Starting phenix.real_space_refine on Sun Jun 22 12:50:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wg8_32480/06_2025/7wg8_32480.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg8_32480/06_2025/7wg8_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_32480/06_2025/7wg8_32480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg8_32480/06_2025/7wg8_32480.map" model { file = "/net/cci-nas-00/data/ceres_data/7wg8_32480/06_2025/7wg8_32480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg8_32480/06_2025/7wg8_32480.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.89, per 1000 atoms: 0.62 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: 6.88 Conformation dependent library (CDL) restraints added in 3.4 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: 3.96 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: 11.42 Time building geometry restraints manager: 8.01 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: 0.00 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 61.940 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.950 ------------------------------------------------------------------------------- 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 : 7.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (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 TRP 0.017 0.001 TRP A 884 HIS 0.002 0.001 HIS B 517 PHE 0.014 0.001 PHE B 454 TYR 0.019 0.001 TYR B 902 ARG 0.006 0.000 ARG C 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 45) link_NAG-ASN : angle 2.50279 ( 135) link_BETA1-4 : bond 0.00290 ( 6) link_BETA1-4 : angle 0.96950 ( 18) hydrogen bonds : bond 0.14600 ( 886) hydrogen bonds : angle 6.35583 ( 2430) SS BOND : bond 0.00189 ( 42) SS BOND : angle 1.16505 ( 84) covalent geometry : bond 0.00347 (26202) covalent geometry : angle 0.59360 (35640) *********************** 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 : 2.791 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: 0.7814 (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: 0.8742 (m) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3352 time to fit residues: 79.2224 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 : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 40.0000 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 HIS ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN A 926 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.095846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.063631 restraints weight = 88884.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.063520 restraints weight = 54792.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063838 restraints weight = 40977.897| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 26295 Z= 0.243 Angle : 0.665 10.507 35877 Z= 0.336 Chirality : 0.046 0.373 4173 Planarity : 0.004 0.074 4557 Dihedral : 7.035 59.869 4488 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.24 % Rotamer: Outliers : 0.61 % Allowed : 7.80 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 3153 helix: 0.67 (0.21), residues: 657 sheet: 0.18 (0.21), residues: 597 loop : -1.75 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 434 HIS 0.003 0.001 HIS B 653 PHE 0.018 0.002 PHE A 925 TYR 0.023 0.002 TYR B 902 ARG 0.005 0.001 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 45) link_NAG-ASN : angle 2.46385 ( 135) link_BETA1-4 : bond 0.00173 ( 6) link_BETA1-4 : angle 1.17142 ( 18) hydrogen bonds : bond 0.05601 ( 886) hydrogen bonds : angle 5.50768 ( 2430) SS BOND : bond 0.00224 ( 42) SS BOND : angle 1.28418 ( 84) covalent geometry : bond 0.00563 (26202) covalent geometry : angle 0.64626 (35640) *********************** 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 122 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 LYS cc_start: 0.8505 (mmtm) cc_final: 0.7724 (pttt) REVERT: B 90 VAL cc_start: 0.8974 (p) cc_final: 0.8729 (m) REVERT: B 582 ILE cc_start: 0.8010 (mm) cc_final: 0.7509 (mm) REVERT: B 985 PRO cc_start: 0.8994 (Cg_exo) cc_final: 0.8743 (Cg_endo) REVERT: A 118 LEU cc_start: 0.9072 (mm) cc_final: 0.8811 (mm) REVERT: A 189 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7275 (tt0) REVERT: A 582 ILE cc_start: 0.8401 (mt) cc_final: 0.7870 (mt) REVERT: C 90 VAL cc_start: 0.9042 (p) cc_final: 0.8733 (m) REVERT: C 184 PHE cc_start: 0.8067 (m-80) cc_final: 0.7769 (m-80) REVERT: C 189 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7006 (mt-10) REVERT: C 957 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9311 (tp) outliers start: 17 outliers final: 12 residues processed: 121 average time/residue: 0.3676 time to fit residues: 74.5766 Evaluate side-chains 106 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1075 THR 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 388 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 175 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** ** 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 = 0.096502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.064005 restraints weight = 88352.