Starting phenix.real_space_refine on Thu Mar 5 22:40:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wg8_32480/03_2026/7wg8_32480.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg8_32480/03_2026/7wg8_32480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wg8_32480/03_2026/7wg8_32480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg8_32480/03_2026/7wg8_32480.map" model { file = "/net/cci-nas-00/data/ceres_data/7wg8_32480/03_2026/7wg8_32480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg8_32480/03_2026/7wg8_32480.cif" } resolution = 3.9 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= 0.001 sd= 0.050 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 117 5.16 5 C 16308 2.51 5 N 4218 2.21 5 O 4986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25629 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "A" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.61, per 1000 atoms: 0.26 Number of scatterers: 25629 At special positions: 0 Unit cell: (149.8, 154.08, 181.9, 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 117 16.00 O 4986 8.00 N 4218 7.00 C 16308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " 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 D 1 " - " NAG D 2 " " 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-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 232 " " NAG A1204 " - " ASN A 280 " " NAG A1205 " - " ASN A 329 " " NAG A1206 " - " ASN A 341 " " NAG A1207 " - " ASN A 601 " " NAG A1208 " - " ASN A 614 " " NAG A1209 " - " ASN A 655 " " NAG A1210 " - " ASN A 707 " " NAG A1211 " - " ASN A1072 " " NAG A1212 " - " ASN A1096 " " NAG A1213 " - " ASN A1132 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 232 " " NAG B1204 " - " ASN B 280 " " NAG B1205 " - " ASN B 329 " " NAG B1206 " - " ASN B 341 " " NAG B1207 " - " ASN B 601 " " NAG B1208 " - " ASN B 614 " " NAG B1209 " - " ASN B 655 " " NAG B1210 " - " ASN B 707 " " NAG B1211 " - " ASN B1072 " " NAG B1212 " - " ASN B1096 " " NAG B1213 " - " ASN B1132 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 232 " " NAG C1204 " - " ASN C 280 " " NAG C1205 " - " ASN C 329 " " NAG C1206 " - " ASN C 341 " " NAG C1207 " - " ASN C 601 " " NAG C1208 " - " ASN C 614 " " NAG C1209 " - " ASN C 655 " " NAG C1210 " - " ASN C 707 " " NAG C1211 " - " ASN C1072 " " NAG C1212 " - " ASN C1096 " " NAG C1213 " - " ASN C1132 " " NAG D 1 " - " ASN B 715 " " NAG E 1 " - " ASN B 799 " " NAG F 1 " - " ASN A 715 " " NAG G 1 " - " ASN A 799 " " NAG H 1 " - " ASN C 715 " " NAG I 1 " - " ASN C 799 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 51 sheets defined 24.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 341 removed outlier: 4.222A pdb=" N VAL B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.391A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 388 removed outlier: 3.557A pdb=" N LYS B 384 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASN B 386 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 387 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 388 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 5.146A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.527A pdb=" N ASN B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.198A pdb=" N LEU B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 781 removed outlier: 3.688A pdb=" N PHE B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.714A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.553A pdb=" N PHE B 853 " --> pdb=" O CYS B 849 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN B 854 " --> pdb=" O ALA B 850 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLY B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 849 through 855' Processing helix chain 'B' and resid 864 through 882 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 905 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.676A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 937 removed outlier: 4.246A pdb=" N ASN B 923 " --> pdb=" O LYS B 919 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 962 Processing helix chain 'B' and resid 963 through 966 removed outlier: 3.807A pdb=" N SER B 966 " --> pdb=" O GLN B 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 963 through 966' Processing helix chain 'B' and resid 974 through 980 Processing helix chain 'B' and resid 981 through 982 No H-bonds generated for 'chain 'B' and resid 981 through 982' Processing helix chain 'B' and resid 983 through 986 Processing helix chain 'B' and resid 987 through 1031 removed outlier: 4.900A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 994 " --> pdb=" O GLN B 990 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B1018 " --> pdb=" O ALA B1014 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B1019 " --> pdb=" O GLU B1015 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1116 No H-bonds generated for 'chain 'B' and resid 1114 through 1116' Processing helix chain 'B' and resid 1139 through 1144 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 335 through 341 removed outlier: 4.156A pdb=" N VAL A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.458A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.503A pdb=" N LYS A 384 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 388 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.881A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.747A pdb=" N ASN A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.700A pdb=" N SER A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 744 through 753 removed outlier: 4.212A pdb=" N LEU A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 781 removed outlier: 4.098A pdb=" N PHE A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.653A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 