Starting phenix.real_space_refine on Tue Oct 27 11:55:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11lq_75813/10_2026/11lq_75813.cif Found real_map, /net/cci-nas-00/data/ceres_data/11lq_75813/10_2026/11lq_75813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11lq_75813/10_2026/11lq_75813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11lq_75813/10_2026/11lq_75813.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11lq_75813/10_2026/11lq_75813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11lq_75813/10_2026/11lq_75813.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 135 5.16 5 C 15198 2.51 5 N 4077 2.21 5 O 4641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24051 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 816 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2723 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 21, 'TRANS': 327} Chain breaks: 2 Chain: "J" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "S" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "R" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 981 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Restraints were copied for chains: F, H, G, I, B, C, L, N, U, Q, M, O, T, V Time building chain proxies: 4.43, per 1000 atoms: 0.18 Number of scatterers: 24051 At special positions: 0 Unit cell: (174.9, 178.2, 112.2, 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 135 16.00 O 4641 8.00 N 4077 7.00 C 15198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 283 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 228 " distance=2.03 Simple disulfide: pdb=" SG CYS C 223 " - pdb=" SG CYS C 252 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 89 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5646 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 78 sheets defined 10.8% alpha, 45.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.632A pdb=" N GLU D 84 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.632A pdb=" N GLU F 84 " --> pdb=" O SER F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.101A pdb=" N ASN A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 272 through 294 removed outlier: 3.778A pdb=" N LYS A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.879A pdb=" N HIS A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.247A pdb=" N ILE A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.265A pdb=" N LEU A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.632A pdb=" N GLU H 84 " --> pdb=" O SER H 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'S' and resid 25 through 30 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 154 through 158 removed outlier: 4.100A pdb=" N ASN B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 272 through 294 removed outlier: 3.778A pdb=" N LYS B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.878A pdb=" N HIS B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 4.246A pdb=" N ILE B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.266A pdb=" N LEU B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 389 " --> pdb=" O MET B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 389' Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 154 through 158 removed outlier: 4.100A pdb=" N ASN C 158 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 272 through 294 removed outlier: 3.778A pdb=" N LYS C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.879A pdb=" N HIS C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 339 removed outlier: 4.246A pdb=" N ILE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 380 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.266A pdb=" N LEU C 388 " --> pdb=" O HIS C 384 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 389' Processing helix chain 'U' and resid 25 through 30 Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.814A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.814A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.814A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'T' and resid 87 through 91 Processing helix chain 'V' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.620A pdb=" N LEU D 107 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA D 85 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.620A pdb=" N LEU D 107 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA D 85 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.643A pdb=" N GLN E 6 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS E 23 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE E 79 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.831A pdb=" N GLY E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 39 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 12 through 13 removed outlier: 4.708A pdb=" N VAL E 113 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER E 100 " --> pdb=" O MET E 111 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET E 111 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.620A pdb=" N LEU F 107 " --> pdb=" O ALA F 85 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA F 85 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.620A pdb=" N LEU F 107 " --> pdb=" O ALA F 85 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA F 85 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.643A pdb=" N GLN G 6 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS G 23 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE G 79 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.830A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG G 39 " --> pdb=" O TRP G 48 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 12 through 13 removed outlier: 4.708A pdb=" N VAL G 113 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER G 100 " --> pdb=" O MET G 111 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET G 111 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.536A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.536A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 316 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 37 through 46 removed outlier: 6.176A pdb=" N LYS A 202 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.671A pdb=" N VAL A 133 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 60 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 148 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.671A pdb=" N VAL A 133 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 60 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 223 through 227 Processing sheet with id=AC1, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AC2, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AC3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.621A pdb=" N LEU H 107 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA H 85 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.621A pdb=" N LEU H 107 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA H 85 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 4 through 8 removed outlier: 3.643A pdb=" N GLN I 6 " --> pdb=" O THR I 24 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS I 23 " --> pdb=" O PHE I 79 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE I 79 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 12 through 13 removed outlier: 3.830A pdb=" N GLY I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG I 39 " --> pdb=" O TRP I 48 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 12 through 13 removed outlier: 4.709A pdb=" N VAL I 113 " --> pdb=" O ARG I 98 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER I 100 " --> pdb=" O MET I 111 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET I 111 " --> pdb=" O SER I 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.374A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.724A pdb=" N GLY J 