Starting phenix.real_space_refine on Mon Aug 25 16:12:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f4p_28856/08_2025/8f4p_28856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f4p_28856/08_2025/8f4p_28856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f4p_28856/08_2025/8f4p_28856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f4p_28856/08_2025/8f4p_28856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f4p_28856/08_2025/8f4p_28856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f4p_28856/08_2025/8f4p_28856.map" } resolution = 3.7 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3104 atoms to isotropic. 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 120 5.16 5 C 16951 2.51 5 N 4399 2.21 5 O 5165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26635 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8375 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 bond proxies already assigned to first conformer: 8551 Chain: "B" Number of atoms: 8524 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 bond proxies already assigned to first conformer: 8708 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 56, 'TRANS': 1010} Chain breaks: 5 Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 868 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} 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: "G" 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: "H" 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: "I" 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: "J" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 459 " occ=0.51 ... (10 atoms not shown) pdb=" OG BSER A 459 " occ=0.49 residue: pdb=" N ASER B 459 " occ=0.67 ... (10 atoms not shown) pdb=" OG BSER B 459 " occ=0.33 Time building chain proxies: 9.88, per 1000 atoms: 0.37 Number of scatterers: 26635 At special positions: 0 Unit cell: (163.572, 162.503, 200.991, 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 120 16.00 O 5165 8.00 N 4399 7.00 C 16951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 331 " " NAG A1203 " - " ASN A 603 " " NAG A1204 " - " ASN A 616 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A 717 " " NAG A1207 " - " ASN A1098 " " NAG A1208 " - " ASN A1134 " " NAG A1209 " - " ASN A 657 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 331 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C 717 " " NAG C1207 " - " ASN C1134 " " NAG C1208 " - " ASN C 343 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN B1134 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 343 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6248 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 47 sheets defined 22.5% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.824A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.944A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.033A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.645A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.840A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 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 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.029A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.524A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.702A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.636A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.640A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (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 988 Processing helix chain 'A' and resid 989 through 1032 removed outlier: 4.303A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.742A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.168A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.790A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.611A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.652A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.921A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.531A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.603A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.386A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (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 removed outlier: 3.604A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.430A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.656A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.827A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.657A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.719A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.609A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.183A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 