Starting phenix.real_space_refine on Sun Oct 25 06:15:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11iw_75729/10_2026/11iw_75729.cif Found real_map, /net/cci-nas-00/data/ceres_data/11iw_75729/10_2026/11iw_75729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11iw_75729/10_2026/11iw_75729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11iw_75729/10_2026/11iw_75729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11iw_75729/10_2026/11iw_75729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11iw_75729/10_2026/11iw_75729.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 106 5.16 5 C 9839 2.51 5 N 2622 2.21 5 O 2978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 15545 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2830 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 23, 'TRANS': 339} Chain breaks: 2 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: "J" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} 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: "I" 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: "G" 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: "F" 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: "H" 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: "B" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2830 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 23, 'TRANS': 339} Chain breaks: 2 Chain: "C" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2830 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 23, 'TRANS': 339} Chain breaks: 2 Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 941 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Time building chain proxies: 3.13, per 1000 atoms: 0.20 Number of scatterers: 15545 At special positions: 0 Unit cell: (138.6, 110.88, 116.16, 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 106 16.00 O 2978 8.00 N 2622 7.00 C 9839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS K 21 " - pdb=" SG CYS K 95 " 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: 1.15 Conformation dependent library (CDL) restraints added in 718.5 milliseconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3646 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 46 sheets defined 14.4% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 90 through 104 removed outlier: 3.663A pdb=" N ASN A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.272A pdb=" N GLU A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.761A pdb=" N ASN A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 removed outlier: 4.124A pdb=" N SER A 166 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 removed outlier: 4.047A pdb=" N ASP A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 267 " --> pdb=" O PHE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 294 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.914A pdb=" N HIS A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.258A pdb=" N ILE A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.942A pdb=" N LEU A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.799A pdb=" N LYS I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.503A pdb=" N LYS G 65 " --> pdb=" O PRO G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 90 through 104 removed outlier: 3.654A pdb=" N ASN B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 104 " --> pdb=" O TRP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.184A pdb=" N GLU B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.751A pdb=" N ASN B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.507A pdb=" N SER B 166 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.688A pdb=" N ASP B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 294 Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.847A pdb=" N HIS B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 4.122A 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: 3.897A pdb=" N LEU B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 105 through 111 removed outlier: 4.117A pdb=" N GLU C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.683A