98 " --> pdb=" O HIS J 93 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 19 through 23 Processing sheet with id=AD3, first strand: chain 'S' and resid 9 through 12 removed outlier: 7.186A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 9 through 12 Processing sheet with id=AD5, first strand: chain 'S' and resid 18 through 23 Processing sheet with id=AD6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.374A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.723A pdb=" N GLY L 98 " --> pdb=" O HIS L 93 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AD9, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.374A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.723A pdb=" N GLY N 98 " --> pdb=" O HIS N 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 19 through 23 Processing sheet with id=AE3, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.536A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.536A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 316 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 37 through 46 removed outlier: 6.177A pdb=" N LYS B 202 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 133 through 135 removed outlier: 3.672A pdb=" N VAL B 133 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 60 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 148 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 133 through 135 removed outlier: 3.672A pdb=" N VAL B 133 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 60 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AE9, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AF1, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AF2, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.536A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.536A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 316 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 37 through 46 removed outlier: 6.176A pdb=" N LYS C 202 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.672A pdb=" N VAL C 133 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 60 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 148 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.672A pdb=" N VAL C 133 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 60 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 223 through 227 Processing sheet with id=AF8, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AF9, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AG1, first strand: chain 'U' and resid 9 through 12 removed outlier: 7.186A pdb=" N TRP U 36 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 9 through 12 Processing sheet with id=AG3, first strand: chain 'U' and resid 18 through 23 Processing sheet with id=AG4, first strand: chain 'Q' and resid 9 through 12 removed outlier: 7.186A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 9 through 12 Processing sheet with id=AG6, first strand: chain 'Q' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AG8, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.811A pdb=" N SER K 121 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA K 40 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.811A pdb=" N SER K 121 " --> pdb=" O GLU K 10 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AH2, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.811A pdb=" N SER M 121 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.811A pdb=" N SER M 121 " --> pdb=" O GLU M 10 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AH5, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.812A pdb=" N SER O 121 " --> pdb=" O GLU O 10 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA O 40 " --> pdb=" O GLY O 44 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY O 44 " --> pdb=" O ALA O 40 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.812A pdb=" N SER O 121 " --> pdb=" O GLU O 10 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 4 through 8 Processing sheet with id=AH8, first strand: chain 'R' and resid 58 through 60 removed outlier: 5.297A pdb=" N TRP R 48 " --> pdb=" O ARG R 39 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG R 39 " --> pdb=" O TRP R 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY R 50 " --> pdb=" O TRP R 37 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS R 96 " --> pdb=" O TRP R 119 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP R 119 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG R 98 " --> pdb=" O GLN R 117 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 58 through 60 removed outlier: 5.297A pdb=" N TRP R 48 " --> pdb=" O ARG R 39 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG R 39 " --> pdb=" O TRP R 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY R 50 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'T' and resid 4 through 8 Processing sheet with id=AI2, first strand: chain 'T' and resid 58 through 60 removed outlier: 5.296A pdb=" N TRP T 48 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG T 39 " --> pdb=" O TRP T 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY T 50 " --> pdb=" O TRP T 37 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N CYS T 96 " --> pdb=" O TRP T 119 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP T 119 " --> pdb=" O CYS T 96 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG T 98 " --> pdb=" O GLN T 117 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'T' and resid 58 through 60 removed outlier: 5.296A pdb=" N TRP T 48 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG T 39 " --> pdb=" O TRP T 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY T 50 " --> pdb=" O TRP T 37 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 4 through 8 Processing sheet with id=AI5, first strand: chain 'V' and resid 58 through 60 removed outlier: 5.297A pdb=" N TRP V 48 " --> pdb=" O ARG V 39 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG V 39 " --> pdb=" O TRP V 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY V 50 " --> pdb=" O TRP V 37 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS V 96 " --> pdb=" O TRP V 119 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP V 119 " --> pdb=" O CYS V 96 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG V 98 " --> pdb=" O GLN V 117 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'V' and resid 58 through 60 removed outlier: 5.297A pdb=" N TRP V 48 " --> pdb=" O ARG V 39 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG V 39 " --> pdb=" O TRP V 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY V 50 " --> pdb=" O TRP V 37 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.63 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7710 1.34 - 1.46: 6405 1.46 - 1.58: 10371 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 24678 Sorted by residual: bond pdb=" CG1 ILE A 134 " pdb=" CD1 ILE A 134 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.39e+00 bond pdb=" CG1 ILE C 134 " pdb=" CD1 ILE C 134 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.38e+00 bond pdb=" CG1 ILE B 134 " pdb=" CD1 ILE B 134 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.33e+00 bond pdb=" N LYS C 1 " pdb=" CA LYS C 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" N LYS B 1 " pdb=" CA LYS B 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.40e+00 ... (remaining 24673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 32623 1.48 - 2.95: 695 2.95 - 4.43: 237 4.43 - 5.90: 21 5.90 - 7.38: 3 Bond angle restraints: 33579 Sorted by residual: angle pdb=" N THR Q 5 " pdb=" CA THR Q 5 " pdb=" C THR Q 5 " ideal model delta sigma weight residual 107.37 114.75 -7.38 2.07e+00 2.33e-01 1.27e+01 angle pdb=" N THR S 5 " pdb=" CA THR S 5 " pdb=" C THR S 5 " ideal model delta sigma weight residual 107.37 114.75 -7.38 2.07e+00 2.33e-01 1.27e+01 angle pdb=" N