removed outlier: 3.527A pdb=" N PHE A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 854' Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.708A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.729A pdb=" N ALA A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 906 removed outlier: 3.594A pdb=" N GLN A 899 " --> pdb=" O PRO A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.633A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 916' Processing helix chain 'A' and resid 917 through 938 removed outlier: 3.563A pdb=" N PHE A 925 " --> pdb=" O ILE A 921 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER A 938 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 962 removed outlier: 3.581A pdb=" N GLN A 952 " --> pdb=" O ASN A 948 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 953 " --> pdb=" O VAL A 949 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 959 " --> pdb=" O GLN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 966 removed outlier: 3.862A pdb=" N SER A 966 " --> pdb=" O GLN A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 963 through 966' Processing helix chain 'A' and resid 974 through 982 Processing helix chain 'A' and resid 983 through 986 removed outlier: 3.617A pdb=" N GLU A 986 " --> pdb=" O ASP A 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 983 through 986' Processing helix chain 'A' and resid 987 through 1031 removed outlier: 4.792A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 362 through 369 removed outlier: 4.502A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.520A pdb=" N LYS C 384 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 4.877A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 409 " --> pdb=" O ARG C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.594A pdb=" N ASN C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 753 removed outlier: 4.234A pdb=" N LEU C 750 " --> pdb=" O GLU C 746 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 781 removed outlier: 4.091A pdb=" N PHE C 780 " --> pdb=" O THR C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.666A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.798A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 905 Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.750A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 938 removed outlier: 3.539A pdb=" N ASN C 923 " --> pdb=" O LYS C 919 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 938 " --> pdb=" O ASP C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 962 Processing helix chain 'C' and resid 963 through 966 removed outlier: 3.886A pdb=" N SER C 966 " --> pdb=" O GLN C 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 963 through 966' Processing helix chain 'C' and resid 974 through 982 Processing helix chain 'C' and resid 983 through 986 removed outlier: 3.736A pdb=" N GLU C 986 " --> pdb=" O ASP C 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 983 through 986' Processing helix chain 'C' and resid 987 through 1031 removed outlier: 4.945A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C1018 " --> pdb=" O ALA C1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C1019 " --> pdb=" O GLU C1015 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1116 No H-bonds generated for 'chain 'C' and resid 1114 through 1116' Processing helix chain 'C' and resid 1139 through 1145 Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.562A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.609A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 67 removed outlier: 5.303A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.621A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 126 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B 128 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 130 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.599A pdb=" N LEU B 648 " --> pdb=" O PHE B 641 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 316 through 317 removed outlier: 3.555A pdb=" N GLY B 591 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 324 Processing sheet with id=AA8, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'B' and resid 359 through 360 removed outlier: 7.430A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AB2, first strand: chain 'B' and resid 652 through 653 removed outlier: 5.903A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 710 through 713 Processing sheet with id=AB4, first strand: chain 'B' and resid 716 through 726 removed outlier: 3.663A pdb=" N GLU B 723 " --> pdb=" O PHE B1060 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY B1057 " --> pdb=" O SER B1053 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER B1053 " --> pdb=" O GLY B1057 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B1059 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B1061 " --> pdb=" O SER B1049 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER B1049 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B1063 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 732 through 734 Processing sheet with id=AB6, first strand: chain 'B' and resid 1079 through 1080 Processing sheet with id=AB7, first strand: chain 'B' and resid 1087 through 1088 Processing sheet with id=AB8, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AB9, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.099A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AC2, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.483A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.761A pdb=" N GLN A 237 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA A 241 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 101 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL A 126 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 