4.151A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.019A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 985 through 1033 removed outlier: 3.871A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.714A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1146' Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.737A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.818A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.701A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 156 removed outlier: 4.379A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.919A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.602A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.667A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.658A pdb=" N ILE A 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.601A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.774A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 53 removed outlier: 4.301A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 160 through 172 removed outlier: 9.225A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.546A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.560A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.542A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.752A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 643 through 645 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.007A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.688A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.474A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.545A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 53 Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.503A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 106 Processing sheet with id=AD8, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.594A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.750A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.429A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 398 through 399 removed outlier: 3.833A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.164A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.530A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.517A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.346A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 99 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP D 100 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.346A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 99 " --> pdb=" O GLY D 33 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2316 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: 4.93 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8530 1.34 - 1.47: 6924 1.47 - 1.60: 11647 1.60 - 1.73: 0 1.73 - 1.86: 152 Bond restraints: 27253 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N SER A 884 " pdb=" CA SER A 884 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.67e+00 bond pdb=" N THR B 167 " pdb=" CA THR B 167 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.17e-02 7.31e+03 6.72e+00 bond pdb=" N VAL D 101 " pdb=" CA VAL D 101 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.58e+00 bond pdb=" N ASP D 100 " pdb=" CA ASP D 100 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.31e-02 5.83e+03 6.07e+00 ... (remaining 27248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 36549 2.14 - 4.28: 497 4.28 - 6.42: 41 6.42 - 8.56: 8 8.56 - 10.70: 2 Bond angle restraints: 37097 Sorted by residual: angle pdb=" C PHE A 55 " pdb=" N LEU A 56 " pdb=" CA LEU A 56 " ideal model delta sigma weight residual 122.65 133.35 -10.70 1.66e+00 3.63e-01 4.15e+01 angle pdb=" CA GLU B 281 " pdb=" CB GLU B 281 " pdb=" CG GLU B 281 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N LEU A 216 " pdb=" CA LEU A 216 " pdb=" C LEU A 216 " ideal model delta sigma weight residual 109.81 116.72 -6.91 2.21e+00 2.05e-01 9.78e+00 angle pdb=" CA ASP D 100 " pdb=" C ASP D 100 " pdb=" O ASP D 100 " ideal model delta sigma weight residual 121.68 118.10 3.58 1.18e+00 7.18e-01 9.19e+00 angle pdb=" N LEU B1141 " pdb=" CA LEU B1141 " pdb=" C LEU B1141 " ideal model delta sigma weight residual 114.62 111.22 3.40 1.14e+00 7.69e-01 8.90e+00 ... (remaining 37092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 15366 24.69 - 49.38: 1072 49.38 - 74.07: 170 74.07 - 98.76: 43 98.76 - 123.45: 32 Dihedral angle restraints: 16683 sinusoidal: 6957 harmonic: 9726 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 18.60 74.40 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 19.29 73.71 1 1.00e+01 1.00e-02 6.91e+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 93.00 22.84 70.16 1 1.00e+01 1.00e-02 6.34e+01 ... (remaining 16680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3476 0.054 - 0.108: 686 0.108 - 0.162: 121 0.162 - 0.216: 2 0.216 - 0.270: 4 Chirality restraints: 4289 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C1 NAG A1207 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1207 " pdb=" O5 NAG A1207 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4286 not shown) Planarity restraints: 4801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO B 987 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 56 " 0.037 5.00e-02 4.00e+02 5.73e-02 5.24e+00 pdb=" N PRO C 57 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO C 987 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.032 5.00e-02 4.00e+02 ... (remaining 4798 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2121 2.74 - 3.28: 26505 3.28 - 3.82: 42594 3.82 - 4.36: 47430 4.36 - 4.90: 83850 Nonbonded interactions: 202500 Sorted by model distance: nonbonded pdb=" OG SER D 7 " pdb=" OG SER D 21 " model vdw 2.197 3.040 nonbonded pdb=" O SER C 975 " pdb=" OG SER C 975 " model vdw 2.198 3.040 nonbonded pdb=" O4 NAG C1201 " pdb=" O7 NAG C1201 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.220 3.040 nonbonded pdb=" O ALA C 352 " pdb=" OG SER C 399 " model vdw 2.220 3.040 ... (remaining 202495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 458 or resid 460 through 476 or resid 478 throu \ gh 675 or resid 690 through 827 or resid 852 through 1146 or resid 1203 through \ 1209)) selection = (chain 'B' and (resid 14 through 458 or resid 460 through 476 or resid 478 throu \ gh 617 or resid 641 through 827 or resid 852 through 940 or resid 944 through 11 \ 46 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 458 or resid 460 through 476 or resid 478 throu \ gh 675 or resid 690 through 827 or resid 852 through 1146 or resid 1203 through \ 1209)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.380 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 : 0.004 0.072 27314 Z= 0.170 Angle : 0.605 10.700 37255 Z= 0.304 Chirality : 0.045 0.270 4289 Planarity : 0.004 0.059 4771 Dihedral : 17.270 123.447 10360 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 0.51 % Allowed : 23.67 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.14), residues: 3314 helix: 1.63 (0.22), residues: 619 sheet: 0.02 (0.22), residues: 587 loop : -1.65 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 995 TYR 0.020 0.001 TYR A1067 PHE 0.015 0.001 PHE C 562 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00360 (27253) covalent geometry : angle 0.59085 (37097) SS BOND : bond 0.00343 ( 25) SS BOND : angle 1.30015 ( 50) hydrogen bonds : bond 0.14375 ( 838) hydrogen bonds : angle 7.21374 ( 2316) link_BETA1-4 : bond 0.00484 ( 6) link_BETA1-4 : angle 2.79098 ( 18) link_NAG-ASN : bond 0.00424 ( 30) link_NAG-ASN : angle 2.27711 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 372 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 ARG cc_start: 0.7552 (tpt-90) cc_final: 0.7219 (ttt-90) REVERT: C 697 MET cc_start: 0.8407 (mtt) cc_final: 0.8057 (mtp) REVERT: C 808 ASP cc_start: 0.8424 (t0) cc_final: 0.8204 (t0) outliers start: 14 outliers final: 6 residues processed: 383 average time/residue: 0.1362 time to fit residues: 85.9419 Evaluate side-chains 363 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 357 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 804 GLN C 856 ASN C 907 ASN C 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.241108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.163711 restraints weight = 66769.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.161104 restraints weight = 28672.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.163911 restraints weight = 20366.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.165129 restraints weight = 14819.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.166060 restraints weight = 12600.418| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27314 Z= 0.175 Angle : 0.618 10.212 37255 Z= 0.305 Chirality : 0.046 0.325 4289 Planarity : 0.004 0.057 4771 Dihedral : 11.147 111.846 4377 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 3.08 % Allowed : 21.45 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.14), residues: 3314 helix: 1.89 (0.21), residues: 622 sheet: -0.01 (0.21), residues: 633 loop : -1.69 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 995 TYR 0.021 0.001 TYR B1067 PHE 0.017 0.001 PHE C 562 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00414 (27253) covalent geometry : angle 0.60465 (37097) SS BOND : bond 0.00358 ( 25) SS BOND : angle 1.39901 ( 50) hydrogen bonds : bond 0.04449 ( 838) hydrogen bonds : angle 5.70226 ( 