pdb=" N ASN C 158 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 269 removed outlier: 3.608A pdb=" N ASP C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 294 Processing helix chain 'C' and resid 298 through 304 removed outlier: 3.848A pdb=" N HIS C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 339 removed outlier: 4.227A 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: 3.811A pdb=" N LEU C 388 " --> pdb=" O HIS C 384 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.315A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 11 removed outlier: 4.315A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 218 removed outlier: 5.007A pdb=" N THR A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS A 202 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 42 " --> pdb=" O THR K 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.785A pdb=" N MET A 56 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 148 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 135 Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 234 Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA8, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.588A pdb=" N ARG A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.581A pdb=" N ASP D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.893A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP D 86 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.358A pdb=" N MET J 11 " --> pdb=" O GLU J 104 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 4 through 8 Processing sheet with id=AB7, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AB8, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.387A pdb=" N TRP E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG E 39 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 4 through 8 Processing sheet with id=AC1, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AC2, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.382A pdb=" N TRP I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG I 39 " --> pdb=" O TRP I 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL I 93 " --> pdb=" O GLN I 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.587A pdb=" N PHE G 79 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AC5, first strand: chain 'G' and resid 58 through 60 removed outlier: 5.613A pdb=" N TRP G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG G 39 " --> pdb=" O TRP G 48 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AC7, first strand: chain 'F' and resid 46 through 49 removed outlier: 7.067A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP F 86 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD1, first strand: chain 'H' and resid 46 through 49 removed outlier: 7.002A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.309A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.309A pdb=" N TYR B 5 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS B 328 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 11 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP B 326 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 216 through 218 removed outlier: 4.972A pdb=" N THR B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS B 202 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET B 44 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 46 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TRP B 240 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 232 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 132 through 135 removed outlier: 3.764A pdb=" N MET B 56 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 148 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 132 through 135 Processing sheet with id=AD7, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AD8, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.577A pdb=" N ARG B 350 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AE1, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.350A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.350A pdb=" N TYR C 5 