THR U 5 " pdb=" CA THR U 5 " pdb=" C THR U 5 " ideal model delta sigma weight residual 107.37 114.73 -7.36 2.07e+00 2.33e-01 1.26e+01 angle pdb=" C ILE A 135 " pdb=" N SER A 136 " pdb=" CA SER A 136 " ideal model delta sigma weight residual 119.78 123.79 -4.01 1.24e+00 6.50e-01 1.05e+01 angle pdb=" C ILE C 135 " pdb=" N SER C 136 " pdb=" CA SER C 136 " ideal model delta sigma weight residual 119.78 123.76 -3.98 1.24e+00 6.50e-01 1.03e+01 ... (remaining 33574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 13224 17.13 - 34.26: 1037 34.26 - 51.40: 169 51.40 - 68.53: 66 68.53 - 85.66: 27 Dihedral angle restraints: 14523 sinusoidal: 5598 harmonic: 8925 Sorted by residual: dihedral pdb=" CD ARG B 346 " pdb=" NE ARG B 346 " pdb=" CZ ARG B 346 " pdb=" NH1 ARG B 346 " ideal model delta sinusoidal sigma weight residual 0.00 -58.60 58.60 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CD ARG C 346 " pdb=" NE ARG C 346 " pdb=" CZ ARG C 346 " pdb=" NH1 ARG C 346 " ideal model delta sinusoidal sigma weight residual 0.00 -58.57 58.57 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CD ARG A 346 " pdb=" NE ARG A 346 " pdb=" CZ ARG A 346 " pdb=" NH1 ARG A 346 " ideal model delta sinusoidal sigma weight residual 0.00 -58.55 58.55 1 1.00e+01 1.00e-02 4.59e+01 ... (remaining 14520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3325 0.077 - 0.155: 314 0.155 - 0.232: 0 0.232 - 0.309: 0 0.309 - 0.387: 3 Chirality restraints: 3642 Sorted by residual: chirality pdb=" CA THR S 5 " pdb=" N THR S 5 " pdb=" C THR S 5 " pdb=" CB THR S 5 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA THR U 5 " pdb=" N THR U 5 " pdb=" C THR U 5 " pdb=" CB THR U 5 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA THR Q 5 " pdb=" N THR Q 5 " pdb=" C THR Q 5 " pdb=" CB THR Q 5 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 3639 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 346 " -0.869 9.50e-02 1.11e+02 3.90e-01 9.30e+01 pdb=" NE ARG C 346 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG C 346 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 346 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 346 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 346 " -0.869 9.50e-02 1.11e+02 3.90e-01 9.29e+01 pdb=" NE ARG B 346 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 346 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 346 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 346 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 346 " -0.868 9.50e-02 1.11e+02 3.89e-01 9.28e+01 pdb=" NE ARG A 346 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 346 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 346 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 346 " -0.018 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2862 2.75 - 3.29: 23626 3.29 - 3.83: 38274 3.83 - 4.36: 45245 4.36 - 4.90: 79390 Nonbonded interactions: 189397 Sorted by model distance: nonbonded pdb=" OE1 GLN S 6 " pdb=" OG1 THR S 105 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLN Q 6 " pdb=" OG1 THR Q 105 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLN U 6 " pdb=" OG1 THR U 105 " model vdw 2.215 3.040 nonbonded pdb=" O LEU Q 96 " pdb=" OG1 THR Q 97 " model vdw 2.273 3.040 nonbonded pdb=" O LEU S 96 " pdb=" OG1 THR S 97 " model vdw 2.273 3.040 ... (remaining 189392 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: 0.07 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'R' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24717 Z= 0.171 Angle : 0.589 7.378 33657 Z= 0.302 Chirality : 0.042 0.387 3642 Planarity : 0.019 0.390 4287 Dihedral : 13.037 85.659 8760 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3069 helix: 1.03 (0.37), residues: 195 sheet: 1.11 (0.15), residues: 1209 loop : 0.04 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 264 TYR 0.044 0.002 TYR V 51 PHE 0.017 0.001 PHE T 53 TRP 0.008 0.001 TRP V 48 HIS 0.008 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (24678) covalent geometry : angle 0.58851 / 0.30 (33579) SS BOND : bond 0.00179 / 0.13 ( 39) SS BOND : angle 0.62605 / 0.44 ( 78) hydrogen bonds : bond 0.22521 / 14.87 ( 888) hydrogen bonds : angle 8.82649 / 6.03 ( 2448) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 28 ASP cc_start: 0.8405 (t70) cc_final: 0.7987 (t70) REVERT: E 73 ASP cc_start: 0.8854 (t0) cc_final: 0.8562 (t0) REVERT: G 28 ASP cc_start: 0.8175 (t70) cc_final: 0.7845 (t0) REVERT: A 27 ASN cc_start: 0.9450 (m-40) cc_final: 0.9233 (m-40) REVERT: A 175 TYR cc_start: 0.8662 (m-80) cc_final: 0.8416 (m-80) REVERT: H 12 ASP cc_start: 0.7109 (t0) cc_final: 0.6623 (t0) REVERT: I 28 ASP cc_start: 0.8466 (t70) cc_final: 0.8062 (t70) REVERT: I 73 ASP cc_start: 0.8867 (t0) cc_final: 0.8660 (t0) REVERT: J 84 GLU cc_start: 0.8593 (tt0) cc_final: 0.8361 (mm-30) REVERT: S 86 ASP cc_start: 0.8893 (m-30) cc_final: 0.8156 (m-30) REVERT: L 17 ARG cc_start: 0.8436 (ptm-80) cc_final: 0.7984 (ptm-80) REVERT: L 76 ILE cc_start: 0.8547 (tp) cc_final: 0.8230 (tp) REVERT: L 96 LEU cc_start: 0.9517 (mp) cc_final: 0.9208 (mp) REVERT: N 17 ARG cc_start: 0.8632 (ptm-80) cc_final: 0.8161 (ptm-80) REVERT: B 291 MET cc_start: 0.8662 (mtp) cc_final: 0.8395 (mtp) REVERT: B 313 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7771 (mmmt) REVERT: C 291 MET cc_start: 0.8792 (mtp) cc_final: 0.8575 (mtp) REVERT: C 382 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8283 (mp10) REVERT: C 385 MET cc_start: 0.8443 (tpt) cc_final: 0.8096 (tpt) REVERT: U 86 ASP cc_start: 0.8840 (m-30) cc_final: 0.8196 (m-30) REVERT: U 94 ASP cc_start: 0.8654 (m-30) cc_final: 0.8404 (m-30) REVERT: Q 86 ASP cc_start: 0.8874 (m-30) cc_final: 0.8211 (m-30) REVERT: K 73 ASP cc_start: 0.8519 (t0) cc_final: 0.8134 (t0) REVERT: K 110 ASP cc_start: 0.8829 (m-30) cc_final: 0.8272 (m-30) REVERT: M 63 LYS cc_start: 0.9480 (ttpt) cc_final: 0.9273 (ttpt) REVERT: M 73 ASP cc_start: 0.8589 (t0) cc_final: 0.8302 (t0) REVERT: M 89 ASP cc_start: 0.8620 (t0) cc_final: 0.8410 (t0) REVERT: O 63 LYS cc_start: 0.9398 (ttpt) cc_final: 0.9039 (ttpt) REVERT: O 73 ASP cc_start: 0.8527 (t0) cc_final: 0.8209 (t0) REVERT: R 31 ASP cc_start: 0.8020 (p0) cc_final: 0.7819 (p0) REVERT: R 47 GLU cc_start: 0.8476 (tt0) cc_final: 0.8217 (tt0) REVERT: R 114 GLU cc_start: 0.8759 (tt0) cc_final: 0.8363 (tt0) outliers start: 0 outliers final: 0 residues processed: 476 average time/residue: 0.1890 time to fit residues: 134.5565 Evaluate side-chains 328 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0020 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.0670 overall best weight: 1.0930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 16 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 377 GLN C 377 GLN U 16 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 GLN T 117 GLN V 117 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.040425 restraints weight = 89150.131| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 3.87 r_work: 0.2489 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24717 Z= 0.148 Angle : 0.669 7.779 33657 Z= 0.351 Chirality : 0.045 0.178 3642 Planarity : 0.005 0.051 4287 Dihedral : 4.827 20.027 3414 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.06 % Allowed : 6.30 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3069 helix: 1.17 (0.38), residues: 195 sheet: 1.15 (0.15), residues: 1181 loop : 0.09 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 77 TYR 0.027 0.002 TYR T 51 PHE 0.015 0.002 PHE B 87 TRP 0.010 0.001 TRP I 114 HIS 0.007 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (24678) covalent geometry : angle 0.66862 / 0.35 (33579) SS BOND : bond 0.00337 / 0.22 ( 39) SS BOND : angle 0.83892 / 0.57 ( 78) hydrogen bonds : bond 0.04492 / 3.00 ( 888) hydrogen bonds : angle 6.54255 / 4.45 ( 2448) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 392 