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064268 restraints weight = 53259.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065082 restraints weight = 36750.349| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26295 Z= 0.157 Angle : 0.580 9.800 35877 Z= 0.292 Chirality : 0.044 0.362 4173 Planarity : 0.004 0.074 4557 Dihedral : 6.486 58.969 4488 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.89 % Rotamer: Outliers : 1.04 % Allowed : 11.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3153 helix: 0.94 (0.21), residues: 657 sheet: 0.27 (0.22), residues: 588 loop : -1.65 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 434 HIS 0.003 0.001 HIS A 49 PHE 0.016 0.001 PHE A 184 TYR 0.018 0.001 TYR C1065 ARG 0.004 0.000 ARG B1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 45) link_NAG-ASN : angle 2.32290 ( 135) link_BETA1-4 : bond 0.00388 ( 6) link_BETA1-4 : angle 1.04562 ( 18) hydrogen bonds : bond 0.04958 ( 886) hydrogen bonds : angle 5.14503 ( 2430) SS BOND : bond 0.00184 ( 42) SS BOND : angle 1.12600 ( 84) covalent geometry : bond 0.00361 (26202) covalent geometry : angle 0.56072 (35640) *********************** 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 130 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 2.839 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8963 (p) cc_final: 0.8699 (m) REVERT: B 582 ILE cc_start: 0.8042 (mm) cc_final: 0.7500 (mm) REVERT: B 985 PRO cc_start: 0.8987 (Cg_exo) cc_final: 0.8723 (Cg_endo) REVERT: B 1102 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8805 (t) REVERT: A 118 LEU cc_start: 0.9117 (mm) cc_final: 0.8876 (mm) REVERT: A 582 ILE cc_start: 0.8457 (mt) cc_final: 0.7935 (mt) REVERT: C 90 VAL cc_start: 0.9002 (p) cc_final: 0.8684 (m) REVERT: C 175 MET cc_start: -0.2334 (mtt) cc_final: -0.3058 (mmt) REVERT: C 184 PHE cc_start: 0.7988 (m-80) cc_final: 0.7693 (m-80) REVERT: C 189 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6955 (mt-10) REVERT: C 867 MET cc_start: 0.9280 (mtt) cc_final: 0.9043 (mtp) outliers start: 29 outliers final: 19 residues processed: 128 average time/residue: 0.3421 time to fit residues: 74.2882 Evaluate side-chains 103 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 3.407 ------------------------------------------------------------------------------- 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 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 A residue 428 THR 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 388 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 866 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 214 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 271 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 193 optimal weight: 0.0020 overall best weight: 2.7394 ------------------------------------------------------------------------------- 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** ** 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 = 0.3766 r_free = 0.3766 target = 0.095831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.063515 restraints weight = 89004.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063514 restraints weight = 54874.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064420 restraints weight = 37973.129| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26295 Z= 0.190 Angle : 0.603 9.649 35877 Z= 0.302 Chirality : 0.044 0.374 4173 Planarity : 0.004 0.074 4557 Dihedral : 6.106 56.615 4488 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.75 % Rotamer: Outliers : 1.73 % Allowed : 13.23 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3153 helix: 0.97 (0.21), residues: 657 sheet: 0.24 (0.22), residues: 579 loop : -1.66 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 434 HIS 0.003 0.001 HIS C1062 PHE 0.015 0.001 PHE B 184 TYR 0.019 0.001 TYR C1065 ARG 0.004 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 45) link_NAG-ASN : angle 2.35468 ( 135) link_BETA1-4 : bond 0.00117 ( 6) link_BETA1-4 : angle 1.09080 ( 18) hydrogen bonds : bond 0.04987 ( 886) hydrogen bonds : angle 5.13144 ( 2430) SS BOND : bond 0.00185 ( 42) SS BOND : angle 1.15543 ( 84) covalent geometry : bond 0.00443 (26202) covalent geometry : angle 0.58438 (35640) *********************** 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 136 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 88 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8948 (p) cc_final: 0.8666 (m) REVERT: B 582 ILE cc_start: 0.8142 (mm) cc_final: 0.7569 (mm) REVERT: B 882 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8348 (t) REVERT: B 985 PRO cc_start: 0.8995 (Cg_exo) cc_final: 0.8730 (Cg_endo) REVERT: A 118 LEU cc_start: 0.9052 (mm) cc_final: 