128 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A 130 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 309 through 312 Processing sheet with id=AC5, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AC6, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AC7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AC8, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AC9, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.179A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 710 through 711 Processing sheet with id=AD2, first strand: chain 'A' and resid 716 through 726 removed outlier: 3.865A pdb=" N GLU A 723 " --> pdb=" O PHE A1060 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A1063 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 716 through 726 removed outlier: 3.865A pdb=" N GLU A 723 " --> pdb=" O PHE A1060 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 732 through 734 Processing sheet with id=AD5, first strand: chain 'A' and resid 1118 through 1119 removed outlier: 3.511A pdb=" N PHE A1119 " --> pdb=" O PHE A1087 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1092 through 1094 Processing sheet with id=AD7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.695A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.595A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 63 through 67 removed outlier: 5.566A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.606A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 126 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE C 128 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 130 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 309 through 312 removed outlier: 3.614A pdb=" N LEU C 648 " --> pdb=" O PHE C 641 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 641 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 316 through 317 Processing sheet with id=AE4, first strand: chain 'C' and resid 322 through 324 Processing sheet with id=AE5, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE6, first strand: chain 'C' and resid 359 through 360 removed outlier: 7.283A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 450 through 452 removed outlier: 3.579A pdb=" N TYR C 451 " --> pdb=" O GLN C 491 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 491 " --> pdb=" O TYR C 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 652 through 653 removed outlier: 5.836A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 710 through 713 Processing sheet with id=AF1, first strand: chain 'C' and resid 716 through 721 Processing sheet with id=AF2, first strand: chain 'C' and resid 716 through 721 removed outlier: 3.645A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 732 through 734 Processing sheet with id=AF4, first strand: chain 'C' and resid 1079 through 1080 Processing sheet with id=AF5, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AF6, first strand: chain 'C' and resid 1092 through 1095 903 hydrogen bonds defined for protein. 2430 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: 6.26 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8175 1.35 - 1.47: 6588 1.47 - 1.59: 11292 1.59 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 26202 Sorted by residual: bond pdb=" C1 NAG C1202 " pdb=" O5 NAG C1202 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" C1 NAG B1207 " pdb=" O5 NAG B1207 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" C1 NAG C1205 " pdb=" O5 NAG C1205 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG A1203 " pdb=" O5 NAG A1203 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C1 NAG B1203 " pdb=" O5 NAG B1203 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 26197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 35097 2.08 - 4.15: 499 4.15 - 6.23: 30 6.23 - 8.30: 11 8.30 - 10.38: 3 Bond angle restraints: 35640 Sorted by residual: angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.78 -4.08 1.22e+00 6.72e-01 1.12e+01 angle pdb=" CA PRO B 984 " pdb=" C PRO B 984 " pdb=" N PRO B 985 " ideal model delta sigma weight residual 117.93 121.22 -3.29 1.20e+00 6.94e-01 7.52e+00 angle pdb=" C ASP C 566 " pdb=" N ILE C 567 " pdb=" CA ILE C 567 " ideal model delta sigma weight residual 121.97 117.05 4.92 1.80e+00 3.09e-01 7.47e+00 angle pdb=" C ASP B 566 " pdb=" N ILE B 567 " pdb=" CA ILE B 567 " ideal model delta sigma weight residual 121.97 117.21 4.76 1.80e+00 3.09e-01 7.00e+00 angle pdb=" N PRO A 984 " pdb=" CA PRO A 984 " pdb=" C PRO A 984 " ideal model delta sigma weight residual 110.70 113.79 -3.09 1.22e+00 6.72e-01 6.43e+00 ... (remaining 35635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 14603 17.70 - 35.40: 1355 35.40 - 53.09: 249 53.09 - 70.79: 55 70.79 - 88.49: 34 Dihedral angle restraints: 16296 sinusoidal: 7023 harmonic: 9273 Sorted by residual: dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 169.63 -76.63 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual 93.00 169.39 -76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS B 478 " pdb=" SG CYS B 478 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual 93.00 168.79 -75.79 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 16293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3684 0.072 - 0.145: 476 0.145 - 0.217: 9 0.217 - 0.290: 3 0.290 - 0.362: 1 Chirality restraints: 4173 Sorted by residual: chirality pdb=" C1 NAG B1210 " pdb=" ND2 ASN B 707 " pdb=" C2 NAG B1210 " pdb=" O5 NAG B1210 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C1 NAG A1202 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1202 " pdb=" O5 NAG A1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C1 NAG B1207 " pdb=" ND2 ASN B 601 " pdb=" C2 NAG B1207 " pdb=" O5 NAG B1207 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4170 not