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.7356 (t0) cc_final: 0.6046 (t0) REVERT: E 28 ASP cc_start: 0.8558 (t70) cc_final: 0.7997 (t70) REVERT: E 73 ASP cc_start: 0.8795 (t0) cc_final: 0.8548 (t0) REVERT: F 12 ASP cc_start: 0.8047 (t0) cc_final: 0.7129 (t0) REVERT: F 79 LEU cc_start: 0.8872 (mp) cc_final: 0.8452 (mp) REVERT: G 44 LYS cc_start: 0.9509 (mppt) cc_final: 0.9281 (mmtm) REVERT: G 73 ASP cc_start: 0.8696 (t0) cc_final: 0.8363 (t0) REVERT: A 175 TYR cc_start: 0.8977 (m-80) cc_final: 0.8653 (m-80) REVERT: A 179 MET cc_start: 0.9017 (mmm) cc_final: 0.8807 (mmm) REVERT: H 12 ASP cc_start: 0.7827 (t0) cc_final: 0.6571 (t0) REVERT: I 28 ASP cc_start: 0.8595 (t70) cc_final: 0.8091 (t70) REVERT: I 47 GLU cc_start: 0.8925 (tt0) cc_final: 0.8194 (pt0) REVERT: I 73 ASP cc_start: 0.8777 (t0) cc_final: 0.8557 (t0) REVERT: J 77 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8125 (tpm170) REVERT: J 84 GLU cc_start: 0.8738 (tt0) cc_final: 0.8463 (mm-30) REVERT: J 106 LYS cc_start: 0.8438 (tppt) cc_final: 0.7974 (tppt) REVERT: S 94 ASP cc_start: 0.8716 (m-30) cc_final: 0.8446 (m-30) REVERT: L 77 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8280 (tpm170) REVERT: L 84 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7846 (mm-30) REVERT: L 96 LEU cc_start: 0.9594 (mp) cc_final: 0.9346 (mp) REVERT: L 106 LYS cc_start: 0.8504 (tppt) cc_final: 0.7660 (tppt) REVERT: N 77 ARG cc_start: 0.8790 (ttp80) cc_final: 0.8322 (tpm170) REVERT: N 84 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7676 (mm-30) REVERT: N 106 LYS cc_start: 0.8469 (tppt) cc_final: 0.7490 (tppt) REVERT: N 107 LEU cc_start: 0.8379 (tt) cc_final: 0.7169 (tp) REVERT: B 175 TYR cc_start: 0.8809 (m-80) cc_final: 0.8489 (m-80) REVERT: B 385 MET cc_start: 0.8824 (tpt) cc_final: 0.8514 (tpt) REVERT: B 396 MET cc_start: 0.8018 (tmm) cc_final: 0.7755 (tmm) REVERT: C 179 MET cc_start: 0.8980 (mmm) cc_final: 0.8737 (mmm) REVERT: C 382 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8455 (mp10) REVERT: Q 107 LEU cc_start: 0.9112 (tt) cc_final: 0.8892 (tt) REVERT: K 23 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7336 (tm-30) REVERT: K 73 ASP cc_start: 0.8574 (t0) cc_final: 0.8159 (t0) REVERT: K 109 ASP cc_start: 0.8204 (t0) cc_final: 0.7967 (t0) REVERT: M 23 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7360 (tm-30) REVERT: M 46 ASP cc_start: 0.8642 (m-30) cc_final: 0.7938 (p0) REVERT: M 73 ASP cc_start: 0.8597 (t0) cc_final: 0.8248 (t0) REVERT: M 116 GLN cc_start: 0.8431 (pt0) cc_final: 0.8046 (pp30) REVERT: O 43 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8875 (mp10) REVERT: O 73 ASP cc_start: 0.8598 (t0) cc_final: 0.8223 (t0) REVERT: R 47 GLU cc_start: 0.9094 (tt0) cc_final: 0.8753 (tt0) REVERT: R 114 GLU cc_start: 0.9326 (tt0) cc_final: 0.9032 (tt0) REVERT: V 17 GLU cc_start: 0.8520 (pt0) cc_final: 0.8294 (pm20) outliers start: 28 outliers final: 23 residues processed: 405 average time/residue: 0.1749 time to fit residues: 108.0244 Evaluate side-chains 356 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 16 GLN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 16 GLN Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain T residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [4, 202, 40, 283, 298, 256, 23, 204, 277, 92, 73] chunk 4 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 204 optimal weight: 0.1980 chunk 277 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 261 HIS H 6 GLN ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 GLN T 78 GLN V 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.052628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.038276 restraints weight = 89762.792| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 3.85 r_work: 0.2420 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24717 Z= 0.202 Angle : 0.644 8.803 33657 Z= 0.339 Chirality : 0.044 0.210 3642 Planarity : 0.005 0.048 4287 Dihedral : 4.851 19.914 3414 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.62 % Allowed : 8.67 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3069 helix: 1.17 (0.38), residues: 195 sheet: 1.17 (0.15), residues: 1143 loop : 0.06 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 87 TYR 0.028 0.002 TYR R 51 PHE 0.015 0.002 PHE V 79 TRP 0.011 0.001 TRP F 36 HIS 0.005 0.001 HIS B 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (24678) covalent geometry : angle 0.64265 / 0.34 (33579) SS BOND : bond 0.00336 / 0.23 ( 39) SS BOND : angle 1.00299 / 0.63 ( 78) hydrogen bonds : bond 0.03978 / 2.66 ( 888) hydrogen bonds : angle 6.05553 / 4.11 ( 2448) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.7632 (t0) cc_final: 0.6878 (t0) REVERT: D 79 LEU cc_start: 0.8525 (mp) cc_final: 0.8209 (mp) REVERT: E 28 ASP cc_start: 0.8636 (t70) cc_final: 0.8052 (t70) REVERT: E 47 GLU cc_start: 0.8876 (tt0) cc_final: 0.8238 (pt0) REVERT: E 73 ASP cc_start: 0.8761 (t0) cc_final: 0.8496 (t0) REVERT: E 102 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.7996 (p0) REVERT: F 12 ASP cc_start: 0.8210 (t0) cc_final: 0.7356 (t0) REVERT: F 79 LEU cc_start: 0.8944 (mp) cc_final: 0.8544 (mp) REVERT: G 28 ASP cc_start: 0.8036 (m-30) cc_final: 0.7681 (m-30) REVERT: A 175 TYR cc_start: 0.9034 (m-80) cc_final: 0.8669 (m-80) REVERT: H 12 ASP cc_start: 0.8078 (t0) cc_final: 0.7579 (t0) REVERT: I 28 ASP cc_start: 0.8713 (t70) cc_final: 0.8210 (t70) REVERT: I 47 GLU cc_start: 0.8975 (tt0) cc_final: 0.8170 (pt0) REVERT: I 73 ASP cc_start: 0.8718 (t0) cc_final: 0.8488 (t0) REVERT: J 75 GLU cc_start: 0.8448 (pm20) cc_final: 0.8182 (pm20) REVERT: J 84 GLU cc_start: 0.8720 (tt0) cc_final: 0.8250 (mm-30) REVERT: S 94 ASP cc_start: 0.8805 (m-30) cc_final: 0.8495 (m-30) REVERT: S 106 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8916 (mmmm) REVERT: L 77 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8355 (tpm170) REVERT: L 96 LEU cc_start: 0.9629 (mp) cc_final: 0.9423 (mp) REVERT: N 76 ILE cc_start: 0.8865 (mm) cc_final: 0.8658 (mm) REVERT: N 77 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8067 (tpm170) REVERT: N 84 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7703 (mm-30) REVERT: N 106 LYS cc_start: 0.8411 (tppt) cc_final: 0.8077 (tppt) REVERT: B 102 MET cc_start: 0.8886 (mmp) cc_final: 0.8520 (ppp) REVERT: B 175 TYR cc_start: 0.8909 (m-80) cc_final: 0.8543 (m-80) REVERT: B 385 MET cc_start: 0.8783 (tpt) cc_final: 0.8432 (tpt) REVERT: B 396 MET cc_start: 0.8089 (tmm) cc_final: 0.7755 (tmm) REVERT: C 141 ASP cc_start: 0.8748 (m-30) cc_final: 0.8133 (p0) REVERT: C 382 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8227 (mp10) REVERT: Q 106 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8978 (tppt) REVERT: K 10 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7428 (tm-30) REVERT: K 12 LYS cc_start: 0.9451 (mttt) cc_final: 0.9101 (mttt) REVERT: K 23 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7503 (tm-30) REVERT: K 31 ASP cc_start: 0.9503 (m-30) cc_final: 0.9178 (m-30) REVERT: K 73 ASP cc_start: 0.8556 (t0) cc_final: 0.8109 (t0) REVERT: K 81 MET cc_start: 0.9178 (tmm) cc_final: 0.8237 (tmm) REVERT: M 23 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7418 (tm-30) REVERT: M 73 ASP cc_start: 0.8583 (t0) cc_final: 0.8191 (t0) REVERT: M 87 ARG cc_start: 0.9192 (mtm110) cc_final: 0.8983 (mtm110) REVERT: M 116 GLN cc_start: 0.8361 (pt0) cc_final: 0.7980 (pp30) REVERT: O 43 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8914 (mp10) REVERT: O 73 ASP cc_start: 0.8641 (t0) cc_final: 0.8305 (t0) REVERT: O 87 ARG cc_start: 0.9129 (mtm110) cc_final: 0.8830 (mtm110) REVERT: R 47 GLU cc_start: 0.9147 (tt0) cc_final: 0.8801 (tt0) REVERT: R 76 LYS cc_start: 0.9196 (mmtm) cc_final: 0.8937 (mmtm) REVERT: R 114 GLU cc_start: 0.9319 (tt0) cc_final: 0.9003 (tt0) REVERT: T 76 LYS cc_start: 0.9382 (mmmm) cc_final: 0.9145 (mmtm) REVERT: V 17 GLU cc_start: 0.8568 (pt0) cc_final: 0.8359 (pm20) REVERT: V 73 ASP cc_start: 0.8750 (t0) cc_final: 0.8525 (t0) REVERT: V 76 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9082 (mmtm) outliers start: 43 outliers final: 20 residues processed: 364 average time/residue: 0.1747 time to fit residues: 97.5222 Evaluate side-chains 336 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 315 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain T residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [33, 27, 263, 22, 30, 259, 288, 13, 240, 265, 78] chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.034850 restraints weight = 90800.885| |-----------------------------------------------------------------------------| r_work (start): 0.2455 rms_B_bonded: 3.82 r_work: 0.2318 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 24717 Z= 0.408 Angle : 0.747 7.342 33657 Z= 0.395 Chirality : 0.047 0.179 3642 Planarity : 0.005 0.050 4287 Dihedral : 5.352 21.073 3414 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.00 % Allowed : 10.29 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3069 helix: 0.68 (0.36), residues: 195 sheet: 0.92 (0.15), residues: 1151 loop : -0.19 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 87 TYR 0.039 0.002 TYR R 51 PHE 0.022 0.002 PHE E 79 TRP 0.013 0.002 TRP D 36 HIS 0.006 0.002 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00936 / 0.41 (24678) covalent geometry : angle 0.74504 / 0.39 (33579) SS BOND : bond 0.00502 / 0.36 ( 39) SS BOND : angle 1.27646 / 0.84 ( 78) hydrogen bonds : bond 0.04320 / 2.92 ( 888) hydrogen bonds : angle 6.12538 / 4.17 ( 2448) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.7869 (t0) cc_final: 0.6995 (t0) REVERT: D 79 LEU cc_start: 0.8816 (mp) cc_final: 0.8531 (mp) REVERT: E 28 ASP cc_start: 0.8807 (t70) cc_final: 0.8154 (t70) REVERT: E 102 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8278 (p0) REVERT: F 12 ASP cc_start: 0.8354 (t0) cc_final: 0.7484 (t0) REVERT: F 16 GLN cc_start: 0.9358 (pm20) cc_final: 0.9106 (pm20) REVERT: F 79 LEU cc_start: 0.9042 (mp) cc_final: 0.8567 (mp) REVERT: F 84 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8207 (mm-30) REVERT: G 28 ASP cc_start: 0.8056 (m-30) cc_final: 0.7827 (m-30) REVERT: G 102 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8439 (p0) REVERT: A 175 TYR cc_start: 0.9026 (m-80) cc_final: 0.8583 (m-80) REVERT: H 12 ASP cc_start: 0.8326 (t0) cc_final: 0.7840 (t0) REVERT: I 28 ASP cc_start: 0.8961 (t70) cc_final: 0.8451 (t70) REVERT: I 47 GLU cc_start: 0.9026 (tt0) cc_final: 0.8208 (pt0) REVERT: L 84 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7979 (mm-30) REVERT: B 102 MET cc_start: 0.8970 (mmp) cc_final: 0.8582 (ppp) REVERT: B 187 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8825 (tpt) REVERT: B 385 MET cc_start: 0.8806 (tpt) cc_final: 0.8474 (tpt) REVERT: B 396 MET cc_start: 0.8372 (tmm) cc_final: 0.7902 (tmm) REVERT: K 10 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7518 (tm-30) REVERT: K 12 LYS cc_start: 0.9475 (mttt) cc_final: 0.9041 (mtmt) REVERT: K 23 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7687 (tm-30) REVERT: K 73 ASP cc_start: 0.8548 (t0) cc_final: 0.8125 (t0) REVERT: M 10 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7768 (tm-30) REVERT: M 23 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7498 (tm-30) REVERT: M 46 ASP cc_start: 0.8693 (m-30) cc_final: 0.8010 (p0) REVERT: M 73 ASP cc_start: 0.8509 (t0) cc_final: 0.8066 (t0) REVERT: O 23 GLU cc_start: 0.9108 (tt0) cc_final: 0.8614 (tm-30) REVERT: O 73 ASP cc_start: 0.8668 (t0) cc_final: 0.8307 (t0) REVERT: R 47 GLU cc_start: 0.9231 (tt0) cc_final: 0.8914 (tt0) REVERT: R 76 LYS cc_start: 0.9304 (mmtm) cc_final: 0.8959 (mmtm) REVERT: R 114 GLU cc_start: 0.9340 (tt0) cc_final: 0.8879 (tt0) outliers start: 53 outliers final: 35 residues processed: 331 average time/residue: 0.1802 time to fit residues: 91.0121 Evaluate side-chains 304 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain T residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [125, 17, 285, 130, 193, 123, 253, 78, 284, 89, 293] chunk 125 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 253 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 293 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN H 16 GLN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.051318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.036977 restraints weight = 88734.489| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 3.82 r_work: 0.2380 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24717 Z= 0.132 Angle : 0.628 9.475 33657 Z= 0.327 Chirality : 0.044 0.203 3642 Planarity : 0.004 0.050 4287 Dihedral : 4.922 18.432 3414 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.36 % Allowed : 11.46 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3069 helix: 1.10 (0.37), residues: 195 sheet: 1.11 (0.15), residues: 1133 loop : -0.17 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 85 TYR 0.031 0.001 TYR V 51 PHE 0.012 0.001 PHE T 79 TRP 0.012 0.001 TRP E 114 HIS 0.005 0.001 HIS R 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (24678) covalent geometry : angle 0.62755 / 0.33 (33579) SS BOND : bond 0.00255 / 0.17 ( 39) SS BOND : angle 0.74427 / 0.49 ( 78) hydrogen bonds : bond 0.03465 / 2.32 ( 888) hydrogen bonds : angle 5.70919 / 3.87 ( 2448) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 319 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.7869 (t0) cc_final: 0.6931 (t0) REVERT: D 79 LEU cc_start: 0.8677 (mp) cc_final: 0.8362 (mp) REVERT: E 28 ASP cc_start: 0.8726 (t70) cc_final: 0.8058 (t70) REVERT: E 102 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8255 (p0) REVERT: F 12 ASP cc_start: 0.8276 (t0) cc_final: 0.7366 (t0) REVERT: F 16 GLN cc_start: 0.9404 (pm20) cc_final: 0.9195 (pm20) REVERT: F 54 LYS cc_start: 0.9325 (ttmm) cc_final: 0.9081 (ttmm) REVERT: F 79 LEU cc_start: 0.9004 (mp) cc_final: 0.8490 (mp) REVERT: F 84 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8219 (mm-30) REVERT: G 28 ASP cc_start: 0.8363 (m-30) cc_final: 0.8058 (m-30) REVERT: G 102 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8239 (p0) REVERT: A 175 TYR cc_start: 0.9123 (m-80) cc_final: 0.8685 (m-10) REVERT: H 12 ASP cc_start: 0.8328 (t0) cc_final: 0.7172 (t0) REVERT: H 16 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: I 28 ASP cc_start: 0.8907 (t70) cc_final: 0.8338 (t0) REVERT: I 47 GLU cc_start: 0.9028 (tt0) cc_final: 0.8223 (pt0) REVERT: J 82 GLU cc_start: 0.8288 (pp20) cc_final: 0.8025 (pp20) REVERT: S 94 ASP cc_start: 0.8894 (m-30) cc_final: 0.8561 (m-30) REVERT: L 84 GLU cc_start: 0.8650 (mt-10) cc_final: 0.7968 (mm-30) REVERT: N 84 GLU cc_start: 0.8723 (mt-10) cc_final: 0.7920 (mm-30) REVERT: N 106 LYS cc_start: 0.8068 (tppt) cc_final: 0.7276 (tppt) REVERT: B 102 MET cc_start: 0.9010 (mmp) cc_final: 0.8574 (ppp) REVERT: B 385 MET cc_start: 0.8857 (tpt) cc_final: 0.8588 (tpt) REVERT: B 396 MET cc_start: 0.8535 (tmm) cc_final: 0.8048 (tmm) REVERT: Q 106 LYS cc_start: 0.9310 (tppp) cc_final: 0.8722 (tppt) REVERT: K 10 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7443 (tm-30) REVERT: K 12 LYS cc_start: 0.9523 (mttt) cc_final: 0.9247 (mttt) REVERT: K 23 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7616 (tm-30) REVERT: K 43 GLN cc_start: 0.9286 (mm-40) cc_final: 0.9064 (mp10) REVERT: K 73 ASP cc_start: 0.8590 (t0) cc_final: 0.8172 (t0) REVERT: K 81 MET cc_start: 0.9191 (tmm) cc_final: 0.8193 (tmm) REVERT: M 23 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7535 (tm-30) REVERT: M 73 ASP cc_start: 0.8536 (t0) cc_final: 0.8147 (t0) REVERT: O 23 GLU cc_start: 0.9083 (tt0) cc_final: 0.8580 (tm-30) REVERT: O 43 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8985 (mp10) REVERT: O 73 ASP cc_start: 0.8692 (t0) cc_final: 0.8314 (t0) REVERT: R 47 GLU cc_start: 0.9209 (tt0) cc_final: 0.8896 (tt0) REVERT: R 76 LYS cc_start: 0.9377 (mmtm) cc_final: 0.9001 (mmtm) REVERT: R 114 GLU cc_start: 0.9284 (tt0) cc_final: 0.8899 (tt0) REVERT: V 73 ASP cc_start: 0.8866 (t0) cc_final: 0.8549 (t0) outliers start: 36 outliers final: 23 residues processed: 341 average time/residue: 0.1782 time to fit residues: 92.7696 Evaluate side-chains 312 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [156, 229, 192, 11, 264, 260, 280, 276, 241, 74, 242] chunk 156 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 280 optimal weight: 0.0870 chunk 276 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 overall best weight: 3.