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS C 328 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU C 11 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP C 326 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 216 through 218 removed outlier: 4.950A pdb=" N THR C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LYS C 202 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET C 44 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 46 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TRP C 240 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.790A pdb=" N MET C 56 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 148 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 132 through 135 Processing sheet with id=AE6, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AE7, first strand: chain 'C' and resid 346 through 347 removed outlier: 3.551A pdb=" N ARG C 350 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AE9, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'K' and resid 57 through 59 removed outlier: 7.184A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TRP K 49 " --> pdb=" O MET K 33 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET K 33 " --> pdb=" O TRP K 49 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY K 32 " --> pdb=" O GLY K 98 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1359 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: 2.72 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4973 1.34 - 1.46: 3989 1.46 - 1.58: 6824 1.58 - 1.70: 0 1.70 - 1.82: 154 Bond restraints: 15940 Sorted by residual: bond pdb=" N LYS A 1 " pdb=" CA LYS A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N LYS B 1 " pdb=" CA LYS B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N LYS C 1 " pdb=" CA LYS C 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.63e+00 bond pdb=" CB VAL J 29 " pdb=" CG1 VAL J 29 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.04e+00 bond pdb=" CD ARG A 346 " pdb=" NE ARG A 346 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.40e-02 5.10e+03 6.42e-01 ... (remaining 15935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 21102 1.44 - 2.89: 397 2.89 - 4.33: 128 4.33 - 5.78: 15 5.78 - 7.22: 1 Bond angle restraints: 21643 Sorted by residual: angle pdb=" C ALA I 89 " pdb=" N ASP I 90 " pdb=" CA ASP I 90 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.70e+00 angle pdb=" N VAL J 33 " pdb=" CA VAL J 33 " pdb=" C VAL J 33 " ideal model delta sigma weight residual 109.63 113.32 -3.69 1.44e+00 4.82e-01 6.57e+00 angle pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" C SER C 136 " ideal model delta sigma weight residual 109.81 115.14 -5.33 2.21e+00 2.05e-01 5.81e+00 angle pdb=" N SER B 136 " pdb=" CA SER B 136 " pdb=" C SER B 136 " ideal model delta sigma weight residual 109.81 114.88 -5.07 2.21e+00 2.05e-01 5.27e+00 angle pdb=" N SER A 136 " pdb=" CA SER A 136 " pdb=" C SER A 136 " ideal model delta sigma weight residual 109.81 114.77 -4.96 2.21e+00 2.05e-01 5.04e+00 ... (remaining 21638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 8598 17.06 - 34.12: 701 34.12 - 51.17: 137 51.17 - 68.23: 28 68.23 - 85.29: 14 Dihedral angle restraints: 9478 sinusoidal: 3741 harmonic: 5737 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 351 " pdb=" CB CYS A 351 " ideal model delta sinusoidal sigma weight residual 93.00 168.46 -75.46 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS C 344 " pdb=" SG CYS C 344 " pdb=" SG CYS C 351 " pdb=" CB CYS C 351 " ideal model delta sinusoidal sigma weight residual 93.00 167.88 -74.88 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS B 344 " pdb=" SG CYS B 344 " pdb=" SG CYS B 351 " pdb=" CB CYS B 351 " ideal model delta sinusoidal sigma weight residual 93.00 167.26 -74.26 1 1.00e+01 1.00e-02 6.99e+01 ... (remaining 9475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1438 0.030 - 0.060: 630 0.060 - 0.090: 123 0.090 - 0.120: 137 0.120 - 0.150: 27 Chirality restraints: 2355 Sorted by residual: chirality pdb=" CA ILE C 373 " pdb=" N ILE C 373 " pdb=" C ILE C 373 " pdb=" CB ILE C 