shown) Planarity restraints: 4602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 984 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO B 985 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 985 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 985 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 984 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 985 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 985 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 985 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.022 2.00e-02 2.50e+03 2.08e-02 5.42e+00 pdb=" CG ASN A 61 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1201 " -0.024 2.00e-02 2.50e+03 ... (remaining 4599 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 885 2.70 - 3.25: 25573 3.25 - 3.80: 39034 3.80 - 4.35: 46744 4.35 - 4.90: 79599 Nonbonded interactions: 191835 Sorted by model distance: nonbonded pdb=" O GLY A 878 " pdb=" OG SER A 882 " model vdw 2.155 3.040 nonbonded pdb=" OG SER A 116 " pdb=" O CYS A 131 " model vdw 2.167 3.040 nonbonded pdb=" O GLY C 878 " pdb=" OG SER C 882 " model vdw 2.202 3.040 nonbonded pdb=" NE2 GLN B 561 " pdb=" O LYS C 41 " model vdw 2.210 3.120 nonbonded pdb=" OG SER B 116 " pdb=" O CYS B 131 " model vdw 2.211 3.040 ... (remaining 191830 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 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: 2.990 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.140 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.003 0.039 26295 Z= 0.167 Angle : 0.614 10.378 35877 Z= 0.306 Chirality : 0.045 0.362 4173 Planarity : 0.004 0.065 4557 Dihedral : 13.845 88.488 10206 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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 are not related in a simple way. whole: -1.10 (0.15), residues: 3153 helix: 0.74 (0.22), residues: 645 sheet: 0.16 (0.21), residues: 606 loop : -1.65 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 317 TYR 0.019 0.001 TYR B 902 PHE 0.014 0.001 PHE B 454 TRP 0.017 0.001 TRP A 884 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd covalent geometry : bond 0.00347 (26202) covalent geometry : angle 0.59360 (35640) SS BOND : bond 0.00189 ( 42) SS BOND : angle 1.16505 ( 84) hydrogen bonds : bond 0.14600 ( 886) hydrogen bonds : angle 6.35583 ( 2430) link_BETA1-4 : bond 0.00290 ( 6) link_BETA1-4 : angle 0.96950 ( 18) link_NAG-ASN : bond 0.00401 ( 45) link_NAG-ASN : angle 2.50279 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 PHE cc_start: 0.7838 (m-80) cc_final: 0.7501 (m-80) REVERT: B 582 ILE cc_start: 0.8065 (mm) cc_final: 0.7813 (mm) REVERT: B 985 PRO cc_start: 0.8905 (Cg_exo) cc_final: 0.8588 (Cg_endo) REVERT: C 90 VAL cc_start: 0.9030 (p) cc_final: 0.8743 (m) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1633 time to fit residues: 38.3285 Evaluate side-chains 92 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.098282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065399 restraints weight = 86269.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.066426 restraints weight = 51202.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066947 restraints weight = 33971.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067096 restraints weight = 32336.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.067432 restraints weight = 28368.330| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26295 Z= 0.121 Angle : 0.568 10.411 35877 Z= 0.285 Chirality : 0.044 0.341 4173 Planarity : 0.004 0.074 4557 Dihedral : 6.805 59.115 4488 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 0.36 % Allowed : 6.29 % Favored : 93.35 % 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 are not related in a simple way. whole: -0.88 (0.15), residues: 3153 helix: 1.09 (0.21), residues: 663 sheet: 0.33 (0.22), residues: 588 loop : -1.59 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 317 TYR 0.017 0.001 TYR C1065 PHE 0.015 0.001 PHE A 79 TRP 0.014 0.001 TRP A 434 HIS 0.002 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00269 (26202) covalent geometry : angle 0.54963 (35640) SS BOND : bond 0.00199 ( 42) SS BOND : angle 1.04134 ( 84) hydrogen bonds : bond 0.04782 ( 886) hydrogen bonds : angle 5.14411 ( 2430) link_BETA1-4 : bond 0.00305 ( 6) link_BETA1-4 : angle 0.82643 ( 18) link_NAG-ASN : bond 0.00450 ( 45) link_NAG-ASN : angle 2.28246 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 LYS cc_start: 0.8431 (mmtm) cc_final: 0.7624 (pttt) REVERT: B 90 VAL cc_start: 0.8974 (p) cc_final: 0.8760 (m) REVERT: B 189 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6799 (tt0) REVERT: B 582 ILE cc_start: 0.8086 (mm) cc_final: 0.7779 (mm) REVERT: B 985 PRO cc_start: 0.8926 (Cg_exo) cc_final: 0.8596 (Cg_endo) REVERT: C 90 VAL cc_start: 0.9005 (p) cc_final: 0.8710 (m) REVERT: C 189 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6882 (mt-10) outliers start: 10 outliers final: 7 residues processed: 120 average time/residue: 0.1711 time to fit residues: 34.0392 Evaluate side-chains 103 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 961 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 86 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 106 optimal weight: 40.0000 chunk 55 optimal weight: 4.9990 chunk 273 optimal weight: 0.0980 chunk 116 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 183 optimal weight: 0.0070 chunk 79 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.098043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.066819 restraints weight = 88554.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.066900 restraints weight = 51184.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067297 restraints weight = 36734.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067687 restraints weight = 34727.