Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 18:29:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwo_23552/04_2023/7lwo_23552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwo_23552/04_2023/7lwo_23552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwo_23552/04_2023/7lwo_23552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwo_23552/04_2023/7lwo_23552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwo_23552/04_2023/7lwo_23552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwo_23552/04_2023/7lwo_23552.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.100 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 101 5.16 5 C 15038 2.51 5 N 3878 2.21 5 O 4539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "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-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23556 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7684 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 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 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 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 chiralities: 2 Chain: "A" 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 chiralities: 10 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 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 chiralities: 10 Time building chain proxies: 14.00, per 1000 atoms: 0.59 Number of scatterers: 23556 At special positions: 0 Unit cell: (128.28, 135.763, 193.489, 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 101 16.00 O 4539 8.00 N 3878 7.00 C 15038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.03 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=2.03 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=1.92 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 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 717 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 801 " " 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 282 " " NAG B1310 " - " ASN B 234 " " 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 331 " " NAG C1310 " - " ASN C 234 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN B1098 " " NAG F 1 " - " ASN C1098 " Time building additional restraints: 9.30 Conformation dependent library (CDL) restraints added in 3.3 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: 73 helices and 44 sheets defined 27.3% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.686A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.449A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.320A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.566A 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: 3.922A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.604A 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: 3.733A 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 918 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: 3.710A 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.111A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.892A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.706A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.097A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.616A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 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: 3.750A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.797A 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 891 removed outlier: 3.780A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.077A 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: 3.636A 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: 4.037A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.160A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) 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 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.004A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.670A 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 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.564A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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: 3.707A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (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 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.597A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.506A 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: 3.679A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.341A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.934A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.512A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.804A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.631A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.372A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.533A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.754A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.585A 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: 6.483A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.262A 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: 4.627A 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: 8.373A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.741A 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: 3.603A 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: 7.007A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.856A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.393A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.206A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.466A 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: 3.773A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.481A 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: 5.969A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.671A 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: 4.431A 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: 4.707A 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: 8.600A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.758A 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: 7.490A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.799A 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 removed outlier: 3.735A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.550A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.791A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.057A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.755A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.988A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.454A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.632A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1054 hydrogen bonds defined for protein. 