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE J 48 " pdb=" N ILE J 48 " pdb=" C ILE J 48 " pdb=" CB ILE J 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2352 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 346 " 0.851 9.50e-02 1.11e+02 3.82e-01 9.91e+01 pdb=" NE ARG A 346 " -0.072 2.00e-02 2.50e+03 pdb=" CZ ARG A 346 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG A 346 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 346 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 95 " -0.559 9.50e-02 1.11e+02 2.52e-01 4.61e+01 pdb=" NE ARG A 95 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 95 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 95 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 95 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 234 " 0.477 9.50e-02 1.11e+02 2.16e-01 3.85e+01 pdb=" NE ARG B 234 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 234 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B 234 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG B 234 " -0.002 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 253 2.64 - 3.21: 14910 3.21 - 3.77: 23429 3.77 - 4.34: 33637 4.34 - 4.90: 54378 Nonbonded interactions: 126607 Sorted by model distance: nonbonded pdb=" O VAL E 86 " pdb=" OG1 THR E 87 " model vdw 2.075 3.040 nonbonded pdb=" O SER B 165 " pdb=" OG SER B 166 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR C 171 " pdb=" O THR C 176 " model vdw 2.250 3.040 nonbonded pdb=" NH2 ARG E 67 " pdb=" O SER E 85 " model vdw 2.264 3.120 nonbonded pdb=" NH2 ARG K 66 " pdb=" O ASN K 84 " model vdw 2.302 3.120 ... (remaining 126602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15969 Z= 0.115 Angle : 0.553 7.221 21701 Z= 0.285 Chirality : 0.042 0.150 2355 Planarity : 0.015 0.382 2761 Dihedral : 12.757 85.291 5745 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.06 % Allowed : 0.06 % Favored : 99.88 % 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: -0.08 (0.18), residues: 1970 helix: -0.78 (0.32), residues: 198 sheet: 0.04 (0.20), residues: 589 loop : 0.16 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.004 ARG A 346 TYR 0.018 0.001 TYR K 100 PHE 0.011 0.001 PHE A 263 TRP 0.013 0.001 TRP C 100 HIS 0.005 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15940) covalent geometry : angle 0.55252 / 0.28 (21643) SS BOND : bond 0.00260 / 0.14 ( 29) SS BOND : angle 0.68331 / 0.44 ( 58) hydrogen bonds : bond 0.24846 / 16.50 ( 507) hydrogen bonds : angle 9.27308 / 6.68 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.463 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: A 179 MET cc_start: 0.8574 (mmm) cc_final: 0.7981 (mmm) REVERT: A 275 GLU cc_start: 0.8522 (mp0) cc_final: 0.7837 (mp0) REVERT: J 79 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7650 (tm-30) REVERT: E 4 HIS cc_start: 0.7371 (m-70) cc_final: 0.6952 (m170) REVERT: G 52 ILE cc_start: 0.9429 (tt) cc_final: 0.9152 (tp) REVERT: F 18 VAL cc_start: 0.9264 (p) cc_final: 0.8568 (p) REVERT: F 33 TYR cc_start: 0.9138 (m-80) cc_final: 0.8747 (m-10) REVERT: F 48 LEU cc_start: 0.9016 (mt) cc_final: 0.8805 (mt) REVERT: F 50 TYR cc_start: 0.7900 (p90) cc_final: 0.7568 (p90) REVERT: F 79 LEU cc_start: 0.7529 (mp) cc_final: 0.7155 (mp) REVERT: F 106 LYS cc_start: 0.8974 (tppp) cc_final: 0.8525 (tppt) REVERT: F 107 LEU cc_start: 0.8143 (tp) cc_final: 0.7188 (tp) REVERT: H 18 VAL cc_start: 0.9238 (p) cc_final: 0.8564 (p) REVERT: B 100 TRP cc_start: 0.7926 (t-100) cc_final: 0.7717 (t-100) REVERT: B 179 MET cc_start: 0.7332 (mmm) cc_final: 0.6879 (mmm) REVERT: K 36 MET cc_start: 0.8325 (mmm) cc_final: 0.8031 (mmm) REVERT: K 56 GLU cc_start: 0.8605 (pp20) cc_final: 0.8355 (pp20) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.1352 time to fit residues: 50.4810 Evaluate side-chains 176 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 77, 122, 91] chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 ASN E 77 ASN H 39 GLN B 383 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.076725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051677 restraints weight = 54760.711| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.93 r_work: 0.2826 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15969 Z= 0.269 Angle : 0.695 9.759 21701 Z= 0.366 Chirality : 0.047 0.195 2355 Planarity : 0.005 0.068 2761 Dihedral : 5.155 22.676 2174 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.04 % Allowed : 8.72 % Favored : 90.24 % 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: 0.18 (0.19), residues: 1970 helix: 0.11 (0.33), residues: 219 sheet: 0.06 (0.20), residues: 610 loop : 0.31 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 17 TYR 0.031 0.002 TYR C 98 PHE 0.021 0.002 PHE E 79 TRP 0.015 0.002 TRP E 35 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.27 (15940) covalent geometry : angle 0.69471 / 0.37 (21643) SS BOND : bond 0.00261 / 0.16 ( 29) SS BOND : angle 0.92493 / 0.59 ( 58) hydrogen bonds : bond 0.04815 / 3.20 ( 507) hydrogen bonds : angle 6.29552 / 4.57 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.560 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: A 102 MET cc_start: 0.9279 (mmm) cc_final: 0.8752 (ptp) REVERT: A 275 GLU cc_start: 0.8931 (mp0) cc_final: 0.8606 (mp0) REVERT: A 385 MET cc_start: 0.8337 (ttp) cc_final: 0.8054 (ttt) REVERT: A 396 MET cc_start: 0.8328 (ttm) cc_final: 0.7921 (ttp) REVERT: D 12 ASP cc_start: 0.8182 (t70) cc_final: 0.7750 (t0) REVERT: D 17 ARG cc_start: 0.8828 (ttt-90) cc_final: 0.8481 (ttp80) REVERT: J 70 ASP cc_start: 0.8538 (m-30) cc_final: 0.8242 (p0) REVERT: J 103 LEU cc_start: 0.9159 (tt) cc_final: 0.8953 (tt) REVERT: E 76 LYS cc_start: 0.9505 (mtpt) cc_final: 0.9208 (mtpp) REVERT: G 28 ASP cc_start: 0.7130 (t0) cc_final: 0.6695 (t0) REVERT: F 33 TYR cc_start: 0.9202 (m-80) cc_final: 0.8780 (m-10) REVERT: F 48 LEU cc_start: 0.9207 (mt) cc_final: 0.8957 (mt) REVERT: F 50 TYR cc_start: 0.8132 (p90) cc_final: 0.7682 (p90) REVERT: F 106 LYS cc_start: 0.9073 (tppp) cc_final: 0.8746 (tppt) REVERT: F 107 LEU cc_start: 0.8266 (tp) cc_final: 0.7834 (tp) REVERT: B 100 TRP cc_start: 0.8264 (t-100) cc_final: 0.7810 (t-100) REVERT: B 236 MET cc_start: 0.8829 (mmm) cc_final: 0.8503 (mmm) REVERT: B 281 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8957 (mm-30) REVERT: B 396 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8117 (ttm) REVERT: C 291 MET cc_start: 0.8851 (mtt) cc_final: 0.8542 (mtp) REVERT: K 36 MET cc_start: 0.9087 (mmm) cc_final: 0.8607 (mmm) REVERT: K 45 LYS cc_start: 0.9466 (mmtm) cc_final: 0.9103 (mmtm) REVERT: K 56 GLU cc_start: 0.9194 (pp20) cc_final: 0.8731 (pp20) outliers start: 18 outliers final: 12 residues processed: 203 average time/residue: 0.1402 time to fit residues: 41.2671 Evaluate side-chains 188 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain B residue 396 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [22, 102, 124, 48, 101, 127, 104, 179, 153, 70, 10] chunk 22 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN B 182 ASN K 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.076629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.052056 restraints weight = 54344.442| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.83 r_work: 0.2840 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15969 Z= 0.189 Angle : 0.607 8.151 21701 Z= 0.320 Chirality : 0.044 0.165 2355 Planarity : 0.004 0.042 2761 Dihedral : 4.916 22.377 2174 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.39 % Allowed : 11.38 % Favored : 87.23 % 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: 0.28 (0.19), residues: 1970 helix: 1.09 (0.37), residues: 183 sheet: 0.02 (0.20), residues: 610 loop : 0.27 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 62 TYR 0.024 0.002 TYR C 98 PHE 0.017 0.001 PHE E 79 TRP 0.013 0.001 TRP E 35 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (15940) covalent geometry : angle 0.60660 / 0.32 (21643) SS BOND : bond 0.00219 / 0.14 ( 29) SS BOND : angle 0.76958 / 0.49 ( 58) hydrogen bonds : bond 0.03976 / 2.64 ( 507) hydrogen bonds : angle 5.75255 / 4.17 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.683 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: A 