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.067853 restraints weight = 29599.427| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26295 Z= 0.118 Angle : 0.541 9.947 35877 Z= 0.272 Chirality : 0.043 0.347 4173 Planarity : 0.004 0.074 4557 Dihedral : 6.212 57.909 4488 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 0.50 % Allowed : 9.17 % Favored : 90.33 % 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 are not related in a simple way. whole: -0.78 (0.15), residues: 3153 helix: 1.25 (0.21), residues: 663 sheet: 0.36 (0.22), residues: 585 loop : -1.54 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 406 TYR 0.018 0.001 TYR A 902 PHE 0.013 0.001 PHE A 79 TRP 0.029 0.001 TRP B 434 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00268 (26202) covalent geometry : angle 0.52346 (35640) SS BOND : bond 0.00169 ( 42) SS BOND : angle 0.92451 ( 84) hydrogen bonds : bond 0.04359 ( 886) hydrogen bonds : angle 4.91352 ( 2430) link_BETA1-4 : bond 0.00275 ( 6) link_BETA1-4 : angle 0.92597 ( 18) link_NAG-ASN : bond 0.00424 ( 45) link_NAG-ASN : angle 2.21971 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8956 (p) cc_final: 0.8712 (m) REVERT: B 325 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8701 (t) REVERT: B 582 ILE cc_start: 0.8103 (mm) cc_final: 0.7763 (mm) REVERT: B 985 PRO cc_start: 0.8900 (Cg_exo) cc_final: 0.8573 (Cg_endo) REVERT: C 90 VAL cc_start: 0.8985 (p) cc_final: 0.8679 (m) REVERT: C 175 MET cc_start: -0.2018 (mtt) cc_final: -0.3243 (mmm) REVERT: C 184 PHE cc_start: 0.7837 (m-80) cc_final: 0.7528 (m-80) REVERT: C 189 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6861 (mt-10) outliers start: 14 outliers final: 8 residues processed: 112 average time/residue: 0.1689 time to fit residues: 31.6951 Evaluate side-chains 97 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 961 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 271 optimal weight: 0.0980 chunk 280 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 250 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.097739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065801 restraints weight = 88350.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065539 restraints weight = 55454.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.066315 restraints weight = 40521.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066577 restraints weight = 35936.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066726 restraints weight = 31599.990| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26295 Z= 0.127 Angle : 0.543 10.079 35877 Z= 0.272 Chirality : 0.043 0.353 4173 Planarity : 0.004 0.075 4557 Dihedral : 5.750 55.999 4488 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 0.90 % Allowed : 11.40 % Favored : 87.70 % 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 are not related in a simple way. whole: -0.72 (0.15), residues: 3153 helix: 1.32 (0.21), residues: 663 sheet: 0.39 (0.23), residues: 546 loop : -1.47 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1105 TYR 0.017 0.001 TYR B 902 PHE 0.013 0.001 PHE B 184 TRP 0.034 0.001 TRP A 434 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00294 (26202) covalent geometry : angle 0.52564 (35640) SS BOND : bond 0.00169 ( 42) SS BOND : angle 0.96631 ( 84) hydrogen bonds : bond 0.04236 ( 886) hydrogen bonds : angle 4.81814 ( 2430) link_BETA1-4 : bond 0.00231 ( 6) link_BETA1-4 : angle 0.94675 ( 18) link_NAG-ASN : bond 0.00418 ( 45) link_NAG-ASN : angle 2.20396 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8957 (p) cc_final: 0.8696 (m) REVERT: B 189 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7094 (mt-10) REVERT: B 193 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8495 (tttt) REVERT: B 582 ILE cc_start: 0.8109 (mm) cc_final: 0.7755 (mm) REVERT: B 985 PRO cc_start: 0.8886 (Cg_exo) cc_final: 0.8555 (Cg_endo) REVERT: B 1102 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8805 (t) REVERT: C 90 VAL cc_start: 0.8997 (p) cc_final: 0.8691 (m) REVERT: C 175 MET cc_start: -0.1929 (mtt) cc_final: -0.3066 (mmm) REVERT: C 184 PHE cc_start: 0.7871 (m-80) cc_final: 0.7559 (m-80) REVERT: C 189 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6903 (mt-10) REVERT: C 325 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8699 (t) outliers start: 25 outliers final: 15 residues processed: 116 average time/residue: 0.1654 time to fit residues: 32.1841 Evaluate side-chains 100 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 961 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 299 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 134 GLN A 205 HIS A 496 GLN A 893 GLN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.094572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.062013 restraints weight = 88756.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.061967 restraints weight = 54882.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.062812 restraints weight = 38644.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.063134 restraints weight = 33614.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.063275 restraints weight = 30205.428| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 26295 Z= 0.322 Angle : 0.726 10.226 35877 Z= 0.366 Chirality : 0.047 0.393 4173 Planarity : 0.004 0.074 4557 Dihedral : 6.182 56.558 4488 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.77 % Rotamer: Outliers : 1.58 % Allowed : 13.66 % Favored : 84.75 % 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 are not related in a simple way. whole: -1.08 (0.15), residues: 3153 helix: 0.83 (0.21), residues: 645 sheet: 0.34 (0.23), residues: 543 loop : -1.66 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1105 TYR 0.022 0.002 TYR C1065 PHE 0.020 0.002 PHE A 925 TRP 0.023 0.002 TRP B 434 HIS 0.005 0.001 HIS C 653 Details of bonding type rmsd covalent geometry : bond 0.00743 (26202) covalent geometry : angle 0.70828 (35640) SS BOND : bond 0.00502 ( 42) SS BOND : angle 1.48702 ( 84) hydrogen bonds : bond 0.05850 ( 886) hydrogen bonds : angle 5.50644 ( 2430) link_BETA1-4 : bond 0.00065 ( 6) link_BETA1-4 : angle 1.40906 ( 18) link_NAG-ASN : bond 0.00521 ( 45) link_NAG-ASN : angle 2.46731 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9010 (p) cc_final: 0.8723 (m) REVERT: B 325 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8885 (t) REVERT: B 582 ILE cc_start: 0.8173 (mm) cc_final: 0.7810 (mm) REVERT: B 985 PRO cc_start: 0.9007 (Cg_exo) cc_final: 0.8733 (Cg_endo) REVERT: A 153 MET cc_start: 0.2586 (tmm) cc_final: 0.2384 (tmm) REVERT: A 366 LEU cc_start: 0.9460 (mm) cc_final: 0.9250 (mp) REVERT: A 582 ILE cc_start: 0.8561 (mt) cc_final: 0.8083 (mt) REVERT: C 90 VAL cc_start: 0.8998 (p) cc_final: 0.8667 (m) REVERT: C 175 MET cc_start: -0.2171 (mtt) cc_final: -0.2687 (mmt) REVERT: C 184 PHE cc_start: 0.7824 (m-80) cc_final: 0.7620 (m-80) outliers start: 44 outliers final: 28 residues processed: 129 average time/residue: 0.1653 time to fit residues: 35.6406 Evaluate side-chains 111 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 272 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 70 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.096369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.063556 restraints weight = 85850.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063601 restraints weight = 55697.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064453 restraints weight = 38518.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064646 restraints weight = 34411.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064826 restraints weight = 30709.603| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26295 Z= 0.143 Angle : 0.573 10.390 35877 Z= 0.287 Chirality : 0.044 0.367 4173 Planarity : 0.004 0.073 4557 Dihedral : 5.698 59.212 4488 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 1.51 % Allowed : 14.85 % Favored : 83.64 % 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 are not related in a simple way. whole: -0.91 (0.15), residues: 3153 helix: 1.13 (0.21), residues: 663 sheet: 0.33 (0.22), residues: 558 loop : -1.61 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.013 0.001 PHE A 495 TRP 0.026 0.001 TRP B 434 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00327 (26202) covalent geometry : angle 0.55426 (35640) SS BOND : bond 0.00210 ( 42) SS BOND : angle 1.21323 ( 84) hydrogen bonds : bond 0.04655 ( 886) hydrogen bonds : angle 4.97860 ( 2430) link_BETA1-4 : bond 0.00277 ( 6) link_BETA1-4 : angle 0.94732 ( 18) link_NAG-ASN : bond 0.00432 ( 45) link_NAG-ASN : angle 2.28977 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8981 (p) cc_final: 0.8697 (m) REVERT: B 193 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8536 (tttt) REVERT: B 325 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8855 (t) REVERT: B 582 ILE cc_start: 0.8120 (mm) cc_final: 0.7522 (mm) REVERT: B 882 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8384 (t) REVERT: B 985 PRO cc_start: 0.8991 (Cg_exo) cc_final: 0.8715 (Cg_endo) REVERT: A 366 LEU cc_start: 0.9455 (mm) cc_final: 0.9238 (mp) REVERT: A 582 ILE cc_start: 0.8536 (mt) cc_final: 0.8013 (mt) REVERT: C 90 VAL cc_start: 0.8984 (p) cc_final: 0.8650 (m) REVERT: C 175 MET cc_start: -0.1993 (mtt) cc_final: -0.3159 (mmm) REVERT: C 184 PHE cc_start: 0.7925 (m-80) cc_final: 0.7675 (m-80) REVERT: C 227 LEU cc_start: 0.9160 (mm) cc_final: 0.8915 (mm) REVERT: C 325 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8812 (t) outliers start: 42 outliers final: 24 residues processed: 130 average time/residue: 0.1597 time to fit residues: 35.0797 Evaluate side-chains 111 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 99 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.095158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062780 restraints weight = 88410.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.062787 restraints weight = 54315.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063556 restraints weight = 37991.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063928 restraints weight = 33231.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064057 restraints weight = 29751.639| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26295 Z= 0.229 Angle : 0.646 10.583 35877 Z= 0.322 Chirality : 0.045 0.386 4173 Planarity : 0.004 0.073 4557 Dihedral : 5.762 52.817 4488 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.10 % Favored : 92.86 % Rotamer: Outliers : 1.62 % Allowed : 15.64 % Favored : 82.74 % 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 are not related in a simple way. whole: -1.04 (0.15), residues: 3153 helix: 1.00 (0.21), residues: 657 sheet: 0.21 (0.22), residues: 558 loop : -1.67 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 406 TYR 0.030 0.001 TYR A 263 PHE 0.030 0.001 PHE A 184 TRP 0.046 0.002 TRP A 434 HIS 0.003 0.001 HIS C 653 Details of bonding type rmsd covalent geometry : bond 0.00533 (26202) covalent geometry : angle 0.62794 (35640) SS BOND : bond 0.00194 ( 42) SS BOND : angle 1.20594 ( 84) hydrogen bonds : bond 0.05161 ( 886) hydrogen bonds : angle 5.22938 ( 2430) link_BETA1-4 : bond 0.00149 ( 6) link_BETA1-4 : angle 1.20237 ( 18) link_NAG-ASN : bond 0.00451 ( 45) link_NAG-ASN : angle 2.38045 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 0.969 Fit side-chains REVERT: B 90 VAL cc_start: 0.8979 (p) cc_final: 0.8680 (m) REVERT: B 325 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8890 (t) REVERT: B 582 ILE cc_start: 0.8163 (mm) cc_final: 0.7551 (mm) REVERT: B 882 