0.8825 (mm) REVERT: A 582 ILE cc_start: 0.8518 (mt) cc_final: 0.7996 (mt) REVERT: C 90 VAL cc_start: 0.8966 (p) cc_final: 0.8633 (m) REVERT: C 175 MET cc_start: -0.2126 (mtt) cc_final: -0.2793 (mmt) REVERT: C 184 PHE cc_start: 0.7921 (m-80) cc_final: 0.7627 (m-80) REVERT: C 325 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8915 (t) REVERT: C 867 MET cc_start: 0.9301 (mtt) cc_final: 0.9082 (mtp) outliers start: 48 outliers final: 30 residues processed: 133 average time/residue: 0.3317 time to fit residues: 75.4093 Evaluate side-chains 116 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 510 VAL 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 893 GLN Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1075 THR 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 949 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 613 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 866 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 162 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 212 optimal weight: 40.0000 chunk 241 optimal weight: 6.9990 chunk 61 optimal weight: 0.0020 chunk 273 optimal weight: 4.9990 chunk 312 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 171 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 = 0.3778 r_free = 0.3778 target = 0.096495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.063457 restraints weight = 86373.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064214 restraints weight = 51721.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064538 restraints weight = 36031.717| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26295 Z= 0.135 Angle : 0.562 10.234 35877 Z= 0.281 Chirality : 0.043 0.367 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.708 55.696 4488 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 1.62 % Allowed : 14.64 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3153 helix: 1.17 (0.21), residues: 663 sheet: 0.34 (0.22), residues: 588 loop : -1.62 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 434 HIS 0.002 0.001 HIS A 49 PHE 0.032 0.001 PHE A 184 TYR 0.016 0.001 TYR C1065 ARG 0.004 0.000 ARG A 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 45) link_NAG-ASN : angle 2.29064 ( 135) link_BETA1-4 : bond 0.00289 ( 6) link_BETA1-4 : angle 0.95081 ( 18) hydrogen bonds : bond 0.04533 ( 886) hydrogen bonds : angle 4.92139 ( 2430) SS BOND : bond 0.00228 ( 42) SS BOND : angle 1.17407 ( 84) covalent geometry : bond 0.00309 (26202) covalent geometry : angle 0.54290 (35640) *********************** 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 137 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 3.076 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8961 (p) cc_final: 0.8675 (m) REVERT: B 189 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7111 (mt-10) REVERT: B 193 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8533 (tttt) REVERT: B 582 ILE cc_start: 0.8118 (mm) cc_final: 0.7517 (mm) REVERT: B 985 PRO cc_start: 0.8994 (Cg_exo) cc_final: 0.8713 (Cg_endo) REVERT: A 118 LEU cc_start: 0.9112 (mm) cc_final: 0.8888 (mm) REVERT: A 582 ILE cc_start: 0.8439 (mt) cc_final: 0.7885 (mt) REVERT: C 90 VAL cc_start: 0.8983 (p) cc_final: 0.8652 (m) REVERT: C 175 MET cc_start: -0.2432 (mtt) cc_final: -0.3531 (mmm) REVERT: C 184 PHE cc_start: 0.7994 (m-80) cc_final: 0.7689 (m-80) REVERT: C 227 LEU cc_start: 0.9221 (mm) cc_final: 0.8983 (mm) REVERT: C 325 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8888 (t) REVERT: C 867 MET cc_start: 0.9281 (mtt) cc_final: 0.9072 (mtp) REVERT: C 924 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7965 (mp10) outliers start: 45 outliers final: 33 residues processed: 133 average time/residue: 0.3458 time to fit residues: 77.7746 Evaluate side-chains 122 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 695 MET Chi-restraints excluded: chain B residue 776 THR 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 1075 THR 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 613 VAL Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1102 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 618 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 882 SER 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 1016 ILE Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 53 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 256 optimal weight: 40.0000 chunk 276 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ** 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 = 0.3781 r_free = 0.3781 target = 0.096663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063704 restraints weight = 85763.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064635 restraints weight = 51411.