side-chains 395 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 366 time to evaluate : 3.600 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2759 time to fit residues: 19.9592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 4.9990 chunk 254 optimal weight: 0.0470 chunk 175 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 161 optimal weight: 0.4980 chunk 227 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 chunk 359 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN C 256 ASN C 483 ASN D 256 ASN D 438 GLN D 483 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 31188 Z= 0.159 Angle : 0.559 8.953 42252 Z= 0.290 Chirality : 0.038 0.140 4708 Planarity : 0.004 0.045 5280 Dihedral : 5.415 51.667 4024 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 1.02 % 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: -0.22 (0.14), residues: 3656 helix: 1.08 (0.11), residues: 2420 sheet: -1.67 (0.33), residues: 192 loop : -2.82 (0.16), residues: 1044 *********************** 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 436 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 402 time to evaluate : 3.770 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 outliers start: 34 outliers final: 8 residues processed: 426 average time/residue: 0.4546 time to fit residues: 309.6477 Evaluate side-chains 369 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 361 time to evaluate : 3.494 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3710 time to fit residues: 10.0574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 9.9990 chunk 204 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 306 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: