Starting phenix.real_space_refine on Tue Mar 19 07:28:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwm_23550/03_2024/7lwm_23550.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwm_23550/03_2024/7lwm_23550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwm_23550/03_2024/7lwm_23550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwm_23550/03_2024/7lwm_23550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwm_23550/03_2024/7lwm_23550.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwm_23550/03_2024/7lwm_23550.pdb" } resolution = 2.83 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= -0.001 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 15046 2.51 5 N 3879 2.21 5 O 4544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23571 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7685 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7697 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7671 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 11.66, per 1000 atoms: 0.49 Number of scatterers: 23571 At special positions: 0 Unit cell: (127.211, 134.694, 194.558, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 4544 8.00 N 3879 7.00 C 15046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.06 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 234 " " NAG A1311 " - " ASN A 61 " " NAG B1301 " - " ASN B1134 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 61 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 61 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN B1098 " " NAG F 1 " - " ASN C1098 " Time building additional restraints: 7.98 Conformation dependent library (CDL) restraints added in 3.7 seconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 27.7% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.724A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.533A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.040A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.689A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.741A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.691A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.775A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.550A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.519A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.269A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.906A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 4.212A pdb=" N GLY B 142 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.195A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.662A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.619A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.836A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.811A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.139A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.553A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.022A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.449A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.897A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.110A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.861A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.053A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.736A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.580A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.795A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.939A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.500A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.640A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.716A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.382A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.805A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.716A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.381A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.544A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.823A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.463A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.530A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.530A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.346A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.182A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.671A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.200A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.860A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.652A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.917A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.348A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.756A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.525A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.813A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.973A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.580A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.604A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.469A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.691A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.379A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.156A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.851A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.525A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.546A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.910A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.409A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.724A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1054 hydrogen bonds defined for protein. 2865 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: 10.11 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5994 1.33 - 1.45: 4625 1.45 - 1.58: 13334 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 24079 Sorted by residual: bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.67e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.48e+01 bond pdb=" C5 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24074 not shown) Histogram of bond angle deviations from ideal: 97.04 - 104.70: 354 104.70 - 112.37: 10551 112.37 - 120.03: 11260 120.03 - 127.70: 10478 127.70 - 135.36: 124 Bond angle restraints: 32767 Sorted by residual: angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 119.35 -6.75 1.00e+00 1.00e+00 4.56e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.84 -6.24 1.00e+00 1.00e+00 3.90e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.87 -6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.55 -5.75 1.00e+00 1.00e+00 3.30e+01 angle pdb=" OE1 GLN B 965 " pdb=" CD GLN B 965 " pdb=" NE2 GLN B 965 " ideal model delta sigma weight residual 122.60 117.17 5.43 1.00e+00 1.00e+00 2.95e+01 ... (remaining 32762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13768 17.91 - 35.81: 785 35.81 - 53.72: 156 53.72 - 71.62: 50 71.62 - 89.53: 26 Dihedral angle restraints: 14785 sinusoidal: 6131 harmonic: 8654 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -163.41 77.41 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.46 75.46 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -158.84 72.84 1 1.00e+01 1.00e-02 6.77e+01 ... (remaining 14782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2945 0.110 - 0.219: 846 0.219 - 0.328: 79 0.328 - 0.438: 5 0.438 - 0.547: 3 Chirality restraints: 3878 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.99e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.74e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.31e+01 ... (remaining 3875 not shown) Planarity restraints: 4211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.378 2.00e-02 2.50e+03 2.05e-01 1.05e+03 pdb=" CG TRP C 886 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.199 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.140 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.037 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.306 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.215 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.069 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.140 2.00e-02 2.50e+03 1.46e-01 2.67e+02 pdb=" CG ASN B 709 " 0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.220 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.124 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CG ASN C 61 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.196 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " -0.157 2.00e-02 2.50e+03 ... (remaining 4208 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 11247 2.99 - 3.47: 22004 3.47 - 3.95: 39373 3.95 - 4.42: 43391 4.42 - 4.90: 73750 Nonbonded interactions: 189765 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.518 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.520 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.524 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.529 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.532 2.440 ... (remaining 189760 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 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 through 215 and (name N or name CA or name C or name \ O or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) \ or resid 481 through 487 or (resid 488 and (name N or name CA or name C or name \ O or name CB )) or resid 489 through 527 or (resid 528 and (name N or name CA o \ r name C or name O or name CB )) or resid 529 through 810 or (resid 811 and (nam \ e N or name CA or name C or name O or name CB )) or resid 813 through 827 or res \ id 855 through 866 or (resid 867 through 868 and (name N or name CA or name C or \ name O or name CB )) or resid 869 through 1141 or (resid 1142 and (name N or na \ me CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid 114 \ 5 through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or resid 16 \ 6 through 168 or (resid 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 195 or (resid 196 through 197 and (nam \ e N or name CA or name C or name O or name CB )) or resid 198 through 241 or (re \ sid 242 through 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 280 or (resid 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 through 483 or resid 485 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 582 o \ r (resid 583 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 84 through 585 or (resid 586 and (name N or name CA or name C or name O or name \ CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name C or \ name O or name CB )) or resid 620 through 676 or resid 690 through 744 or (resi \ d 745 and (name N or name CA or name C or name O or name CB )) or resid 746 thro \ ugh 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) o \ r resid 749 through 810 or (resid 811 and (name N or name CA or name C or name O \ or name CB )) or resid 813 or (resid 814 and (name N or name CA or name C or na \ me O or name CB )) or resid 815 through 827 or resid 855 through 866 or (resid 8 \ 67 through 868 and (name N or name CA or name C or name O or name CB )) or resid \ 869 through 1091 or (resid 1092 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1093 through 1143 or (resid 1144 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 or resid 1301 through 13 \ 10)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 195 or (resid 196 th \ rough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 213 or (resid 214 through 215 and (name N or name CA or name C or name O \ or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (name \ N or name CA or name C or name O or name CB )) or resid 240 through 308 or (resi \ d 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) o \ r resid 481 through 483 or resid 485 through 487 or (resid 488 and (name N or na \ me CA or name C or name O or name CB )) or resid 489 through 527 or (resid 528 a \ nd (name N or name CA or name C or name O or name CB )) or resid 529 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 through 582 or (resid 583 and (name N or name CA or name C or name O or nam \ e CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or name C \ or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N or na \ me CA or name C or name O or name CB )) or resid 620 through 813 or (resid 814 a \ nd (name N or name CA or name C or name O or name CB )) or resid 815 through 109 \ 1 or (resid 1092 and (name N or name CA or name C or name O or name CB )) or res \ id 1093 through 1141 or (resid 1142 and (name N or name CA or name C or name O o \ r name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 7.140 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 59.310 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.077 24079 Z= 0.872 Angle : 1.779 9.859 32767 Z= 1.197 Chirality : 0.095 0.547 3878 Planarity : 0.013 0.235 4177 Dihedral : 12.750 89.530 9095 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.27 % Favored : 94.36 % Rotamer: Outliers : 0.59 % Allowed : 2.24 % Favored : 97.17 % Cbeta Deviations : 0.14 % 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: -0.71 (0.14), residues: 2924 helix: -0.88 (0.17), residues: 687 sheet: 0.86 (0.20), residues: 577 loop : -0.74 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.378 0.029 TRP C 886 HIS 0.015 0.003 HIS A1048 PHE 0.095 0.013 PHE A 718 TYR 0.125 0.019 TYR B 495 ARG 0.012 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 358 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7610 (t60) cc_final: 0.7301 (t60) REVERT: A 114 THR cc_start: 0.8237 (m) cc_final: 0.8015 (p) REVERT: A 116 SER cc_start: 0.7964 (p) cc_final: 0.7615 (m) REVERT: A 126 VAL cc_start: 0.7561 (t) cc_final: 0.7270 (p) REVERT: A 207 HIS cc_start: 0.7383 (m170) cc_final: 0.7010 (t70) REVERT: A 230 PRO cc_start: 0.8923 (Cg_endo) cc_final: 0.8721 (Cg_exo) REVERT: A 378 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7481 (mmtp) REVERT: A 563 GLN cc_start: 0.7608 (mt0) cc_final: 0.6944 (mp10) REVERT: B 304 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7590 (mtmm) REVERT: B 319 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7209 (ttp-110) REVERT: B 569 ILE cc_start: 0.8088 (mm) cc_final: 0.7754 (tp) REVERT: B 935 GLN cc_start: 0.7822 (tt0) cc_final: 0.7512 (tt0) REVERT: C 117 LEU cc_start: 0.7440 (mp) cc_final: 0.6844 (tt) REVERT: C 129 LYS cc_start: 0.6724 (mttt) cc_final: 0.5942 (mppt) REVERT: C 321 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7469 (mm-40) REVERT: C 370 ASN cc_start: 0.7268 (m-40) cc_final: 0.6962 (p0) REVERT: C 378 LYS cc_start: 0.7513 (mmtt) cc_final: 0.7212 (mmmm) REVERT: C 455 LEU cc_start: 0.8128 (tp) cc_final: 0.7911 (tp) outliers start: 15 outliers final: 4 residues processed: 372 average time/residue: 1.1341 time to fit residues: 494.1354 Evaluate side-chains 206 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 202 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 1094 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 269 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 954 GLN A1005 GLN A1101 HIS B 334 ASN B 764 ASN B 957 GLN B1002 GLN B1088 HIS C 81 ASN C 165 ASN C 360 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 481 ASN C 603 ASN C 607 GLN C 804 GLN C1002 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24079 Z= 0.194 Angle : 0.631 8.260 32767 Z= 0.340 Chirality : 0.047 0.390 3878 Planarity : 0.004 0.035 4177 Dihedral : 6.724 58.034 3956 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.46 % Favored : 97.44 % Rotamer: Outliers : 1.89 % Allowed : 7.55 % Favored : 90.57 % 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: 0.32 (0.15), residues: 2924 helix: 1.44 (0.21), residues: 651 sheet: 0.72 (0.18), residues: 704 loop : -0.54 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.004 0.001 HIS B 49 PHE 0.026 0.002 PHE B 201 TYR 0.023 0.002 TYR B 369 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 242 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8371 (m) cc_final: 0.8148 (p) REVERT: A 314 GLN cc_start: 0.7670 (mt0) cc_final: 0.7454 (tt0) REVERT: A 347 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: A 378 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7742 (mmtp) REVERT: A 394 ASN cc_start: 0.7364 (m-40) cc_final: 0.6931 (m110) REVERT: A 465 GLU cc_start: 0.6921 (tt0) cc_final: 0.6690 (tt0) REVERT: A 563 GLN cc_start: 0.7608 (mt0) cc_final: 0.6962 (mp10) REVERT: A 985 ASP cc_start: 0.7345 (p0) cc_final: 0.7143 (p0) REVERT: A 988 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7092 (pt0) REVERT: A 994 ASP cc_start: 0.7533 (t0) cc_final: 0.7239 (m-30) REVERT: B 200 TYR cc_start: 0.4642 (m-10) cc_final: 0.4106 (m-10) REVERT: B 271 GLN cc_start: 0.8546 (mt0) cc_final: 0.8174 (mt0) REVERT: B 319 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7184 (ttp-110) REVERT: B 556 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.8044 (p0) REVERT: B 569 ILE cc_start: 0.8281 (mm) cc_final: 0.7753 (tp) REVERT: B 969 ASN cc_start: 0.8174 (m-40) cc_final: 0.7913 (m-40) REVERT: C 28 TYR cc_start: 0.7572 (m-80) cc_final: 0.6985 (m-80) REVERT: C 271 GLN cc_start: 0.7834 (mt0) cc_final: 0.7628 (mt0) REVERT: C 370 ASN cc_start: 0.7418 (m-40) cc_final: 0.6948 (p0) REVERT: C 376 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7152 (p) REVERT: C 455 LEU cc_start: 0.7907 (tp) cc_final: 0.7221 (pt) REVERT: C 514 SER cc_start: 0.8110 (OUTLIER) cc_final: 0.7858 (p) REVERT: C 731 MET cc_start: 0.8779 (mtm) cc_final: 0.8561 (mtp) REVERT: C 950 ASP cc_start: 0.7659 (m-30) cc_final: 0.7295 (m-30) REVERT: C 954 GLN cc_start: 0.8082 (mt0) cc_final: 0.7879 (mt0) REVERT: C 985 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7144 (p0) outliers start: 48 outliers final: 14 residues processed: 272 average time/residue: 1.0637 time to fit residues: 343.9543 Evaluate side-chains 209 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 224 optimal weight: 0.1980 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 267 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1048 HIS B 49 HIS B 804 GLN B 901 GLN B 914 ASN B1010 GLN B1048 HIS C 165 ASN C 360 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 440 ASN C 901 GLN C1048 HIS C1135 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24079 Z= 0.243 Angle : 0.580 8.188 32767 Z= 0.308 Chirality : 0.046 0.306 3878 Planarity : 0.004 0.038 4177 Dihedral : 6.246 58.635 3952 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 2.04 % Allowed : 8.81 % Favored : 89.15 % 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 (0.15), residues: 2924 helix: 1.69 (0.21), residues: 661 sheet: 0.62 (0.19), residues: 669 loop : -0.50 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 886 HIS 0.006 0.001 HIS A 207 PHE 0.021 0.002 PHE A 456 TYR 0.022 0.002 TYR C1067 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 215 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8349 (m) cc_final: 0.7915 (p) REVERT: A 347 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6542 (m-80) REVERT: A 378 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7747 (mmtp) REVERT: A 394 ASN cc_start: 0.7348 (m-40) cc_final: 0.7072 (m-40) REVERT: A 465 GLU cc_start: 0.6994 (tt0) cc_final: 0.6723 (tt0) REVERT: A 985 ASP cc_start: 0.7432 (p0) cc_final: 0.7211 (p0) REVERT: A 988 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7067 (pt0) REVERT: A 994 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: B 271 GLN cc_start: 0.8606 (mt0) cc_final: 0.8268 (mt0) REVERT: B 321 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7716 (mm-40) REVERT: B 556 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.8025 (p0) REVERT: B 567 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7014 (mtt180) REVERT: B 569 ILE cc_start: 0.8244 (mm) cc_final: 0.7765 (tp) REVERT: B 969 ASN cc_start: 0.8209 (m-40) cc_final: 0.7953 (m-40) REVERT: B 985 ASP cc_start: 0.7543 (p0) cc_final: 0.7318 (p0) REVERT: C 28 TYR cc_start: 0.7569 (m-80) cc_final: 0.7018 (m-80) REVERT: C 52 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 271 GLN cc_start: 0.7829 (mt0) cc_final: 0.7603 (OUTLIER) REVERT: C 356 LYS cc_start: 0.7797 (tptt) cc_final: 0.7359 (tptt) REVERT: C 370 ASN cc_start: 0.7587 (m-40) cc_final: 0.7084 (p0) REVERT: C 376 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7248 (p) REVERT: C 455 LEU cc_start: 0.7912 (tp) cc_final: 0.7151 (pt) REVERT: C 731 MET cc_start: 0.8692 (mtm) cc_final: 0.8451 (mtp) REVERT: C 950 ASP cc_start: 0.7638 (m-30) cc_final: 0.7206 (m-30) REVERT: C 985 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.7030 (p0) outliers start: 52 outliers final: 20 residues processed: 248 average time/residue: 1.0268 time to fit residues: 306.3429 Evaluate side-chains 209 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 140 optimal weight: 0.0670 chunk 29 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 0.5980 chunk 287 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 256 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B1010 GLN C 165 ASN C 321 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 439 ASN C 440 ASN C 804 GLN C 969 ASN C1135 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24079 Z= 0.214 Angle : 0.537 6.610 32767 Z= 0.284 Chirality : 0.045 0.318 3878 Planarity : 0.004 0.041 4177 Dihedral : 5.859 56.834 3951 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 2.48 % Allowed : 10.10 % Favored : 87.42 % 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: 0.47 (0.15), residues: 2924 helix: 1.85 (0.21), residues: 662 sheet: 0.65 (0.19), residues: 676 loop : -0.48 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.028 0.001 PHE C 168 TYR 0.020 0.001 TYR C 170 ARG 0.007 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 203 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: A 114 THR cc_start: 0.8270 (m) cc_final: 0.7892 (p) REVERT: A 347 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6644 (OUTLIER) REVERT: A 378 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7737 (mmtp) REVERT: A 394 ASN cc_start: 0.7404 (m-40) cc_final: 0.7132 (m-40) REVERT: A 465 GLU cc_start: 0.7033 (tt0) cc_final: 0.6721 (tt0) REVERT: A 804 GLN cc_start: 0.8130 (mp10) cc_final: 0.7711 (mp-120) REVERT: A 994 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: B 227 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.7144 (p) REVERT: B 271 GLN cc_start: 0.8632 (mt0) cc_final: 0.8228 (mt0) REVERT: B 321 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7739 (mm-40) REVERT: B 556 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7506 (p0) REVERT: B 558 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7537 (mmtp) REVERT: B 567 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7046 (mtt180) REVERT: B 569 ILE cc_start: 0.8214 (mm) cc_final: 0.7712 (tp) REVERT: B 969 ASN cc_start: 0.8191 (m-40) cc_final: 0.7941 (m-40) REVERT: C 28 TYR cc_start: 0.7636 (m-80) cc_final: 0.7114 (m-80) REVERT: C 190 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6299 (mtt180) REVERT: C 271 GLN cc_start: 0.7856 (mt0) cc_final: 0.7620 (OUTLIER) REVERT: C 324 GLU cc_start: 0.7334 (pm20) cc_final: 0.7129 (pm20) REVERT: C 356 LYS cc_start: 0.7699 (tptt) cc_final: 0.7319 (tptt) REVERT: C 370 ASN cc_start: 0.7500 (m-40) cc_final: 0.7007 (p0) REVERT: C 376 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7322 (p) REVERT: C 455 LEU cc_start: 0.7876 (tp) cc_final: 0.7080 (pt) REVERT: C 661 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: C 950 ASP cc_start: 0.7685 (m-30) cc_final: 0.7258 (m-30) REVERT: C 985 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6924 (p0) outliers start: 63 outliers final: 23 residues processed: 244 average time/residue: 1.1021 time to fit residues: 319.0644 Evaluate side-chains 214 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 213 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 779 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1106 GLN C 165 ASN C 321 GLN C 439 ASN C 440 ASN C 804 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24079 Z= 0.232 Angle : 0.550 16.532 32767 Z= 0.289 Chirality : 0.045 0.294 3878 Planarity : 0.004 0.043 4177 Dihedral : 5.781 57.475 3951 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 2.44 % Allowed : 10.89 % Favored : 86.67 % 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: 0.46 (0.15), residues: 2924 helix: 1.80 (0.21), residues: 669 sheet: 0.65 (0.19), residues: 680 loop : -0.49 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 PHE 0.028 0.001 PHE A 140 TYR 0.021 0.001 TYR A 170 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 192 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8452 (tt0) cc_final: 0.8234 (tt0) REVERT: A 88 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: A 114 THR cc_start: 0.8264 (m) cc_final: 0.7899 (p) REVERT: A 347 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6531 (OUTLIER) REVERT: A 378 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7744 (mmtp) REVERT: A 394 ASN cc_start: 0.7380 (m-40) cc_final: 0.7137 (m-40) REVERT: A 465 GLU cc_start: 0.6993 (tt0) cc_final: 0.6677 (tt0) REVERT: A 988 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7025 (pt0) REVERT: A 994 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: B 321 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7711 (mm-40) REVERT: B 556 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7532 (p0) REVERT: B 558 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7504 (mmtp) REVERT: B 567 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7107 (mtt180) REVERT: B 569 ILE cc_start: 0.8190 (mm) cc_final: 0.7690 (tp) REVERT: B 583 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: B 779 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: B 969 ASN cc_start: 0.8226 (m-40) cc_final: 0.7976 (m-40) REVERT: C 28 TYR cc_start: 0.7671 (m-80) cc_final: 0.7231 (m-80) REVERT: C 102 ARG cc_start: 0.7410 (tpp80) cc_final: 0.6789 (tpp-160) REVERT: C 190 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6342 (mtt180) REVERT: C 271 GLN cc_start: 0.7857 (mt0) cc_final: 0.7624 (OUTLIER) REVERT: C 356 LYS cc_start: 0.7654 (tptt) cc_final: 0.7286 (tttm) REVERT: C 370 ASN cc_start: 0.7446 (m-40) cc_final: 0.7051 (p0) REVERT: C 376 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7334 (p) REVERT: C 386 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7409 (mmmt) REVERT: C 455 LEU cc_start: 0.7858 (tp) cc_final: 0.7072 (pt) REVERT: C 506 GLN cc_start: 0.7551 (mt0) cc_final: 0.7076 (mp10) REVERT: C 661 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: C 950 ASP cc_start: 0.7696 (m-30) cc_final: 0.7256 (m-30) outliers start: 62 outliers final: 28 residues processed: 234 average time/residue: 1.1259 time to fit residues: 311.1309 Evaluate side-chains 216 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.0370 chunk 258 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 168 optimal weight: 4.9990 chunk 70 optimal weight: 0.0020 chunk 287 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 133 optimal weight: 40.0000 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 overall best weight: 0.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 779 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN C 165 ASN C 321 GLN C 440 ASN C 762 GLN C 804 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 24079 Z= 0.129 Angle : 0.497 10.531 32767 Z= 0.261 Chirality : 0.043 0.278 3878 Planarity : 0.003 0.041 4177 Dihedral : 5.430 55.465 3951 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 1.65 % Allowed : 12.11 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 2924 helix: 2.10 (0.21), residues: 670 sheet: 0.65 (0.19), residues: 669 loop : -0.37 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS B1088 PHE 0.025 0.001 PHE C 453 TYR 0.021 0.001 TYR A 170 ARG 0.008 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: A 114 THR cc_start: 0.8172 (m) cc_final: 0.7820 (p) REVERT: A 347 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6551 (m-80) REVERT: A 378 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7756 (mmtp) REVERT: A 394 ASN cc_start: 0.7354 (m-40) cc_final: 0.7061 (m-40) REVERT: A 988 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6987 (pt0) REVERT: B 227 VAL cc_start: 0.7475 (OUTLIER) cc_final: 0.7190 (p) REVERT: B 271 GLN cc_start: 0.8569 (mt0) cc_final: 0.8303 (mt0) REVERT: B 321 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7661 (mm-40) REVERT: B 556 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7367 (p0) REVERT: B 558 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7535 (mmtp) REVERT: B 569 ILE cc_start: 0.8136 (mm) cc_final: 0.7606 (tp) REVERT: B 583 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: B 779 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: B 969 ASN cc_start: 0.8196 (m-40) cc_final: 0.7944 (m-40) REVERT: C 28 TYR cc_start: 0.7627 (m-80) cc_final: 0.7198 (m-80) REVERT: C 102 ARG cc_start: 0.7420 (tpp80) cc_final: 0.7169 (tpp-160) REVERT: C 129 LYS cc_start: 0.6586 (mttt) cc_final: 0.5827 (mppt) REVERT: C 190 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6248 (mtt90) REVERT: C 271 GLN cc_start: 0.7829 (mt0) cc_final: 0.7623 (OUTLIER) REVERT: C 356 LYS cc_start: 0.7628 (tptt) cc_final: 0.7206 (tttm) REVERT: C 370 ASN cc_start: 0.7624 (m-40) cc_final: 0.6995 (p0) REVERT: C 455 LEU cc_start: 0.7821 (tp) cc_final: 0.7035 (pt) REVERT: C 950 ASP cc_start: 0.7508 (m-30) cc_final: 0.7079 (m-30) REVERT: C 990 GLU cc_start: 0.7396 (tt0) cc_final: 0.6953 (mt-10) REVERT: C 994 ASP cc_start: 0.7745 (t70) cc_final: 0.7439 (m-30) outliers start: 42 outliers final: 13 residues processed: 249 average time/residue: 1.0750 time to fit residues: 318.6051 Evaluate side-chains 218 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 286 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 165 ASN C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 24079 Z= 0.148 Angle : 0.492 9.595 32767 Z= 0.258 Chirality : 0.043 0.279 3878 Planarity : 0.003 0.040 4177 Dihedral : 5.291 55.575 3951 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 1.26 % Allowed : 13.44 % Favored : 85.30 % 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: 0.72 (0.15), residues: 2924 helix: 2.12 (0.21), residues: 676 sheet: 0.72 (0.19), residues: 692 loop : -0.35 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS A1064 PHE 0.028 0.001 PHE C 453 TYR 0.022 0.001 TYR A 170 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: A 114 THR cc_start: 0.8174 (m) cc_final: 0.7857 (p) REVERT: A 347 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: A 378 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7805 (mmtp) REVERT: A 394 ASN cc_start: 0.7381 (m-40) cc_final: 0.7095 (m-40) REVERT: A 988 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6981 (pt0) REVERT: B 227 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7241 (p) REVERT: B 271 GLN cc_start: 0.8554 (mt0) cc_final: 0.8323 (mt0) REVERT: B 321 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7688 (mm-40) REVERT: B 569 ILE cc_start: 0.8162 (mm) cc_final: 0.7673 (tp) REVERT: B 583 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: B 779 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: B 969 ASN cc_start: 0.8200 (m-40) cc_final: 0.7956 (m-40) REVERT: C 28 TYR cc_start: 0.7637 (m-80) cc_final: 0.7188 (m-80) REVERT: C 102 ARG cc_start: 0.7466 (tpp80) cc_final: 0.6973 (tpp-160) REVERT: C 129 LYS cc_start: 0.6487 (mttt) cc_final: 0.5779 (mppt) REVERT: C 190 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6266 (mtt90) REVERT: C 271 GLN cc_start: 0.7835 (mt0) cc_final: 0.7612 (OUTLIER) REVERT: C 356 LYS cc_start: 0.7629 (tptt) cc_final: 0.7215 (tttm) REVERT: C 370 ASN cc_start: 0.7640 (m-40) cc_final: 0.7002 (p0) REVERT: C 455 LEU cc_start: 0.7779 (tp) cc_final: 0.7058 (pt) REVERT: C 506 GLN cc_start: 0.7412 (mt0) cc_final: 0.6859 (mp10) REVERT: C 661 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7741 (pt0) REVERT: C 950 ASP cc_start: 0.7614 (m-30) cc_final: 0.7159 (m-30) REVERT: C 994 ASP cc_start: 0.7752 (t70) cc_final: 0.7362 (m-30) outliers start: 32 outliers final: 15 residues processed: 231 average time/residue: 1.0486 time to fit residues: 287.8442 Evaluate side-chains 220 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 5.9990 chunk 114 optimal weight: 0.0870 chunk 170 optimal weight: 0.0370 chunk 86 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 overall best weight: 1.3840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 165 ASN C 321 GLN C 690 GLN C 804 GLN C1010 GLN C1083 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24079 Z= 0.221 Angle : 0.521 8.613 32767 Z= 0.272 Chirality : 0.044 0.292 3878 Planarity : 0.004 0.040 4177 Dihedral : 5.370 56.956 3951 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 1.73 % Allowed : 13.36 % Favored : 84.91 % 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: 0.60 (0.15), residues: 2924 helix: 1.90 (0.21), residues: 681 sheet: 0.71 (0.18), residues: 705 loop : -0.42 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 PHE 0.032 0.001 PHE C 453 TYR 0.023 0.001 TYR C 170 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: A 114 THR cc_start: 0.8165 (m) cc_final: 0.7841 (p) REVERT: A 378 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7808 (mmtp) REVERT: A 393 THR cc_start: 0.8272 (m) cc_final: 0.8027 (p) REVERT: A 394 ASN cc_start: 0.7387 (m-40) cc_final: 0.7100 (m-40) REVERT: A 900 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8379 (mtm) REVERT: A 988 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6976 (pt0) REVERT: B 227 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7247 (p) REVERT: B 271 GLN cc_start: 0.8578 (mt0) cc_final: 0.8256 (mt0) REVERT: B 569 ILE cc_start: 0.8275 (mm) cc_final: 0.7763 (tp) REVERT: B 583 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: B 779 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: B 969 ASN cc_start: 0.8189 (m-40) cc_final: 0.7933 (m-40) REVERT: C 28 TYR cc_start: 0.7671 (m-80) cc_final: 0.7131 (m-80) REVERT: C 102 ARG cc_start: 0.7460 (tpp80) cc_final: 0.7146 (tpp-160) REVERT: C 129 LYS cc_start: 0.6478 (mttt) cc_final: 0.5790 (mppt) REVERT: C 190 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6325 (mtt90) REVERT: C 192 PHE cc_start: 0.7580 (m-80) cc_final: 0.7291 (m-80) REVERT: C 271 GLN cc_start: 0.7845 (mt0) cc_final: 0.7623 (OUTLIER) REVERT: C 331 ASN cc_start: 0.7209 (p0) cc_final: 0.7007 (p0) REVERT: C 356 LYS cc_start: 0.7645 (tptt) cc_final: 0.7233 (tttm) REVERT: C 370 ASN cc_start: 0.7562 (m-40) cc_final: 0.6943 (p0) REVERT: C 455 LEU cc_start: 0.7778 (tp) cc_final: 0.7034 (pt) REVERT: C 661 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: C 886 TRP cc_start: 0.7650 (p90) cc_final: 0.7014 (p90) REVERT: C 950 ASP cc_start: 0.7785 (m-30) cc_final: 0.7293 (m-30) REVERT: C 994 ASP cc_start: 0.7795 (t70) cc_final: 0.7455 (m-30) outliers start: 44 outliers final: 19 residues processed: 229 average time/residue: 1.0115 time to fit residues: 277.8677 Evaluate side-chains 227 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 265 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 165 ASN C 321 GLN C 690 GLN C 804 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24079 Z= 0.280 Angle : 0.550 8.409 32767 Z= 0.288 Chirality : 0.046 0.292 3878 Planarity : 0.004 0.042 4177 Dihedral : 5.553 58.055 3951 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 1.77 % Allowed : 13.40 % Favored : 84.83 % 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: 0.42 (0.15), residues: 2924 helix: 1.69 (0.21), residues: 686 sheet: 0.60 (0.18), residues: 716 loop : -0.51 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS C1083 PHE 0.035 0.002 PHE A 347 TYR 0.020 0.002 TYR C1067 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 202 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: A 114 THR cc_start: 0.8293 (m) cc_final: 0.7956 (p) REVERT: A 378 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7845 (mmtp) REVERT: A 393 THR cc_start: 0.8280 (m) cc_final: 0.7993 (p) REVERT: A 394 ASN cc_start: 0.7324 (m-40) cc_final: 0.7071 (m-40) REVERT: A 988 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6966 (pt0) REVERT: B 227 