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064937 restraints weight = 35557.478| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26295 Z= 0.127 Angle : 0.554 10.173 35877 Z= 0.278 Chirality : 0.043 0.367 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.393 55.435 4488 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.05 % Allowed : 15.53 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3153 helix: 1.32 (0.21), residues: 663 sheet: 0.26 (0.22), residues: 588 loop : -1.56 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 434 HIS 0.002 0.000 HIS A 49 PHE 0.023 0.001 PHE A 184 TYR 0.015 0.001 TYR A1065 ARG 0.004 0.000 ARG A 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 45) link_NAG-ASN : angle 2.26069 ( 135) link_BETA1-4 : bond 0.00265 ( 6) link_BETA1-4 : angle 0.93803 ( 18) hydrogen bonds : bond 0.04308 ( 886) hydrogen bonds : angle 4.82714 ( 2430) SS BOND : bond 0.00181 ( 42) SS BOND : angle 1.04080 ( 84) covalent geometry : bond 0.00293 (26202) covalent geometry : angle 0.53520 (35640) *********************** 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 148 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 91 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8959 (p) cc_final: 0.8668 (m) REVERT: B 189 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7083 (mt-10) REVERT: B 193 LYS cc_start: 0.8829 (ttmt) cc_final: 0.8533 (tttt) REVERT: B 263 TYR cc_start: 0.7872 (p90) cc_final: 0.7575 (p90) REVERT: B 406 ARG cc_start: 0.8711 (pmt-80) cc_final: 0.8450 (pmt-80) REVERT: B 582 ILE cc_start: 0.8155 (mm) cc_final: 0.7547 (mm) REVERT: B 985 PRO cc_start: 0.8992 (Cg_exo) cc_final: 0.8711 (Cg_endo) REVERT: A 101 ILE cc_start: 0.9111 (mp) cc_final: 0.8813 (tp) REVERT: A 118 LEU cc_start: 0.9107 (mm) cc_final: 0.8890 (mm) REVERT: A 153 MET cc_start: 0.2771 (tmm) cc_final: 0.2552 (tmm) REVERT: A 898 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7812 (pmm) REVERT: C 90 VAL cc_start: 0.8951 (p) cc_final: 0.8621 (m) REVERT: C 175 MET cc_start: -0.2530 (mtt) cc_final: -0.2988 (mmt) REVERT: C 184 PHE cc_start: 0.7944 (m-80) cc_final: 0.7681 (m-80) REVERT: C 189 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7028 (mt-10) REVERT: C 227 LEU cc_start: 0.9141 (mm) cc_final: 0.8887 (mm) REVERT: C 325 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8825 (t) REVERT: C 867 MET cc_start: 0.9271 (mtt) cc_final: 0.9068 (mtp) REVERT: C 924 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8007 (mp10) outliers start: 57 outliers final: 41 residues processed: 145 average time/residue: 0.3936 time to fit residues: 97.7688 Evaluate side-chains 131 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 310 ILE 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 654 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 776 THR 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 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 191 VAL Chi-restraints excluded: chain A residue 313 THR 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 647 CYS Chi-restraints excluded: chain A residue 722 THR 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 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 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 618 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 882 SER 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 1016 ILE 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 51 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 288 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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** B1009 GLN ** 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 = 0.3778 r_free = 0.3778 target = 0.096553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.063507 restraints weight = 86418.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.064410 restraints weight = 52123.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064921 restraints weight = 35864.159| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1653 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= 0.138 Angle : 0.565 11.406 35877 Z= 0.280 Chirality : 0.043 0.370 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.254 54.852 4488 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 1.87 % Allowed : 15.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3153 helix: 1.32 (0.21), residues: 663 sheet: 0.21 (0.21), residues: 618 loop : -1.60 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 434 HIS 0.002 0.000 HIS A 49 PHE 0.024 0.001 PHE A 184 TYR 0.031 0.001 TYR A 263 ARG 0.003 0.000 ARG A 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 45) link_NAG-ASN : angle 2.25925 ( 135) link_BETA1-4 : bond 0.00347 ( 6) link_BETA1-4 : angle 0.98035 ( 18) hydrogen bonds : bond 0.04304 ( 886) hydrogen bonds : angle 4.82246 ( 2430) SS BOND : bond 0.00167 ( 42) SS BOND : angle 1.06258 ( 84) covalent geometry : bond 0.00319 (26202) covalent geometry : angle 0.54674 (35640) *********************** 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 146 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 94 time to evaluate : 4.181 Fit side-chains REVERT: B 90 VAL cc_start: 0.8988 (p) cc_final: 0.8695 (m) REVERT: B 193 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8537 (tttt) REVERT: B 263 TYR cc_start: 0.7810 (p90) cc_final: 0.7589 (p90) REVERT: B 406 ARG cc_start: 0.8676 (pmt-80) cc_final: 0.8427 (pmt-80) REVERT: B 582 ILE cc_start: 0.8174 (mm) cc_final: 0.7547 (mm) REVERT: B 985 PRO cc_start: 0.8991 (Cg_exo) cc_final: 0.8715 (Cg_endo) REVERT: A 101 ILE cc_start: 0.9130 (mp) cc_final: 0.8835 (tp) REVERT: A 118 LEU cc_start: 0.9095 (mm) cc_final: 0.8886 (mm) REVERT: A 898 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7832 (pmm) REVERT: C 41 LYS cc_start: 0.8196 (ptmt) cc_final: 0.7797 (ptmt) REVERT: C 90 VAL cc_start: 0.8946 (p) cc_final: 0.8613 (m) REVERT: C 175 MET cc_start: -0.2470 (mtt) cc_final: -0.3489 (mmm) REVERT: C 184 PHE cc_start: 0.7864 (m-80) cc_final: 0.7612 (m-80) REVERT: C 189 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7022 (mt-10) REVERT: C 227 LEU cc_start: 0.9143 (mm) cc_final: 0.8883 (mm) REVERT: C 325 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8837 (t) REVERT: C 924 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8007 (mp10) outliers start: 52 outliers final: 42 residues processed: 142 average time/residue: 0.3907 time to fit residues: 95.7880 Evaluate side-chains 133 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 4.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 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 613 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 776 THR 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 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 191 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 647 CYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 913 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 306 VAL 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 618 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 882 SER 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 1016 ILE 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 204 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 291 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 310 optimal weight: 0.5980 chunk 267 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 134 GLN A 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.096071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.063113 restraints weight = 86098.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.063712 restraints weight = 52800.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064573 restraints weight = 34930.908| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26295 Z= 0.164 Angle : 0.582 10.688 35877 Z= 0.290 Chirality : 0.044 0.375 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.267 53.708 4488 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.77 % Favored : 94.20 % Rotamer: Outliers : 1.91 % Allowed : 16.36 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3153 helix: 1.24 (0.21), residues: 663 sheet: 0.19 (0.22), residues: 588 loop : -1.58 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 434 HIS 0.002 0.001 HIS A 49 PHE 0.049 0.001 PHE B 184 TYR 0.015 0.001 TYR C1065 ARG 0.003 0.000 ARG A 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 45) link_NAG-ASN : angle 2.27982 ( 135) link_BETA1-4 : bond 0.00172 ( 6) link_BETA1-4 : angle 1.00036 ( 18) hydrogen bonds : bond 0.04508 ( 886) hydrogen bonds : angle 4.91473 ( 2430) SS BOND : bond 0.00154 ( 42) SS BOND : angle 1.20888 ( 84) covalent geometry : bond 0.00384 (26202) covalent geometry : angle 0.56312 (35640) *********************** 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 146 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 93 time to evaluate : 2.980 Fit side-chains REVERT: B 90 VAL cc_start: 0.8997 (p) cc_final: 0.8705 (m) REVERT: B 193 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8555 (tttt) REVERT: B 406 ARG cc_start: 0.8658 (pmt-80) cc_final: 0.8444 (pmt-80) REVERT: B 582 ILE cc_start: 0.8208 (mm) cc_final: 0.7578 (mm) REVERT: B 985 PRO cc_start: 0.9008 (Cg_exo) cc_final: 0.8724 (Cg_endo) REVERT: A 101 ILE cc_start: 0.9081 (mp) cc_final: 0.8840 (tp) REVERT: A 898 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7917 (pmm) REVERT: C 41 LYS cc_start: 0.8222 (ptmt) cc_final: 0.7826 (ptmt) REVERT: C 90 VAL cc_start: 0.8950 (p) cc_final: 0.8617 (m) REVERT: C 175 MET cc_start: -0.2247 (mtt) cc_final: -0.3294 (mmm) REVERT: C 184 PHE cc_start: 0.7706 (m-80) cc_final: 0.7469 (m-80) REVERT: C 227 LEU cc_start: 0.9124 (mm) cc_final: 0.8852 (mm) REVERT: C 325 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8870 (t) REVERT: C 924 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7945 (mp10) outliers start: 53 outliers