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN C 377 GLN ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.035465 restraints weight = 90248.726| |-----------------------------------------------------------------------------| r_work (start): 0.2468 rms_B_bonded: 3.82 r_work: 0.2329 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 24717 Z= 0.316 Angle : 0.684 9.559 33657 Z= 0.359 Chirality : 0.045 0.183 3642 Planarity : 0.005 0.049 4287 Dihedral : 5.076 19.367 3414 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.00 % Allowed : 12.52 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3069 helix: 0.89 (0.37), residues: 195 sheet: 0.86 (0.15), residues: 1134 loop : -0.27 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 17 TYR 0.034 0.002 TYR V 51 PHE 0.017 0.002 PHE E 79 TRP 0.011 0.001 TRP C 335 HIS 0.005 0.001 HIS T 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.32 (24678) covalent geometry : angle 0.68282 / 0.36 (33579) SS BOND : bond 0.00446 / 0.30 ( 39) SS BOND : angle 1.11518 / 0.72 ( 78) hydrogen bonds : bond 0.03833 / 2.59 ( 888) hydrogen bonds : angle 5.79449 / 3.93 ( 2448) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.8071 (t0) cc_final: 0.7253 (t0) REVERT: D 79 LEU cc_start: 0.8877 (mp) cc_final: 0.8605 (mp) REVERT: E 28 ASP cc_start: 0.8844 (t70) cc_final: 0.8192 (t70) REVERT: E 102 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8428 (p0) REVERT: F 12 ASP cc_start: 0.8386 (t0) cc_final: 0.7408 (t0) REVERT: F 16 GLN cc_start: 0.9425 (pm20) cc_final: 0.9162 (pm20) REVERT: F 79 LEU cc_start: 0.9062 (mp) cc_final: 0.8530 (mp) REVERT: F 84 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8299 (mm-30) REVERT: G 28 ASP cc_start: 0.8409 (m-30) cc_final: 0.8101 (m-30) REVERT: G 102 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8386 (p0) REVERT: A 175 TYR cc_start: 0.9160 (m-80) cc_final: 0.8668 (m-10) REVERT: H 12 ASP cc_start: 0.8508 (t0) cc_final: 0.7592 (t0) REVERT: I 28 ASP cc_start: 0.9025 (t70) cc_final: 0.8509 (t70) REVERT: I 47 GLU cc_start: 0.9033 (tt0) cc_final: 0.8182 (pt0) REVERT: J 77 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8304 (tpm170) REVERT: J 82 GLU cc_start: 0.8250 (pp20) cc_final: 0.7988 (pp20) REVERT: S 106 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8831 (mmmm) REVERT: L 84 GLU cc_start: 0.8649 (mt-10) cc_final: 0.7999 (mm-30) REVERT: N 77 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8244 (tpm170) REVERT: N 84 GLU cc_start: 0.8700 (mt-10) cc_final: 0.7831 (mm-30) REVERT: N 106 LYS cc_start: 0.8060 (tppt) cc_final: 0.7811 (tppt) REVERT: B 102 MET cc_start: 0.9091 (mmp) cc_final: 0.8691 (ppp) REVERT: B 396 MET cc_start: 0.8566 (tmm) cc_final: 0.8055 (tmm) REVERT: C 179 MET cc_start: 0.8889 (mmm) cc_final: 0.8643 (mmm) REVERT: C 376 MET cc_start: 0.9040 (tpp) cc_final: 0.8800 (tpp) REVERT: Q 106 LYS cc_start: 0.9337 (tppp) cc_final: 0.8738 (tppt) REVERT: K 10 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7271 (tm-30) REVERT: K 12 LYS cc_start: 0.9535 (mttt) cc_final: 0.9206 (mtmt) REVERT: K 23 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7754 (tm-30) REVERT: K 73 ASP cc_start: 0.8604 (t0) cc_final: 0.8176 (t0) REVERT: K 81 MET cc_start: 0.9166 (tmm) cc_final: 0.8183 (tmm) REVERT: M 23 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7521 (tm-30) REVERT: M 73 ASP cc_start: 0.8525 (t0) cc_final: 0.8113 (t0) REVERT: M 81 MET cc_start: 0.9099 (tmm) cc_final: 0.7941 (tmm) REVERT: O 23 GLU cc_start: 0.9115 (tt0) cc_final: 0.8602 (tm-30) REVERT: O 73 ASP cc_start: 0.8686 (t0) cc_final: 0.8284 (t0) REVERT: R 47 GLU cc_start: 0.9239 (tt0) cc_final: 0.8953 (tt0) REVERT: R 114 GLU cc_start: 0.9338 (tt0) cc_final: 0.8923 (tt0) REVERT: V 73 ASP cc_start: 0.8820 (t0) cc_final: 0.8441 (t0) outliers start: 53 outliers final: 41 residues processed: 320 average time/residue: 0.1762 time to fit residues: 86.0872 Evaluate side-chains 310 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [184, 171, 242, 267, 73, 227, 141, 296, 207, 66, 18] chunk 184 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 296 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.051136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.036841 restraints weight = 88817.103| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 3.81 r_work: 0.2385 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24717 Z= 0.132 Angle : 0.626 8.428 33657 Z= 0.325 Chirality : 0.043 0.212 3642 Planarity : 0.004 0.050 4287 Dihedral : 4.826 18.388 3414 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.62 % Allowed : 13.12 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3069 helix: 1.04 (0.38), residues: 195 sheet: 1.00 (0.15), residues: 1133 loop : -0.29 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 85 TYR 0.027 0.001 TYR H 50 PHE 0.012 0.001 PHE R 79 TRP 0.011 0.001 TRP K 50 HIS 0.004 0.001 HIS R 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (24678) covalent geometry : angle 0.62520 / 0.32 (33579) SS BOND : bond 0.00266 / 0.18 ( 39) SS BOND : angle 0.77911 / 0.50 ( 78) hydrogen bonds : bond 0.03299 / 2.21 ( 888) hydrogen bonds : angle 5.53436 / 3.75 ( 2448) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 299 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.8068 (t70) cc_final: 0.7217 (t0) REVERT: D 79 LEU cc_start: 0.8681 (mp) cc_final: 0.8382 (mp) REVERT: E 28 ASP cc_start: 0.8763 (t70) cc_final: 0.8081 (t70) REVERT: E 102 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8329 (p0) REVERT: F 12 ASP cc_start: 0.8301 (t0) cc_final: 0.7370 (t0) REVERT: F 54 LYS cc_start: 0.9276 (ttmm) cc_final: 0.9024 (ttmm) REVERT: F 79 LEU cc_start: 0.9004 (mp) cc_final: 0.8451 (mp) REVERT: G 2 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8349 (tm-30) REVERT: G 28 ASP cc_start: 0.8500 (m-30) cc_final: 0.8111 (m-30) REVERT: G 102 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8324 (p0) REVERT: A 175 TYR cc_start: 0.9163 (m-80) cc_final: 0.8694 (m-10) REVERT: A 396 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7976 (tmm) REVERT: H 12 ASP cc_start: 0.8244 (t0) cc_final: 0.7575 (t0) REVERT: I 28 ASP cc_start: 0.8935 (t70) cc_final: 0.8344 (t0) REVERT: I 47 GLU cc_start: 0.9025 (tt0) cc_final: 0.8204 (pt0) REVERT: J 82 GLU cc_start: 0.8198 (pp20) cc_final: 0.7979 (pp20) REVERT: J 84 GLU cc_start: 0.8716 (mt-10) cc_final: 0.7918 (mm-30) REVERT: L 84 GLU cc_start: 0.8670 (mt-10) cc_final: 0.7990 (mm-30) REVERT: L 107 LEU cc_start: 0.8990 (tt) cc_final: 0.8306 (tt) REVERT: N 84 GLU cc_start: 0.8724 (mt-10) cc_final: 0.7882 (mm-30) REVERT: N 106 LYS cc_start: 0.8128 (tppt) cc_final: 0.7726 (tppt) REVERT: B 187 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8208 (tpt) REVERT: B 396 MET cc_start: 0.8588 (tmm) cc_final: 0.8078 (tmm) REVERT: C 179 MET cc_start: 0.8894 (mmm) cc_final: 0.8597 (mmm) REVERT: C 376 MET cc_start: 0.8985 (tpp) cc_final: 0.8735 (tpp) REVERT: Q 106 LYS cc_start: 0.9325 (tppp) cc_final: 0.8757 (tppt) REVERT: K 10 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7166 (tm-30) REVERT: K 12 LYS cc_start: 0.9580 (mttt) cc_final: 0.9305 (mtmt) REVERT: K 23 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7721 (tm-30) REVERT: K 73 ASP cc_start: 0.8610 (t0) cc_final: 0.8195 (t0) REVERT: K 81 MET cc_start: 0.9220 (tmm) cc_final: 0.8227 (tmm) REVERT: M 10 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7471 (tm-30) REVERT: M 12 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8920 (ptpt) REVERT: M 23 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7474 (tm-30) REVERT: M 73 ASP cc_start: 0.8539 (t0) cc_final: 0.8138 (t0) REVERT: O 10 GLU cc_start: 0.8062 (tm-30) cc_final: 0.6884 (tm-30) REVERT: O 23 GLU cc_start: 0.9090 (tt0) cc_final: 0.8578 (tm-30) REVERT: O 43 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8988 (mp10) REVERT: O 73 ASP cc_start: 0.8695 (t0) cc_final: 0.8298 (t0) REVERT: R 47 GLU cc_start: 0.9215 (tt0) cc_final: 0.8922 (tt0) REVERT: R 76 LYS cc_start: 0.9394 (mmtm) cc_final: 0.9032 (mmtm) REVERT: R 114 GLU cc_start: 0.9304 (tt0) cc_final: 0.8953 (tt0) REVERT: V 73 ASP cc_start: 0.8840 (t0) cc_final: 0.8506 (t0) outliers start: 43 outliers final: 34 residues processed: 331 average time/residue: 0.1805 time to fit residues: 90.6130 Evaluate side-chains 318 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain M residue 12 LYS Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain V residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [256, 81, 178, 137, 35, 194, 181, 50, 71, 79, 226] chunk 256 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.036299 restraints weight = 89157.509| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 3.79 r_work: 0.2368 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24717 Z= 0.212 Angle : 0.644 8.743 33657 Z= 0.335 Chirality : 0.043 0.208 3642 Planarity : 0.004 0.049 4287 Dihedral : 4.834 18.034 3414 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.00 % Allowed : 13.01 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 3069 helix: 1.02 (0.38), residues: 195 sheet: 0.93 (0.15), residues: 1130 loop : -0.33 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 87 TYR 0.027 0.001 TYR V 51 PHE 0.014 0.001 PHE V 79 TRP 0.011 0.001 TRP S 36 HIS 0.004 0.001 HIS T 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (24678) covalent geometry : angle 0.64291 / 0.33 (33579) SS BOND : bond 0.00307 / 0.21 ( 39) SS BOND : angle 0.90695 / 0.58 ( 78) hydrogen bonds : bond 0.03429 / 2.31 ( 888) hydrogen bonds : angle 5.54597 / 3.76 ( 2448) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 293 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.8057 (t70) cc_final: 0.7197 (t0) REVERT: D 79 LEU cc_start: 0.8714 (mp) cc_final: 0.8413 (mp) REVERT: E 28 ASP cc_start: 0.8784 (t70) cc_final: 0.8100 (t70) REVERT: E 102 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8412 (p0) REVERT: F 12 ASP cc_start: 0.8275 (t0) cc_final: 0.7527 (t0) REVERT: F 54 LYS cc_start: 0.9272 (ttmm) cc_final: 0.8997 (ttmm) REVERT: F 79 LEU cc_start: 0.9055 (mp) cc_final: 0.8543 (mp) REVERT: G 28 ASP cc_start: 0.8493 (m-30) cc_final: 0.8279 (m-30) REVERT: G 102 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8347 (p0) REVERT: A 175 TYR cc_start: 0.9182 (m-80) cc_final: 0.8693 (m-10) REVERT: A 396 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7972 (tmm) REVERT: H 12 ASP cc_start: 0.8253 (t0) cc_final: 0.7714 (t0) REVERT: I 28 ASP cc_start: 0.8965 (t70) cc_final: 0.8437 (t70) REVERT: I 47 GLU cc_start: 0.9028 (tt0) cc_final: 0.8215 (pt0) REVERT: J 77 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8289 (tpm170) REVERT: J 84 GLU cc_start: 0.8721 (mt-10) cc_final: 0.7933 (mm-30) REVERT: N 84 GLU cc_start: 0.8711 (mt-10) cc_final: 0.7799 (mm-30) REVERT: B 102 MET cc_start: 0.8921 (mmp) cc_final: 0.8703 (ppp) REVERT: B 396 MET cc_start: 0.8602 (tmm) cc_final: 0.8077 (tmm) REVERT: C 179 MET cc_start: 0.8845 (mmm) cc_final: 0.8582 (mmm) REVERT: Q 106 LYS cc_start: 0.9333 (tppp) cc_final: 0.8764 (tppt) REVERT: K 10 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7145 (tm-30) REVERT: K 12 LYS cc_start: 0.9575 (mttt) cc_final: 0.9288 (mtmt) REVERT: K 23 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7770 (tm-30) REVERT: K 73 ASP cc_start: 0.8617 (t0) cc_final: 0.8184 (t0) REVERT: K 81 MET cc_start: 0.9211 (tmm) cc_final: 0.8615 (tmm) REVERT: M 23 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7493 (tm-30) REVERT: M 73 ASP cc_start: 0.8534 (t0) cc_final: 0.8128 (t0) REVERT: M 81 MET cc_start: 0.9117 (tmm) cc_final: 0.7953 (tmm) REVERT: O 10 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7703 (tm-30) REVERT: O 23 GLU cc_start: 0.9104 (tt0) cc_final: 0.8590 (tm-30) REVERT: O 43 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8852 (mp10) REVERT: O 73 ASP cc_start: 0.8697 (t0) cc_final: 0.8294 (t0) REVERT: R 47 GLU cc_start: 0.9246 (tt0) cc_final: 0.8963 (tt0) REVERT: R 114 GLU cc_start: 0.9324 (tt0) cc_final: 0.8996 (tt0) REVERT: V 73 ASP cc_start: 0.8849 (t0) cc_final: 0.8525 (t0) outliers start: 53 outliers final: 41 residues processed: 330 average time/residue: 0.1855 time to fit residues: 93.0912 Evaluate side-chains 324 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 80 GLN Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 80 GLN Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [92, 206, 153, 12, 100, 280, 219, 3, 284, 6, 211] chunk 92 optimal weight: 0.0980 chunk 206 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 284 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 173 HIS ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.051862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.037541 restraints weight = 88608.981| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 3.81 r_work: 0.2408 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24717 Z= 0.121 Angle : 0.633 9.441 33657 Z= 0.325 Chirality : 0.043 0.200 3642 Planarity : 0.004 0.050 4287 Dihedral : 4.629 16.912 3414 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.55 % Allowed : 13.69 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3069 helix: 0.69 (0.36), residues: 213 sheet: 1.01 (0.15), residues: 1130 loop : -0.23 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 87 TYR 0.026 0.001 TYR H 50 PHE 0.013 0.001 PHE T 79 TRP 0.012 0.001 TRP K 50 HIS 0.003 0.001 HIS T 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (24678) covalent geometry : angle 0.63321 / 0.32 (33579) SS BOND : bond 0.00254 / 0.16 ( 39) SS BOND : angle 0.68643 / 0.44 ( 78) hydrogen bonds : bond 0.03075 / 2.06 ( 888) hydrogen bonds : angle 5.36888 / 3.64 ( 2448) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 314 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.7991 (t70) cc_final: 0.7074 (t0) REVERT: D 79 LEU cc_start: 0.8392 (mp) cc_final: 0.7989 (mp) REVERT: E 6 GLN cc_start: 0.9278 (tp-100) cc_final: 0.9022 (tp-100) REVERT: E 28 ASP cc_start: 0.8648 (t70) cc_final: 0.8075 (t0) REVERT: E 102 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8343 (p0) REVERT: F 12 ASP cc_start: 0.8289 (t0) cc_final: 0.7636 (t0) REVERT: F 79 LEU cc_start: 0.8926 (mp) cc_final: 0.8473 (mp) REVERT: G 28 ASP cc_start: 0.8553 (m-30) cc_final: 0.8312 (m-30) REVERT: G 102 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8331 (p0) REVERT: A 175 TYR cc_start: 0.9199 (m-80) cc_final: 0.8687 (m-10) REVERT: A 396 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8039 (tmm) REVERT: H 12 ASP cc_start: 0.8270 (t0) cc_final: 0.7402 (t0) REVERT: H 16 GLN cc_start: 0.9449 (pm20) cc_final: 0.9231 (pm20) REVERT: I 28 ASP cc_start: 0.8905 (t70) cc_final: 0.8309 (t0) REVERT: I 30 MET cc_start: 0.9158 (mtp) cc_final: 0.8940 (tpp) REVERT: I 44 LYS cc_start: 0.9285 (mppt) cc_final: 0.8974 (mppt) REVERT: I 47 GLU cc_start: 0.9024 (tt0) cc_final: 0.8193 (pt0) REVERT: J 20 ILE cc_start: 0.8849 (mt) cc_final: 0.8533 (tp) REVERT: J 84 GLU cc_start: 0.8743 (mt-10) cc_final: 0.7930 (mm-30) REVERT: S 94 ASP cc_start: 0.8910 (m-30) cc_final: 0.8634 (m-30) REVERT: L 17 