102 MET cc_start: 0.9306 (mmm) cc_final: 0.8676 (ptp) REVERT: A 179 MET cc_start: 0.8625 (mmm) cc_final: 0.7732 (mmm) REVERT: A 274 GLU cc_start: 0.8641 (pm20) cc_final: 0.8185 (pm20) REVERT: A 275 GLU cc_start: 0.9042 (mp0) cc_final: 0.8244 (mp0) REVERT: A 396 MET cc_start: 0.8303 (ttm) cc_final: 0.7943 (ttp) REVERT: D 12 ASP cc_start: 0.8058 (t70) cc_final: 0.7786 (t0) REVERT: D 17 ARG cc_start: 0.8802 (ttt-90) cc_final: 0.8549 (ttp80) REVERT: D 50 TYR cc_start: 0.8470 (p90) cc_final: 0.8239 (p90) REVERT: J 4 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8453 (mtm) REVERT: J 39 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8518 (p0) REVERT: J 42 GLN cc_start: 0.8485 (mp10) cc_final: 0.8054 (mp10) REVERT: J 103 LEU cc_start: 0.9202 (tt) cc_final: 0.8921 (tt) REVERT: E 76 LYS cc_start: 0.9455 (mtpt) cc_final: 0.9174 (mtpp) REVERT: I 28 ASP cc_start: 0.8901 (m-30) cc_final: 0.8491 (m-30) REVERT: F 50 TYR cc_start: 0.8139 (p90) cc_final: 0.7550 (p90) REVERT: F 106 LYS cc_start: 0.9134 (tppp) cc_final: 0.8812 (tppt) REVERT: F 107 LEU cc_start: 0.8374 (tp) cc_final: 0.8075 (tp) REVERT: B 100 TRP cc_start: 0.8308 (t-100) cc_final: 0.7803 (t-100) REVERT: B 236 MET cc_start: 0.8881 (mmm) cc_final: 0.8542 (mmm) REVERT: B 281 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8933 (mm-30) REVERT: B 396 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8289 (ttm) REVERT: C 291 MET cc_start: 0.8734 (mtt) cc_final: 0.7943 (mmm) REVERT: C 385 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7964 (ttp) REVERT: K 36 MET cc_start: 0.9082 (mmm) cc_final: 0.8667 (mmm) REVERT: K 45 LYS cc_start: 0.9490 (mmtm) cc_final: 0.9127 (mmtm) REVERT: K 56 GLU cc_start: 0.9176 (pp20) cc_final: 0.8690 (pp20) outliers start: 24 outliers final: 7 residues processed: 208 average time/residue: 0.1402 time to fit residues: 42.3978 Evaluate side-chains 189 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 385 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [98, 143, 73, 78, 71, 28, 69, 132, 24, 4, 18] chunk 98 optimal weight: 9.9990 chunk 143 optimal weight: 0.0770 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN E 2 GLN I 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.076296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051752 restraints weight = 54504.696| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.84 r_work: 0.2840 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15969 Z= 0.188 Angle : 0.604 8.402 21701 Z= 0.315 Chirality : 0.044 0.159 2355 Planarity : 0.004 0.044 2761 Dihedral : 4.854 22.052 2174 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.39 % Allowed : 13.46 % Favored : 85.15 % 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: 0.23 (0.19), residues: 1970 helix: 0.84 (0.35), residues: 201 sheet: 0.01 (0.20), residues: 625 loop : 0.24 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 62 TYR 0.025 0.001 TYR C 98 PHE 0.016 0.002 PHE E 79 TRP 0.013 0.001 TRP G 35 HIS 0.004 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (15940) covalent geometry : angle 0.60328 / 0.31 (21643) SS BOND : bond 0.00217 / 0.13 ( 29) SS BOND : angle 0.79143 / 0.51 ( 58) hydrogen bonds : bond 0.03654 / 2.44 ( 507) hydrogen bonds : angle 5.49165 / 3.97 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.546 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: A 102 MET cc_start: 0.9402 (mmm) cc_final: 0.8796 (ptp) REVERT: A 134 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8240 (pt) REVERT: A 396 MET cc_start: 0.8363 (ttm) cc_final: 0.8027 (ttp) REVERT: D 12 ASP cc_start: 0.8128 (t70) cc_final: 0.7805 (t0) REVERT: D 17 ARG cc_start: 0.8786 (ttt-90) cc_final: 0.8506 (tmm-80) REVERT: D 50 TYR cc_start: 0.8547 (p90) cc_final: 0.8316 (p90) REVERT: J 39 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8309 (p0) REVERT: J 42 GLN cc_start: 0.8578 (mp10) cc_final: 0.8197 (mp10) REVERT: E 76 LYS cc_start: 0.9471 (mtpt) cc_final: 0.9156 (mtpp) REVERT: I 28 ASP cc_start: 0.8864 (m-30) cc_final: 0.8488 (m-30) REVERT: G 111 MET cc_start: 0.8739 (mtt) cc_final: 0.8362 (mtt) REVERT: F 50 TYR cc_start: 