final: 46 residues processed: 141 average time/residue: 0.3405 time to fit residues: 81.5256 Evaluate side-chains 134 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 85 time to evaluate : 3.125 ------------------------------------------------------------------------------- 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 388 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 776 THR 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 1006 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 191 VAL Chi-restraints excluded: chain A residue 313 THR 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 647 CYS Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 913 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 306 VAL 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 618 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 882 SER 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 1016 ILE Chi-restraints excluded: chain C residue 1102 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 26 optimal weight: 4.9990 chunk 256 optimal weight: 30.0000 chunk 168 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 458 ASN ** B 899 GLN ** 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 = 0.3755 r_free = 0.3755 target = 0.095263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.062300 restraints weight = 87799.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.062732 restraints weight = 54663.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.063511 restraints weight = 36653.112| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26295 Z= 0.204 Angle : 0.624 10.919 35877 Z= 0.311 Chirality : 0.045 0.385 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.429 51.425 4488 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.53 % Rotamer: Outliers : 2.01 % Allowed : 16.58 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3153 helix: 1.03 (0.21), residues: 663 sheet: 0.30 (0.23), residues: 546 loop : -1.57 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 434 HIS 0.002 0.001 HIS C 653 PHE 0.017 0.001 PHE A 184 TYR 0.017 0.001 TYR C1065 ARG 0.005 0.000 ARG A1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 45) link_NAG-ASN : angle 2.34816 ( 135) link_BETA1-4 : bond 0.00096 ( 6) link_BETA1-4 : angle 1.08736 ( 18) hydrogen bonds : bond 0.04907 ( 886) hydrogen bonds : angle 5.08307 ( 2430) SS BOND : bond 0.00180 ( 42) SS BOND : angle 1.36477 ( 84) covalent geometry : bond 0.00477 (26202) covalent geometry : angle 0.60478 (35640) *********************** 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 147 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 91 time to evaluate : 2.888 Fit side-chains REVERT: B 90 VAL cc_start: 0.9009 (p) cc_final: 0.8706 (m) REVERT: B 193 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8541 (tttt) REVERT: B 582 ILE cc_start: 0.8195 (mm) cc_final: 0.7542 (mm) REVERT: B 882 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8402 (t) REVERT: B 985 PRO cc_start: 0.9011 (Cg_exo) cc_final: 0.8722 (Cg_endo) REVERT: A 101 ILE cc_start: 0.9162 (mp) cc_final: 0.8895 (tp) REVERT: A 898 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7795 (mtm) REVERT: C 41 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7872 (ptmt) REVERT: C 90 VAL cc_start: 0.8967 (p) cc_final: 0.8623 (m) REVERT: C 175 MET cc_start: -0.2390 (mtt) cc_final: -0.3326 (mmm) REVERT: C 184 PHE cc_start: 0.7893 (m-80) cc_final: 0.7633 (m-80) REVERT: C 227 LEU cc_start: 0.9173 (mm) cc_final: 0.8893 (mm) REVERT: C 325 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8896 (t) REVERT: C 924 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7857 (mp10) outliers start: 56 outliers final: 49 residues processed: 141 average time/residue: 0.3413 time to fit residues: 83.1472 Evaluate side-chains 139 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 86 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 310 ILE 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 613 VAL Chi-restraints excluded: chain B residue 654 VAL 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 1006 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 191 VAL Chi-restraints excluded: chain A residue 313 THR 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 647 CYS Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 MET 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 949 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 306 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 618 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 882 SER 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 1016 ILE 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 255 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 118 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 269 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.095922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.063261 restraints weight = 86491.