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8421 (t) REVERT: A 582 ILE cc_start: 0.8565 (mt) cc_final: 0.8060 (mt) REVERT: A 898 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7655 (mtm) REVERT: C 41 LYS cc_start: 0.8206 (ptmt) cc_final: 0.7851 (ptmt) REVERT: C 90 VAL cc_start: 0.8972 (p) cc_final: 0.8652 (m) REVERT: C 175 MET cc_start: -0.2242 (mtt) cc_final: -0.3221 (mmm) REVERT: C 184 PHE cc_start: 0.7859 (m-80) cc_final: 0.7616 (m-80) REVERT: C 189 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7107 (mt-10) REVERT: C 227 LEU cc_start: 0.9153 (mm) cc_final: 0.8884 (mm) REVERT: C 325 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8866 (t) REVERT: C 924 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7930 (mp10) outliers start: 45 outliers final: 32 residues processed: 134 average time/residue: 0.1570 time to fit residues: 35.6816 Evaluate side-chains 122 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 86 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 315 optimal weight: 8.9990 chunk 48 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN B 205 HIS ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.097158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.064271 restraints weight = 86434.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065191 restraints weight = 51497.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065482 restraints weight = 35549.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.065923 restraints weight = 33610.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.065996 restraints weight = 29355.367| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26295 Z= 0.104 Angle : 0.558 10.760 35877 Z= 0.277 Chirality : 0.043 0.359 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.171 52.172 4488 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 1.29 % Allowed : 16.22 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 3153 helix: 1.37 (0.21), residues: 663 sheet: 0.31 (0.22), residues: 558 loop : -1.55 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 406 TYR 0.015 0.001 TYR A1065 PHE 0.022 0.001 PHE A 184 TRP 0.032 0.001 TRP A 434 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00232 (26202) covalent geometry : angle 0.53959 (35640) SS BOND : bond 0.00222 ( 42) SS BOND : angle 1.10761 ( 84) hydrogen bonds : bond 0.04048 ( 886) hydrogen bonds : angle 4.73445 ( 2430) link_BETA1-4 : bond 0.00301 ( 6) link_BETA1-4 : angle 0.75615 ( 18) link_NAG-ASN : bond 0.00443 ( 45) link_NAG-ASN : angle 2.23585 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8973 (p) cc_final: 0.8677 (m) REVERT: B 171 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8505 (pp30) REVERT: B 263 TYR cc_start: 0.7837 (p90) cc_final: 0.7602 (p90) REVERT: B 325 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8789 (t) REVERT: B 582 ILE cc_start: 0.8175 (mm) cc_final: 0.7553 (mm) REVERT: B 882 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8261 (t) REVERT: B 985 PRO cc_start: 0.8973 (Cg_exo) cc_final: 0.8698 (Cg_endo) REVERT: C 41 LYS cc_start: 0.8162 (ptmt) cc_final: 0.7769 (ptmt) REVERT: C 90 VAL cc_start: 0.8958 (p) cc_final: 0.8642 (m) REVERT: C 175 MET cc_start: -0.2547 (mtt) cc_final: -0.2903 (mmt) REVERT: C 184 PHE cc_start: 0.7896 (m-80) cc_final: 0.7624 (m-80) REVERT: C 189 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7129 (mt-10) REVERT: C 227 LEU cc_start: 0.9148 (mm) cc_final: 0.8897 (mm) REVERT: C 325 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8762 (t) REVERT: C 924 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8040 (mp10) outliers start: 36 outliers final: 25 residues processed: 127 average time/residue: 0.1598 time to fit residues: 34.4148 Evaluate side-chains 120 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 298 optimal weight: 0.4980 chunk 204 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 216 optimal weight: 4.9990 chunk 304 optimal weight: 0.9980 chunk 317 optimal weight: 0.9990 chunk 259 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.096732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064811 restraints weight = 88226.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064683 restraints weight = 55027.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.065397 restraints weight = 39084.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065737 restraints weight = 35280.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065848 restraints weight = 30767.722| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26295 Z= 0.133 Angle : 0.569 10.899 35877 Z= 0.282 Chirality : 0.043 0.370 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.087 52.332 4488 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 1.29 % Allowed : 16.40 % Favored : 82.31 % 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 are not related in a simple way. whole: -0.78 (0.15), residues: 3153 helix: 1.37 (0.21), residues: 663 sheet: 0.31 (0.22), residues: 558 loop : -1.55 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 406 TYR 0.027 0.001 TYR A 263 PHE 0.020 0.001 PHE A 184 TRP 0.030 0.001 TRP A 434 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00310 (26202) covalent geometry : angle 0.55145 (35640) SS BOND : bond 0.00175 ( 42) SS BOND : angle 1.06864 ( 84) hydrogen bonds : bond 0.04150 ( 886) hydrogen bonds : angle 4.78770 ( 2430) link_BETA1-4 : bond 0.00246 ( 6) link_BETA1-4 : angle 0.91722 ( 18) link_NAG-ASN : bond 0.00408 ( 45) link_NAG-ASN : angle 2.24476 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8971 (p) cc_final: 0.8673 (m) REVERT: B 263 TYR cc_start: 0.7841 (p90) cc_final: 0.7606 (p90) REVERT: B 325 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8833 (t) REVERT: B 582 ILE cc_start: 0.8187 (mm) cc_final: 0.7570 (mm) REVERT: B 882 