0.8086 (p90) cc_final: 0.7355 (p90) REVERT: F 62 ARG cc_start: 0.8777 (ptp90) cc_final: 0.8431 (mtm-85) REVERT: F 106 LYS cc_start: 0.9196 (tppp) cc_final: 0.8813 (tppt) REVERT: F 107 LEU cc_start: 0.8420 (tp) cc_final: 0.7898 (tp) REVERT: H 76 ILE cc_start: 0.8054 (mm) cc_final: 0.7726 (mt) REVERT: B 100 TRP cc_start: 0.8368 (t-100) cc_final: 0.7807 (t-100) REVERT: B 236 MET cc_start: 0.8909 (mmm) cc_final: 0.8564 (mmm) REVERT: B 281 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8918 (mm-30) REVERT: B 396 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8328 (ttm) REVERT: C 385 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7781 (ttp) REVERT: C 396 MET cc_start: 0.8762 (tpt) cc_final: 0.8538 (tpp) REVERT: K 36 MET cc_start: 0.9029 (mmm) cc_final: 0.8698 (mmm) REVERT: K 45 LYS cc_start: 0.9479 (mmtm) cc_final: 0.9057 (mmtm) REVERT: K 47 MET cc_start: 0.8966 (mtm) cc_final: 0.8503 (mtm) REVERT: K 56 GLU cc_start: 0.9179 (pp20) cc_final: 0.8845 (pp20) REVERT: K 62 ASP cc_start: 0.8556 (t0) cc_final: 0.7961 (t0) outliers start: 24 outliers final: 13 residues processed: 200 average time/residue: 0.1334 time to fit residues: 38.9868 Evaluate side-chains 192 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 385 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [143, 107, 93, 97, 63, 31, 168, 27, 123, 131, 138] chunk 143 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 2 GLN I 2 GLN H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.077212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052794 restraints weight = 53946.842| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.84 r_work: 0.2870 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15969 Z= 0.128 Angle : 0.584 8.403 21701 Z= 0.301 Chirality : 0.043 0.156 2355 Planarity : 0.004 0.043 2761 Dihedral : 4.607 21.033 2174 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.44 % Allowed : 14.44 % Favored : 84.11 % 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: 0.26 (0.19), residues: 1970 helix: 0.82 (0.35), residues: 207 sheet: 0.13 (0.21), residues: 615 loop : 0.20 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 62 TYR 0.022 0.001 TYR C 98 PHE 0.012 0.001 PHE E 79 TRP 0.011 0.001 TRP I 35 HIS 0.004 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15940) covalent geometry : angle 0.58408 / 0.30 (21643) SS BOND : bond 0.00186 / 0.12 ( 29) SS BOND : angle 0.67024 / 0.44 ( 58) hydrogen bonds : bond 0.03309 / 2.20 ( 507) hydrogen bonds : angle 5.23373 / 3.78 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.456 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: A 102 MET cc_start: 0.9419 (mmm) cc_final: 0.8792 (ptp) REVERT: A 275 GLU cc_start: 0.9053 (mp0) cc_final: 0.8757 (pm20) REVERT: A 396 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8057 (ttp) REVERT: D 12 ASP cc_start: 0.7993 (t70) cc_final: 0.7651 (t0) REVERT: D 17 ARG cc_start: 0.8785 (ttt-90) cc_final: 0.8468 (ttp80) REVERT: J 31 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.9091 (p) REVERT: J 39 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8270 (p0) REVERT: J 42 GLN cc_start: 0.8495 (mp10) cc_final: 0.8059 (mp10) REVERT: J 79 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8407 (tm-30) REVERT: E 76 LYS cc_start: 0.9459 (mtpt) cc_final: 0.9151 (mtpp) REVERT: I 28 ASP cc_start: 0.8882 (m-30) cc_final: 0.8653 (m-30) REVERT: I 65 LYS cc_start: 0.9117 (mttm) cc_final: 0.8864 (mmtt) REVERT: G 2 GLN cc_start: 0.7451 (pm20) cc_final: 0.7106 (pp30) REVERT: G 17 GLU cc_start: 0.9361 (mp0) cc_final: 0.9145 (mp0) REVERT: G 30 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8208 (mpt) REVERT: G 111 MET cc_start: 0.8687 (mtt) cc_final: 0.8270 (mtt) REVERT: F 50 TYR cc_start: 0.8079 (p90) cc_final: 0.7214 (p90) REVERT: F 62 ARG cc_start: 0.8805 (ptp90) cc_final: 0.8360 (ptp90) REVERT: F 106 LYS cc_start: 0.9174 (tppp) cc_final: 0.8914 (tppt) REVERT: H 17 ARG cc_start: 0.8172 (tmm-80) cc_final: 0.7659 (tmm-80) REVERT: H 61 ASP cc_start: 0.8972 (p0) cc_final: 0.8301 (t0) REVERT: H 76 ILE cc_start: 0.8006 (mm) cc_final: 0.7733 (mm) REVERT: B 100 TRP