2868 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: 10.07 Time building geometry restraints manager: 10.11 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: 6176 1.33 - 1.46: 4484 1.46 - 1.58: 13279 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24064 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.62e+01 bond pdb=" C5 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.41e+01 bond pdb=" C5 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 24059 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.61: 246 103.61 - 111.55: 8721 111.55 - 119.49: 10721 119.49 - 127.43: 12907 127.43 - 135.37: 152 Bond angle restraints: 32747 Sorted by residual: angle pdb=" OE1 GLN A1106 " pdb=" CD GLN A1106 " pdb=" NE2 GLN A1106 " ideal model delta sigma weight residual 122.60 116.43 6.17 1.00e+00 1.00e+00 3.81e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" OE1 GLN B 965 " pdb=" CD GLN B 965 " pdb=" NE2 GLN B 965 " ideal model delta sigma weight residual 122.60 116.87 5.73 1.00e+00 1.00e+00 3.28e+01 angle pdb=" CA PHE A 58 " pdb=" CB PHE A 58 " pdb=" CG PHE A 58 " ideal model delta sigma weight residual 113.80 119.53 -5.73 1.00e+00 1.00e+00 3.28e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 118.28 -5.68 1.00e+00 1.00e+00 3.23e+01 ... (remaining 32742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13118 17.97 - 35.94: 707 35.94 - 53.91: 111 53.91 - 71.88: 44 71.88 - 89.85: 24 Dihedral angle restraints: 14004 sinusoidal: 5350 harmonic: 8654 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.05 79.05 1 1.00e+01 1.00e-02 7.78e+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 -150.73 64.73 1 1.00e+01 1.00e-02 5.50e+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 93.00 154.73 -61.73 1 1.00e+01 1.00e-02 5.05e+01 ... (remaining 14001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2820 0.103 - 0.205: 955 0.205 - 0.308: 80 0.308 - 0.410: 16 0.410 - 0.513: 2 Chirality restraints: 3873 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 -2.56 0.16 2.00e-02 2.50e+03 6.27e+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 -2.55 0.15 2.00e-02 2.50e+03 5.80e+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 -2.52 0.12 2.00e-02 2.50e+03 3.60e+01 ... (remaining 3870 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.371 2.00e-02 2.50e+03 2.01e-01 1.01e+03 pdb=" CG TRP C 886 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.190 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.138 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.303 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.212 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.070 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.251 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.140 2.00e-02 2.50e+03 1.52e-01 2.89e+02 pdb=" CG ASN A 331 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.237 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.140 2.00e-02 2.50e+03 1.48e-01 2.75e+02 pdb=" CG ASN B1074 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.228 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.176 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11011 2.99 - 3.47: 22005 3.47 - 3.94: 39116 3.94 - 4.42: 43250 4.42 - 4.90: 73642 Nonbonded interactions: 189024 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.511 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.523 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.527 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.531 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.546 2.440 ... (remaining 189019 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 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 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 na \ me 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 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 479 or (resid 480 and (name N or name CA or name C or name O o \ r name CB )) or resid 481 through 487 or (resid 488 and (name N or name CA or na \ me C or name O or name CB )) or resid 489 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 throug \ h 827 or resid 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 name CA or name C or name O or name CB )) or resid 1143 through 1144 o \ r (resid 1145 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 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 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 or 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 or (resid \ 583 and (name N or name CA or name C or name O or name CB )) or resid 584 throug \ h 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 o \ r name CB )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and \ (name N or name CA or name C or name O or name CB )) or resid 746 through 747 o \ r (resid 748 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 49 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 name O or n \ ame CB )) or resid 815 through 827 or resid 855 through 866 or (resid 867 throug \ h 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thro \ ugh 1091 or (resid 1092 and (name N or name CA or name C or name O or name CB )) \ or resid 1093 through 1143 or (resid 1144 through 1146 and (name N or name CA o \ r name C or name O or name CB )) or resid 1147 or resid 1301 through 1310)) 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 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r 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 23 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 483 or resid 485 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 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 n \ ame O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name C \ A 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 813 or \ (resid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name \ CB )) or resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C \ or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N o \ r 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.830 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 