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7245 (p) REVERT: B 271 GLN cc_start: 0.8550 (mt0) cc_final: 0.8301 (mt0) REVERT: B 569 ILE cc_start: 0.8311 (mm) cc_final: 0.7804 (tp) REVERT: B 583 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: B 779 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: C 28 TYR cc_start: 0.7682 (m-80) cc_final: 0.7147 (m-80) REVERT: C 102 ARG cc_start: 0.7478 (tpp80) cc_final: 0.7169 (tpp-160) REVERT: C 190 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6374 (mtt90) REVERT: C 192 PHE cc_start: 0.7616 (m-80) cc_final: 0.7322 (m-80) REVERT: C 271 GLN cc_start: 0.7849 (mt0) cc_final: 0.7645 (OUTLIER) REVERT: C 331 ASN cc_start: 0.7036 (p0) cc_final: 0.6818 (p0) REVERT: C 356 LYS cc_start: 0.7788 (tptt) cc_final: 0.7331 (tttp) REVERT: C 370 ASN cc_start: 0.7492 (m-40) cc_final: 0.6871 (p0) REVERT: C 455 LEU cc_start: 0.7770 (tp) cc_final: 0.7427 (tp) REVERT: C 506 GLN cc_start: 0.7711 (mt0) cc_final: 0.6950 (mp10) REVERT: C 661 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: C 790 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8262 (mtpt) REVERT: C 904 TYR cc_start: 0.7890 (m-10) cc_final: 0.7572 (m-10) REVERT: C 950 ASP cc_start: 0.7825 (m-30) cc_final: 0.7329 (m-30) REVERT: C 994 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: C 1010 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7923 (tt0) outliers start: 45 outliers final: 26 residues processed: 229 average time/residue: 0.9878 time to fit residues: 272.1746 Evaluate side-chains 229 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.7980 chunk 282 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 165 ASN C 321 GLN C 690 GLN C 804 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24079 Z= 0.164 Angle : 0.506 7.935 32767 Z= 0.266 Chirality : 0.044 0.298 3878 Planarity : 0.003 0.042 4177 Dihedral : 5.420 58.478 3951 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 1.22 % Allowed : 13.99 % Favored : 84.79 % 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: 0.59 (0.15), residues: 2924 helix: 1.90 (0.21), residues: 680 sheet: 0.66 (0.19), residues: 690 loop : -0.39 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS A1064 PHE 0.031 0.001 PHE C 453 TYR 0.027 0.001 TYR B 200 ARG 0.004 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: A 114 THR cc_start: 0.8262 (m) cc_final: 0.7924 (p) REVERT: A 378 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7829 (mmtp) REVERT: A 393 THR cc_start: 0.8203 (m) cc_final: 0.7938 (p) REVERT: A 394 ASN cc_start: 0.7245 (m-40) cc_final: 0.7001 (m-40) REVERT: A 988 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6969 (pt0) REVERT: B 227 VAL cc_start: 0.7548 (OUTLIER) cc_final: 0.7305 (p) REVERT: B 271 GLN cc_start: 0.8592 (mt0) cc_final: 0.8306 (mt0) REVERT: B 569 ILE cc_start: 0.8311 (mm) cc_final: 0.7778 (tp) REVERT: B 583 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: B 779 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: B 969 ASN cc_start: 0.8208 (m-40) cc_final: 0.7952 (m-40) REVERT: C 28 TYR cc_start: 0.7647 (m-80) cc_final: 0.7101 (m-80) REVERT: C 102 ARG cc_start: 0.7584 (tpp80) cc_final: 0.7285 (tpp-160) REVERT: C 190 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6289 (mtt90) REVERT: C 192 PHE cc_start: 0.7642 (m-80) cc_final: 0.7364 (m-80) REVERT: C 271 GLN cc_start: 0.7869 (mt0) cc_final: 0.7641 (OUTLIER) REVERT: C 356 LYS cc_start: 0.7828 (tptt) cc_final: 0.7339 (tttp) REVERT: C 370 ASN cc_start: 0.7527 (m-40) cc_final: 0.6916 (p0) REVERT: C 455 LEU cc_start: 0.7649 (tp) cc_final: 0.7384 (tp) REVERT: C 506 GLN cc_start: 0.7680 (mt0) cc_final: 0.7024 (mp10) REVERT: C 790 LYS cc_start: 0.8437 (mtpp) cc_final: 0.8220 (mtpt) REVERT: C 886 TRP cc_start: 0.7547 (p90) cc_final: 0.7011 (p90) REVERT: C 950 ASP cc_start: 0.7773 (m-30) cc_final: 0.7295 (m-30) REVERT: C 990 GLU cc_start: 0.7446 (tt0) cc_final: 0.6993 (mt-10) REVERT: C 994 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7457 (m-30) outliers start: 31 outliers final: 17 residues processed: 222 average time/residue: 1.0493 time to fit residues: 275.8726 Evaluate side-chains 219 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 217 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 165 ASN C 321 GLN C 409 GLN C 603 ASN C 690 GLN C 804 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.182987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113404 restraints weight = 27410.953| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.41 r_work: 0.3047 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24079 Z= 0.208 Angle : 0.520 7.629 32767 Z= 0.272 Chirality : 0.045 0.292 3878 Planarity : 0.004 0.042 4177 Dihedral : 5.413 56.704 3951 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 1.42 % Allowed : 13.76 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 2924 helix: 1.90 (0.21), residues: 674 sheet: 0.63 (0.18), residues: 700 loop : -0.46 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 PHE 0.032 0.001 PHE C 453 TYR 0.023 0.001 TYR C 904 ARG 0.007 0.000 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6859.96 seconds wall clock time: 122 minutes 57.08 seconds (7377.08 seconds total)