2316) link_BETA1-4 : bond 0.00503 ( 6) link_BETA1-4 : angle 2.15975 ( 18) link_NAG-ASN : bond 0.00405 ( 30) link_NAG-ASN : angle 2.36514 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 371 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 821 LEU cc_start: 0.8679 (tt) cc_final: 0.8434 (tt) REVERT: A 935 GLN cc_start: 0.8682 (tt0) cc_final: 0.8414 (tt0) REVERT: A 979 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: A 1107 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7087 (mpp-170) REVERT: C 228 ASP cc_start: 0.6217 (m-30) cc_final: 0.5804 (m-30) REVERT: C 353 TRP cc_start: -0.1164 (OUTLIER) cc_final: -0.1884 (m-90) REVERT: C 385 THR cc_start: 0.2438 (OUTLIER) cc_final: 0.2207 (m) REVERT: C 697 MET cc_start: 0.8383 (mtt) cc_final: 0.8050 (mtp) REVERT: C 808 ASP cc_start: 0.8366 (t0) cc_final: 0.7993 (t0) REVERT: C 996 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8518 (mp) REVERT: C 1029 MET cc_start: 0.8864 (tpp) cc_final: 0.7985 (ttt) REVERT: C 1125 ASN cc_start: 0.8456 (p0) cc_final: 0.7619 (p0) outliers start: 89 outliers final: 45 residues processed: 427 average time/residue: 0.1360 time to fit residues: 96.0842 Evaluate side-chains 405 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 355 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 93 optimal weight: 0.6980 chunk 321 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 230 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 254 optimal weight: 0.4980 chunk 222 optimal weight: 6.9990 chunk 280 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 992 GLN C 804 GLN C 856 ASN C 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.242959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.164430 restraints weight = 80057.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.164155 restraints weight = 31959.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.164864 restraints weight = 22880.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.166711 restraints weight = 17113.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.170959 restraints weight = 13715.989| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27314 Z= 0.128 Angle : 0.579 9.795 37255 Z= 0.284 Chirality : 0.046 0.399 4289 Planarity : 0.004 0.056 4771 Dihedral : 8.900 105.859 4374 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 3.36 % Allowed : 21.38 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3314 helix: 2.05 (0.21), residues: 628 sheet: -0.07 (0.21), residues: 649 loop : -1.59 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.022 0.001 TYR A1067 PHE 0.016 0.001 PHE A 559 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00295 (27253) covalent geometry : angle 0.56213 (37097) SS BOND : bond 0.00355 ( 25) SS BOND : angle 1.29919 ( 50) hydrogen bonds : bond 0.03963 ( 838) hydrogen bonds : angle 5.33032 ( 2316) link_BETA1-4 : bond 0.00558 ( 6) link_BETA1-4 : angle 2.38722 ( 18) link_NAG-ASN : bond 0.00477 ( 30) link_NAG-ASN : angle 2.53375 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 375 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9152 (ptt) cc_final: 0.8869 (ptt) REVERT: A 825 LYS cc_start: 0.8382 (tptp) cc_final: 0.8066 (tptp) REVERT: A 979 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: A 1107 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7093 (mpp-170) REVERT: B 457 ARG cc_start: 0.7914 (tpt-90) cc_final: 0.7700 (tpt-90) REVERT: B 512 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8651 (t) REVERT: B 790 LYS cc_start: 0.8807 (mttt) cc_final: 0.8299 (mttm) REVERT: C 228 ASP cc_start: 0.6440 (m-30) cc_final: 0.6033 (m-30) REVERT: C 353 TRP cc_start: -0.1188 (OUTLIER) cc_final: -0.1880 (m-90) REVERT: C 385 THR cc_start: 0.2448 (OUTLIER) cc_final: 0.2215 (m) REVERT: C 697 MET cc_start: 0.8335 (mtt) cc_final: 0.7986 (mtp) REVERT: C 808 ASP cc_start: 0.8359 (t0) cc_final: 0.7976 (t0) REVERT: C 1029 MET cc_start: 0.8727 (tpp) cc_final: 0.8012 (ttt) REVERT: C 1125 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8130 (p0) REVERT: D 3 GLN cc_start: 0.7201 (mt0) cc_final: 0.6994 (mt0) outliers start: 97 outliers final: 52 residues processed: 438 average time/residue: 0.1280 time to fit residues: 93.9589 Evaluate side-chains 417 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 359 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 105 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 295 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.0070 chunk 181 optimal weight: 0.4980 chunk 290 optimal weight: 0.0980 chunk 280 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 804 GLN C 856 ASN C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.242866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.163565 restraints weight = 66372.