62.100 Find NCS groups from input model: 1.760 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 0.079 24064 Z= 0.875 Angle : 1.787 9.100 32747 Z= 1.202 Chirality : 0.095 0.513 3873 Planarity : 0.013 0.201 4176 Dihedral : 12.725 89.855 8317 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.55 % Favored : 95.14 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.22 % 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: -0.78 (0.14), residues: 2924 helix: -0.98 (0.17), residues: 692 sheet: 0.67 (0.20), residues: 581 loop : -0.70 (0.14), residues: 1651 *********************** 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 407 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 392 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 405 average time/residue: 1.1709 time to fit residues: 555.9404 Evaluate side-chains 249 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 242 time to evaluate : 2.582 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 3.6304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 232 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 532 ASN A 703 ASN A 779 GLN A 954 GLN A1005 GLN B 540 ASN B 764 ASN B1048 HIS B1106 GLN B1125 ASN B1135 ASN C 211 ASN C 239 GLN C 394 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN C1048 HIS C1119 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 24064 Z= 0.227 Angle : 0.647 11.532 32747 Z= 0.344 Chirality : 0.048 0.557 3873 Planarity : 0.004 0.061 4176 Dihedral : 5.560 29.048 3173 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer Outliers : 2.40 % 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: 0.25 (0.15), residues: 2924 helix: 1.19 (0.20), residues: 673 sheet: 0.69 (0.19), residues: 687 loop : -0.50 (0.15), residues: 1564 *********************** 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 327 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 266 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 23 residues processed: 302 average time/residue: 1.0313 time to fit residues: 372.9922 Evaluate side-chains 238 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.2170 time to fit residues: 5.7907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 270 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 216 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 544 ASN A 954 GLN A1005 GLN A1048 HIS C 239 GLN C 271 GLN C 314 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1010 GLN C1088 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 24064 Z= 0.259 Angle : 0.600 14.101 32747 Z= 0.314 Chirality : 0.047 0.333 3873 Planarity : 0.004 0.038 4176 Dihedral : 5.089 29.981 3173 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.09 % Rotamer Outliers : 2.63 % 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: 1.41 (0.20), residues: 678 sheet: 0.63 (0.18), residues: 683 loop : -0.50 (0.15), residues: 1563 *********************** 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 288 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 221 time to evaluate : 2.799 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 33 residues processed: 265 average time/residue: 1.1413 time to fit residues: 358.6599 Evaluate side-chains 226 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 26 residues processed: 7 average time/residue: 0.6800 time to fit residues: 9.8735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.4980 chunk 203 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 181 optimal weight: 0.3980 chunk 271 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 256 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 52 GLN A 207 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 901 GLN C 239 GLN C 271 GLN C 564 GLN C 762 GLN C 901 GLN C1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 24064 Z= 0.141 Angle : 0.521 11.541 32747 Z= 0.270 Chirality : 0.044 0.328 3873 Planarity : 0.004 0.051 4176 Dihedral : 4.542 28.269 3173 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.39 % Favored : 97.47 % Rotamer Outliers : 2.56 % 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: 0.56 (0.15), residues: 2924 helix: 1.84 (0.21), residues: 671 sheet: 0.65 (0.18), residues: 673 loop : -0.37 (0.15), residues: 1580 *********************** 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 288 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 223 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 29 residues processed: 266 average time/residue: 1.1154 time to fit residues: 354.3960 Evaluate side-chains 224 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 2.442 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 0.2092 time to fit residues: 5.8294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 5.9990 chunk 162 optimal weight: 0.1980 chunk 4 optimal weight: 0.0020 chunk 213 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 257 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 115 GLN A 207 HIS A 675 GLN A1005 GLN A1010 GLN B 532 ASN B 901 GLN B1010 GLN C 239 GLN C 271 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.108 24064 Z= 0.233 Angle : 0.547 10.595 32747 Z= 0.284 Chirality : 0.045 0.316 3873 Planarity : 0.004 0.055 4176 Dihedral : 4.512 24.698 3173 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.99 % Rotamer Outliers : 2.67 % 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: 0.47 (0.15), residues: 2924 helix: 1.69 (0.21), residues: 679 sheet: 0.61 (0.18), residues: 669 loop : -0.41 (0.15), residues: 1576 *********************** 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 277 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 209 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 40 residues processed: 252 average time/residue: 1.1653 time to fit residues: 349.3129 Evaluate side-chains 237 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.666 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 29 residues processed: 11 average time/residue: 0.6389 time to fit residues: 12.9765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 287 optimal weight: 0.9990 chunk 238 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 675 GLN A 914 ASN A1005 GLN B 901 GLN B 957 GLN C 239 GLN C 271 GLN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 24064 Z= 0.169 Angle : 0.510 11.209 32747 Z= 0.264 Chirality : 0.044 0.381 3873 Planarity : 0.003 0.067 4176 Dihedral : 4.313 21.032 3173 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.74 % Favored : 97.13 % Rotamer Outliers : 2.56 % 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: 0.57 (0.15), residues: 2924 helix: 1.81 (0.21), residues: 678 sheet: 0.56 (0.18), residues: 687 loop : -0.32 (0.15), residues: 1559 *********************** 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 267 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 202 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 40 residues processed: 247 average time/residue: 1.1313 time to fit residues: 332.6852 Evaluate side-chains 231 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 3.158 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 9 average time/residue: 0.7970 time to fit residues: 12.9094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 163 optimal weight: 0.9980 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 914 ASN A 969 ASN A1005 GLN B 532 ASN C 239 GLN C 271 GLN C 532 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 24064 Z= 0.295 Angle : 0.569 9.805 32747 Z= 0.295 Chirality : 0.046 0.267 3873 Planarity : 0.004 0.077 4176 Dihedral : 4.519 25.378 3173 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Rotamer Outliers : 2.56 % 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: 0.36 (0.15), residues: 2924 helix: 1.55 (0.21), residues: 681 sheet: 0.51 (0.18), residues: 686 loop : -0.44 (0.15), residues: 1557 *********************** 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 266 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 201 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 41 residues processed: 247 average time/residue: 1.1395 time to fit residues: 335.3177 Evaluate side-chains 231 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 7 average time/residue: 0.4423 time to fit residues: 7.9838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 170 optimal weight: 0.3980 chunk 86 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 675 GLN A1005 GLN B 751 ASN B 804 GLN C 239 GLN C 271 GLN C 935 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 24064 Z= 0.170 Angle : 0.504 11.338 32747 Z= 0.262 Chirality : 0.044 0.240 3873 Planarity : 0.003 0.050 4176 Dihedral : 4.252 25.213 3173 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer Outliers : 1.97 % 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: 1.76 (0.21), residues: 679 sheet: 0.51 (0.18), residues: 697 loop : -0.32 (0.15), residues: 1548 *********************** 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 245 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 195 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 37 residues processed: 236 average time/residue: 1.1814 time to fit residues: 331.7369 Evaluate side-chains 231 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 2.624 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 5 average time/residue: 0.7630 time to fit residues: 8.5510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.7980 chunk 274 optimal weight: 2.9990 chunk 250 optimal weight: 0.5980 chunk 266 optimal weight: 0.0370 chunk 160 optimal weight: 0.4980 chunk 116 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 252 optimal weight: 0.3980 chunk 265 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 969 ASN A1005 GLN C 239 GLN C 271 GLN C 580 GLN C 935 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 24064 Z= 0.126 Angle : 0.480 11.411 32747 Z= 0.249 Chirality : 0.043 0.252 3873 Planarity : 0.003 0.073 4176 Dihedral : 4.027 25.128 3173 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.56 % Favored : 97.30 % Rotamer Outliers : 1.49 % 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: 0.77 (0.15), residues: 2924 helix: 2.06 (0.21), residues: 667 sheet: 0.64 (0.19), residues: 692 loop : -0.19 (0.15), residues: 1565 *********************** 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 245 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 31 residues processed: 241 average time/residue: 1.1569 time to fit residues: 331.8262 Evaluate side-chains 229 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 198 time to evaluate : 2.741 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 1 average time/residue: 0.2319 time to fit residues: 4.0706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 133 optimal weight: 0.0770 chunk 196 optimal weight: 0.9990 chunk 295 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 675 GLN A 914 ASN A 969 ASN A1005 GLN C 271 GLN C 804 GLN C 935 GLN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 24064 Z= 0.223 Angle : 0.522 11.234 32747 Z= 0.271 Chirality : 0.044 0.267 3873 Planarity : 0.004 0.094 4176 Dihedral : 4.169 23.587 3173 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer Outliers : 1.57 % 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: 0.63 (0.15), residues: 2924 helix: 1.84 (0.21), residues: 678 sheet: 0.59 (0.18), residues: 703 loop : -0.27 (0.15), residues: 1543 ********************** 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 238 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 32 residues processed: 233 average time/residue: 1.1672 time to fit residues: 327.0741 Evaluate side-chains 225 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 193 time to evaluate : 2.647 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.3487 time to fit residues: 4.8680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.9980 chunk 250 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 217 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 235 optimal weight: 0.0970 chunk 98 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 969 ASN B 271 GLN C 271 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.189897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122092 restraints weight = 27242.441| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.44 r_work: 0.3087 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 24064 Z= 0.147 Angle : 0.485 11.391 32747 Z= 0.251 Chirality : 0.043 0.266 3873 Planarity : 0.004 0.079 4176 Dihedral : 4.005 23.478 3173 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.63 % Favored : 97.23 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 2924 helix: 1.99 (0.21), residues: 670 sheet: 0.60 (0.18), residues: 694 loop : -0.16 (0.15), residues: 1560 =============================================================================== Job complete usr+sys time: 7311.90 seconds wall clock time: 131 minutes 25.27 seconds (7885.27 seconds total)