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.063642 restraints weight = 53374.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.064523 restraints weight = 35856.250| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26295 Z= 0.156 Angle : 0.588 10.964 35877 Z= 0.293 Chirality : 0.044 0.379 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.298 51.237 4488 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 1.91 % Allowed : 16.83 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3153 helix: 1.14 (0.21), residues: 663 sheet: 0.17 (0.22), residues: 588 loop : -1.60 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 434 HIS 0.002 0.001 HIS C 49 PHE 0.018 0.001 PHE A 184 TYR 0.016 0.001 TYR C1065 ARG 0.006 0.000 ARG A 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 45) link_NAG-ASN : angle 2.31045 ( 135) link_BETA1-4 : bond 0.00311 ( 6) link_BETA1-4 : angle 0.96544 ( 18) hydrogen bonds : bond 0.04542 ( 886) hydrogen bonds : angle 4.92591 ( 2430) SS BOND : bond 0.00189 ( 42) SS BOND : angle 1.24944 ( 84) covalent geometry : bond 0.00364 (26202) covalent geometry : angle 0.56917 (35640) ********************** 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 142 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 89 time to evaluate : 2.666 Fit side-chains REVERT: B 90 VAL cc_start: 0.9006 (p) cc_final: 0.8703 (m) REVERT: B 193 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8567 (tttt) REVERT: B 263 TYR cc_start: 0.7966 (p90) cc_final: 0.7723 (p90) REVERT: B 582 ILE cc_start: 0.8196 (mm) cc_final: 0.7544 (mm) REVERT: B 882 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8369 (t) REVERT: A 101 ILE cc_start: 0.9145 (mp) cc_final: 0.8885 (tp) REVERT: A 125 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8734 (p0) REVERT: A 898 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7870 (pmm) REVERT: C 41 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7878 (ptmt) REVERT: C 175 MET cc_start: -0.2388 (mtt) cc_final: -0.3477 (mmm) REVERT: C 184 PHE cc_start: 0.7856 (m-80) cc_final: 0.7598 (m-80) REVERT: C 227 LEU cc_start: 0.9160 (mm) cc_final: 0.8878 (mm) REVERT: C 325 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8879 (t) REVERT: C 882 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8610 (t) REVERT: C 924 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7962 (mp10) outliers start: 53 outliers final: 47 residues processed: 137 average time/residue: 0.3920 time to fit residues: 91.3557 Evaluate side-chains 140 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 87 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 310 ILE 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 613 VAL Chi-restraints excluded: chain B residue 654 VAL 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 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 125 ASN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 313 THR 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 647 CYS Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 722 THR 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 949 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 306 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 618 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 882 SER 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 1016 ILE 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 258 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.095856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.063799 restraints weight = 88615.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063907 restraints weight = 53921.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.064693 restraints weight = 37422.141| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 26295 Z= 0.219 Angle : 0.721 59.189 35877 Z= 0.393 Chirality : 0.046 0.679 4173 Planarity : 0.004 0.072 4557 Dihedral : 5.298 51.228 4488 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 1.94 % Allowed : 16.90 % Favored : 81.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3153 helix: 1.14 (0.21), residues: 663 sheet: 0.17 (0.22), residues: 588 loop : -1.60 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 434 HIS 0.002 0.001 HIS C 49 PHE 0.016 0.001 PHE A 184 TYR 0.023 0.001 TYR A 202 ARG 0.003 0.000 ARG A 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 45) link_NAG-ASN : angle 2.31170 ( 135) link_BETA1-4 : bond 0.00286 ( 6) link_BETA1-4 : angle 0.96903 ( 18) hydrogen bonds : bond 0.04614 ( 886) hydrogen bonds : angle 4.93316 ( 2430) SS BOND : bond 0.00168 ( 42) SS BOND : angle 1.21885 ( 84) covalent geometry : bond 0.00491 (26202) covalent geometry : angle 0.70623 (35640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7204.23 seconds wall clock time: 129 minutes 33.65 seconds (7773.65 seconds total)