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7605 (ttp80) REVERT: L 20 ILE cc_start: 0.8996 (mt) cc_final: 0.8504 (tp) REVERT: L 84 GLU cc_start: 0.8696 (mt-10) cc_final: 0.7972 (mm-30) REVERT: N 84 GLU cc_start: 0.8697 (mt-10) cc_final: 0.7796 (mm-30) REVERT: B 102 MET cc_start: 0.8960 (mmp) cc_final: 0.8706 (ppp) REVERT: B 396 MET cc_start: 0.8693 (tmm) cc_final: 0.8244 (tmm) REVERT: C 179 MET cc_start: 0.8833 (mmm) cc_final: 0.8527 (mmm) REVERT: Q 106 LYS cc_start: 0.9302 (tppp) cc_final: 0.8762 (tppt) REVERT: K 12 LYS cc_start: 0.9584 (mttt) cc_final: 0.9361 (mtmt) REVERT: K 23 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7697 (tm-30) REVERT: K 73 ASP cc_start: 0.8606 (t0) cc_final: 0.8190 (t0) REVERT: K 81 MET cc_start: 0.9220 (tmm) cc_final: 0.8630 (tmm) REVERT: M 23 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7467 (tm-30) REVERT: M 73 ASP cc_start: 0.8494 (t0) cc_final: 0.8105 (t0) REVERT: O 10 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7766 (tm-30) REVERT: O 23 GLU cc_start: 0.9097 (tt0) cc_final: 0.8572 (tm-30) REVERT: O 43 GLN cc_start: 0.9236 (mm-40) cc_final: 0.9023 (mp10) REVERT: O 73 ASP cc_start: 0.8687 (t0) cc_final: 0.8286 (t0) REVERT: R 47 GLU cc_start: 0.9227 (tt0) cc_final: 0.8949 (tt0) REVERT: R 76 LYS cc_start: 0.9389 (mmtm) cc_final: 0.9058 (mmtm) REVERT: R 114 GLU cc_start: 0.9302 (tt0) cc_final: 0.9003 (tt0) REVERT: V 73 ASP cc_start: 0.8795 (t0) cc_final: 0.8434 (t0) outliers start: 41 outliers final: 34 residues processed: 342 average time/residue: 0.1805 time to fit residues: 93.7784 Evaluate side-chains 331 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 294 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 80 GLN Chi-restraints excluded: chain Q residue 80 GLN Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [19, 7, 48, 124, 135, 71, 187, 299, 218, 156, 67] chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 135 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 187 optimal weight: 0.3980 chunk 299 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 156 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS H 94 ASN ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.038046 restraints weight = 88453.947| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 3.84 r_work: 0.2424 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24717 Z= 0.112 Angle : 0.639 9.955 33657 Z= 0.326 Chirality : 0.043 0.194 3642 Planarity : 0.004 0.048 4287 Dihedral : 4.513 17.356 3414 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.43 % Allowed : 14.14 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3069 helix: 0.95 (0.38), residues: 195 sheet: 1.07 (0.15), residues: 1165 loop : -0.30 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 17 TYR 0.026 0.001 TYR H 50 PHE 0.013 0.001 PHE T 79 TRP 0.012 0.001 TRP K 50 HIS 0.003 0.001 HIS T 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (24678) covalent geometry : angle 0.63861 / 0.33 (33579) SS BOND : bond 0.00227 / 0.14 ( 39) SS BOND : angle 0.65971 / 0.42 ( 78) hydrogen bonds : bond 0.02963 / 1.99 ( 888) hydrogen bonds : angle 5.28593 / 3.58 ( 2448) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.7963 (t70) cc_final: 0.7042 (t0) REVERT: D 79 LEU cc_start: 0.8311 (mp) cc_final: 0.7913 (mp) REVERT: E 6 GLN cc_start: 0.9288 (tp-100) cc_final: 0.9018 (tp-100) REVERT: E 28 ASP cc_start: 0.8634 (t70) cc_final: 0.8274 (t0) REVERT: E 47 GLU cc_start: 0.9007 (tt0) cc_final: 0.8557 (pt0) REVERT: E 102 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8331 (p0) REVERT: F 12 ASP cc_start: 0.8254 (t0) cc_final: 0.7469 (t0) REVERT: F 79 LEU cc_start: 0.8941 (mp) cc_final: 0.8482 (mp) REVERT: G 28 ASP cc_start: 0.8546 (m-30) cc_final: 0.8326 (m-30) REVERT: G 102 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8353 (p0) REVERT: A 175 TYR cc_start: 0.9231 (m-80) cc_final: 0.8735 (m-10) REVERT: A 396 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8060 (tmm) REVERT: H 12 ASP cc_start: 0.8217 (t0) cc_final: 0.7342 (t0) REVERT: H 16 GLN cc_start: 0.9446 (pm20) cc_final: 0.9241 (pm20) REVERT: I 28 ASP cc_start: 0.8820 (t70) cc_final: 0.8255 (t0) REVERT: I 44 LYS cc_start: 0.9309 (mppt) cc_final: 0.8956 (mppt) REVERT: I 47 GLU cc_start: 0.9017 (tt0) cc_final: 0.8205 (pt0) REVERT: J 20 ILE cc_start: 0.8884 (mt) cc_final: 0.8545 (tp) REVERT: J 84 GLU cc_start: 0.8702 (mt-10) cc_final: 0.7912 (mm-30) REVERT: S 94 ASP cc_start: 0.8916 (m-30) cc_final: 0.8664 (m-30) REVERT: L 20 ILE cc_start: 0.9019 (mt) cc_final: 0.8528 (tp) REVERT: L 77 ARG cc_start: 0.8948 (ttp80) cc_final: 0.8513 (tpm170) REVERT: L 84 GLU cc_start: 0.8678 (mt-10) cc_final: 0.7948 (mm-30) REVERT: N 84 GLU cc_start: 0.8675 (mt-10) cc_final: 0.7766 (mm-30) REVERT: B 102 MET cc_start: 0.8995 (mmp) cc_final: 0.8644 (ppp) REVERT: B 396 MET cc_start: 0.8749 (tmm) cc_final: 0.8313 (tmm) REVERT: C 179 MET cc_start: 0.8834 (mmm) cc_final: 0.8530 (mmm) REVERT: C 263 PHE cc_start: 0.8815 (m-80) cc_final: 0.8509 (m-80) REVERT: C 264 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8638 (mpt-90) REVERT: Q 106 LYS cc_start: 0.9290 (tppp) cc_final: 0.8748 (tppt) REVERT: K 23 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7690 (tm-30) REVERT: K 73 ASP cc_start: 0.8594 (t0) cc_final: 0.8166 (t0) REVERT: K 81 MET cc_start: 0.9235 (tmm) cc_final: 0.8652 (tmm) REVERT: M 10 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7396 (tm-30) REVERT: M 23 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7453 (tm-30) REVERT: M 73 ASP cc_start: 0.8482 (t0) cc_final: 0.8092 (t0) REVERT: O 10 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7677 (tm-30) REVERT: O 23 GLU cc_start: 0.9101 (tt0) cc_final: 0.8570 (tm-30) REVERT: O 73 ASP cc_start: 0.8641 (t0) cc_final: 0.8255 (t0) REVERT: O 87 ARG cc_start: 0.8844 (mtm110) cc_final: 0.7969 (mtm110) REVERT: R 47 GLU cc_start: 0.9232 (tt0) cc_final: 0.8946 (tt0) REVERT: R 76 LYS cc_start: 0.9380 (mmtm) cc_final: 0.9056 (mmtm) REVERT: R 114 GLU cc_start: 0.9293 (tt0) cc_final: 0.9055 (tt0) REVERT: V 51 TYR cc_start: 0.9318 (p90) cc_final: 0.9095 (p90) outliers start: 38 outliers final: 32 residues processed: 343 average time/residue: 0.1783 time to fit residues: 93.0755 Evaluate side-chains 334 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 299 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 80 GLN Chi-restraints excluded: chain Q residue 80 GLN Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: [297, 224, 104, 140, 149, 127, 38, 206, 244, 208, 252] chunk 297 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 127 optimal weight: 0.0170 chunk 38 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.051241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.036861 restraints weight = 89554.924| |-----------------------------------------------------------------------------| r_work (start): 0.2515 rms_B_bonded: 3.81 r_work: 0.2377 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24717 Z= 0.198 Angle : 0.673 11.068 33657 Z= 0.344 Chirality : 0.043 0.189 3642 Planarity : 0.005 0.057 4287 Dihedral : 4.659 18.975 3414 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.40 % Allowed : 14.37 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3069 helix: 1.00 (0.39), residues: 195 sheet: 1.02 (0.15), residues: 1130 loop : -0.34 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 85 TYR 0.034 0.001 TYR R 51 PHE 0.014 0.001 PHE V 79 TRP 0.010 0.001 TRP Q 36 HIS 0.004 0.001 HIS T 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (24678) covalent geometry : angle 0.67276 / 0.34 (33579) SS BOND : bond 0.00291 / 0.20 ( 39) SS BOND : angle 0.87607 / 0.57 ( 78) hydrogen bonds : bond 0.03231 / 2.17 ( 888) hydrogen bonds : angle 5.35101 / 3.63 ( 2448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4942.43 seconds wall clock time: 85 minutes 42.92 seconds (5142.92 seconds total)