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.161812 restraints weight = 29705.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.166423 restraints weight = 19053.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.167442 restraints weight = 12996.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.170571 restraints weight = 11236.740| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27314 Z= 0.127 Angle : 0.568 9.757 37255 Z= 0.280 Chirality : 0.045 0.327 4289 Planarity : 0.004 0.089 4771 Dihedral : 8.161 101.741 4374 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 3.49 % Allowed : 21.34 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.14), residues: 3314 helix: 2.10 (0.21), residues: 629 sheet: -0.12 (0.21), residues: 641 loop : -1.58 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.021 0.001 TYR A1067 PHE 0.019 0.001 PHE A 559 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00298 (27253) covalent geometry : angle 0.55242 (37097) SS BOND : bond 0.00340 ( 25) SS BOND : angle 1.51196 ( 50) hydrogen bonds : bond 0.03795 ( 838) hydrogen bonds : angle 5.16414 ( 2316) link_BETA1-4 : bond 0.00559 ( 6) link_BETA1-4 : angle 2.44177 ( 18) link_NAG-ASN : bond 0.00466 ( 30) link_NAG-ASN : angle 2.33737 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 378 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9188 (ptt) cc_final: 0.8899 (ptt) REVERT: A 825 LYS cc_start: 0.8327 (tptp) cc_final: 0.7974 (tptp) REVERT: A 979 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: A 1107 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7013 (mpp-170) REVERT: B 508 TYR cc_start: 0.7607 (m-80) cc_final: 0.7230 (m-80) REVERT: B 512 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8657 (t) REVERT: B 790 LYS cc_start: 0.8785 (mttt) cc_final: 0.8410 (mtpp) REVERT: B 804 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8426 (mm-40) REVERT: C 228 ASP cc_start: 0.6387 (m-30) cc_final: 0.5998 (m-30) REVERT: C 353 TRP cc_start: -0.1333 (OUTLIER) cc_final: -0.2011 (m-90) REVERT: C 385 THR cc_start: 0.2416 (OUTLIER) cc_final: 0.2181 (m) REVERT: C 808 ASP cc_start: 0.8460 (t0) cc_final: 0.8036 (t0) REVERT: C 996 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8481 (mp) REVERT: C 1029 MET cc_start: 0.8798 (tpp) cc_final: 0.7952 (ttm) REVERT: C 1125 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8163 (p0) REVERT: D 3 GLN cc_start: 0.7181 (mt0) cc_final: 0.6973 (mt0) outliers start: 101 outliers final: 63 residues processed: 446 average time/residue: 0.1290 time to fit residues: 96.3417 Evaluate side-chains 434 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 364 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2796 > 50: distance: 55 - 77: 5.026 distance: 59 - 82: 7.207 distance: 66 - 90: 5.598 distance: 72 - 77: 5.247 distance: 73 - 99: 7.918 distance: 77 - 78: 7.893 distance: 78 - 81: 11.283 distance: 79 - 80: 5.674 distance: 79 - 82: 5.134 distance: 80 - 110: 7.664 distance: 83 - 86: 6.668 distance: 84 - 85: 4.987 distance: 85 - 118: 11.736 distance: 86 - 87: 6.999 distance: 87 - 88: 4.666 distance: 87 - 89: 8.814 distance: 91 - 92: 3.048 distance: 91 - 94: 3.520 distance: 93 - 124: 11.424 distance: 96 - 97: 3.962 distance: 96 - 98: 5.339 distance: 100 - 101: 4.833 distance: 100 - 103: 5.347 distance: 101 - 102: 4.732 distance: 101 - 110: 3.223 distance: 102 - 129: 7.099 distance: 103 - 104: 5.655 distance: 104 - 105: 4.973 distance: 104 - 106: 5.572 distance: 105 - 107: 4.397 distance: 106 - 108: 4.043 distance: 107 - 109: 3.895 distance: 108 - 109: 4.839 distance: 110 - 111: 6.743 distance: 111 - 112: 4.213 distance: 111 - 114: 7.104 distance: 112 - 113: 5.645 distance: 113 - 137: 26.006 distance: 114 - 115: 5.884 distance: 115 - 116: 4.211 distance: 115 - 117: 7.466 distance: 119 - 120: 6.426 distance: 119 - 122: 4.842 distance: 120 - 121: 4.180 distance: 120 - 124: 6.036 distance: 121 - 141: 18.101 distance: 122 - 123: 8.799 distance: 125 - 126: 8.909 distance: 125 - 128: 11.538 distance: 126 - 127: 10.595 distance: 126 - 129: 3.527 distance: 129 - 130: 25.464 distance: 130 - 131: 19.566 distance: 130 - 133: 21.550 distance: 131 - 132: 7.190 distance: 131 - 137: 55.451 distance: 133 - 134: 31.361 distance: 133 - 135: 17.082 distance: 134 - 136: 23.990 distance: 137 - 138: 8.157 distance: 138 - 139: 32.677 distance: 139 - 140: 3.215 distance: 139 - 141: 20.025 distance: 141 - 142: 7.759 distance: 142 - 143: 8.484 distance: 142 - 145: 10.376 distance: 143 - 144: 7.295 distance: 143 - 150: 5.512 distance: 144 - 170: 4.656 distance: 145 - 146: 3.430 distance: 146 - 147: 4.301 distance: 147 - 148: 6.686 distance: 148 - 149: 6.381