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8283 (t) REVERT: B 985 PRO cc_start: 0.8974 (Cg_exo) cc_final: 0.8697 (Cg_endo) REVERT: A 153 MET cc_start: 0.2801 (tmm) cc_final: 0.2528 (tmm) REVERT: C 41 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7777 (ptmt) REVERT: C 90 VAL cc_start: 0.8962 (p) cc_final: 0.8627 (m) REVERT: C 175 MET cc_start: -0.2426 (mtt) cc_final: -0.3658 (mmm) REVERT: C 184 PHE cc_start: 0.7819 (m-80) cc_final: 0.7533 (m-80) REVERT: C 189 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7053 (mt-10) REVERT: C 227 LEU cc_start: 0.9144 (mm) cc_final: 0.8882 (mm) REVERT: C 325 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8747 (t) REVERT: C 924 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7996 (mp10) outliers start: 36 outliers final: 26 residues processed: 119 average time/residue: 0.1632 time to fit residues: 32.8744 Evaluate side-chains 116 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 219 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 269 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 181 optimal weight: 0.4980 chunk 278 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.095933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.063412 restraints weight = 87429.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.063617 restraints weight = 53764.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.064548 restraints weight = 36674.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.064862 restraints weight = 31991.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065006 restraints weight = 28738.794| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26295 Z= 0.160 Angle : 0.587 10.988 35877 Z= 0.292 Chirality : 0.044 0.375 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.116 51.784 4488 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 1.29 % Allowed : 16.43 % Favored : 82.27 % 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 are not related in a simple way. whole: -0.79 (0.15), residues: 3153 helix: 1.27 (0.21), residues: 663 sheet: 0.43 (0.23), residues: 516 loop : -1.52 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 406 TYR 0.015 0.001 TYR C1065 PHE 0.017 0.001 PHE A 184 TRP 0.029 0.001 TRP A 434 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00372 (26202) covalent geometry : angle 0.56792 (35640) SS BOND : bond 0.00164 ( 42) SS BOND : angle 1.23596 ( 84) hydrogen bonds : bond 0.04504 ( 886) hydrogen bonds : angle 4.89856 ( 2430) link_BETA1-4 : bond 0.00192 ( 6) link_BETA1-4 : angle 0.99260 ( 18) link_NAG-ASN : bond 0.00416 ( 45) link_NAG-ASN : angle 2.28549 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 1.040 Fit side-chains REVERT: B 90 VAL cc_start: 0.8981 (p) cc_final: 0.8678 (m) REVERT: B 153 MET cc_start: 0.3477 (tmm) cc_final: 0.3210 (tpt) REVERT: B 263 TYR cc_start: 0.7954 (p90) cc_final: 0.7669 (p90) REVERT: B 325 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8852 (t) REVERT: B 582 ILE cc_start: 0.8201 (mm) cc_final: 0.7573 (mm) REVERT: B 882 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8322 (t) REVERT: B 985 PRO cc_start: 0.9002 (Cg_exo) cc_final: 0.8719 (Cg_endo) REVERT: A 153 MET cc_start: 0.2687 (tmm) cc_final: 0.2412 (tmm) REVERT: C 41 LYS cc_start: 0.8229 (ptmt) cc_final: 0.7802 (ptmt) REVERT: C 90 VAL cc_start: 0.8971 (p) cc_final: 0.8631 (m) REVERT: C 175 MET cc_start: -0.2320 (mtt) cc_final: -0.3565 (mmm) REVERT: C 184 PHE cc_start: 0.7827 (m-80) cc_final: 0.7544 (m-80) REVERT: C 189 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7150 (mt-10) REVERT: C 227 LEU cc_start: 0.9160 (mm) cc_final: 0.8883 (mm) REVERT: C 325 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8758 (t) REVERT: C 924 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7952 (mp10) outliers start: 36 outliers final: 29 residues processed: 123 average time/residue: 0.1622 time to fit residues: 34.0888 Evaluate side-chains 122 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 79 optimal weight: 2.9990 chunk 297 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 271 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 274 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.096117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063170 restraints weight = 85817.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063925 restraints weight = 52024.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.064613 restraints weight = 34714.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065014 restraints weight = 31082.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.065058 restraints weight = 28069.013| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26295 Z= 0.153 Angle : 0.583 11.032 35877 Z= 0.290 Chirality : 0.044 0.375 4173 Planarity : 0.004 0.071 4557 Dihedral : 5.069 51.546 4488 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.32 % Rotamer: Outliers : 1.33 % Allowed : 16.58 % Favored : 82.09 % 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 are not related in a simple way. whole: -0.84 (0.15), residues: 3153 helix: 1.26 (0.21), residues: 663 sheet: 0.30 (0.22), residues: 558 loop : -1.57 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 406 TYR 0.015 0.001 TYR C1065 PHE 0.016 0.001 PHE A 390 TRP 0.029 0.001 TRP A 434 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00358 (26202) covalent geometry : angle 0.56496 (35640) SS BOND : bond 0.00174 ( 42) SS BOND : angle 1.20980 ( 84) hydrogen bonds : bond 0.04423 ( 886) hydrogen bonds : angle 4.86200 ( 2430) link_BETA1-4 : bond 0.00233 ( 6) link_BETA1-4 : angle 0.96424 ( 18) link_NAG-ASN : bond 0.00415 ( 45) link_NAG-ASN : angle 2.27583 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3688.24 seconds wall clock time: 65 minutes 7.03 seconds (3907.03 seconds total)