cc_start: 0.8347 (t-100) cc_final: 0.7773 (t-100) REVERT: B 236 MET cc_start: 0.8896 (mmm) cc_final: 0.8539 (mmm) REVERT: B 281 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8963 (mm-30) REVERT: B 396 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8401 (ttm) REVERT: C 275 GLU cc_start: 0.9084 (mp0) cc_final: 0.8831 (mp0) REVERT: C 385 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7664 (ttp) REVERT: C 396 MET cc_start: 0.8781 (tpt) cc_final: 0.8558 (tpp) REVERT: K 36 MET cc_start: 0.9037 (mmm) cc_final: 0.8696 (mmm) REVERT: K 45 LYS cc_start: 0.9484 (mmtm) cc_final: 0.8983 (mmtm) REVERT: K 47 MET cc_start: 0.9065 (mtm) cc_final: 0.8513 (mtm) REVERT: K 56 GLU cc_start: 0.9180 (pp20) cc_final: 0.8818 (pp20) REVERT: K 62 ASP cc_start: 0.8562 (t0) cc_final: 0.7830 (t0) outliers start: 25 outliers final: 13 residues processed: 205 average time/residue: 0.1330 time to fit residues: 39.9397 Evaluate side-chains 197 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 385 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [86, 42, 136, 9, 150, 35, 144, 11, 7, 59, 134] chunk 86 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 136 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 35 optimal weight: 0.0050 chunk 144 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 134 optimal weight: 30.0000 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 2 GLN H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.076365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.051839 restraints weight = 54096.188| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.84 r_work: 0.2845 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15969 Z= 0.180 Angle : 0.598 9.557 21701 Z= 0.308 Chirality : 0.043 0.157 2355 Planarity : 0.004 0.044 2761 Dihedral : 4.655 21.252 2174 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.14 % Allowed : 15.19 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.22 (0.19), residues: 1970 helix: 1.03 (0.36), residues: 201 sheet: -0.01 (0.21), residues: 629 loop : 0.21 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 62 TYR 0.023 0.001 TYR C 98 PHE 0.017 0.002 PHE E 79 TRP 0.013 0.001 TRP G 35 HIS 0.004 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (15940) covalent geometry : angle 0.59737 / 0.31 (21643) SS BOND : bond 0.00192 / 0.11 ( 29) SS BOND : angle 0.70917 / 0.45 ( 58) hydrogen bonds : bond 0.03335 / 2.21 ( 507) hydrogen bonds : angle 5.23768 / 3.77 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.546 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: A 102 MET cc_start: 0.9456 (mmm) cc_final: 0.8726 (ptp) REVERT: A 134 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8315 (pt) REVERT: A 179 MET cc_start: 0.8662 (mmm) cc_final: 0.8459 (mmm) REVERT: A 275 GLU cc_start: 0.9077 (mp0) cc_final: 0.8724 (pm20) REVERT: A 396 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7930 (ttp) REVERT: D 12 ASP cc_start: 0.8052 (t70) cc_final: 0.7720 (t0) REVERT: D 17 ARG cc_start: 0.8753 (ttt-90) cc_final: 0.8473 (ttp80) REVERT: J 31 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9092 (p) REVERT: J 39 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.7916 (p0) REVERT: J 42 GLN cc_start: 0.8553 (mp10) cc_final: 0.8098 (mp10) REVERT: E 76 LYS cc_start: 0.9485 (mtpt) cc_final: 0.9221 (mtpp) REVERT: I 28 ASP cc_start: 0.8810 (m-30) cc_final: 0.8569 (m-30) REVERT: G 2 GLN cc_start: 0.7396 (pm20) cc_final: 0.7093 (pp30) REVERT: G 17 GLU cc_start: 0.9323 (mp0) cc_final: 0.9099 (mp0) REVERT: G 30 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8247 (mpt) REVERT: G 111 MET cc_start: 0.8748 (mtt) cc_final: 0.8357 (mtt) REVERT: F 50 TYR cc_start: 0.8136 (p90) cc_final: 0.7271 (p90) REVERT: F 79 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7223 (tt) REVERT: F 106 LYS cc_start: 0.9235 (tppp) cc_final: 0.8894 (tppt) REVERT: H 17 ARG cc_start: 0.8111 (tmm-80) cc_final: 0.7445 (ttp80) REVERT: H 61 ASP cc_start: 0.8984 (p0) cc_final: 0.8392 (t0) REVERT: H 62 ARG cc_start: 0.8772 (ptp90) cc_final: 0.8487 (ptp90) REVERT: H 76 ILE cc_start: 0.8040 (mm) cc_final: 0.7567 (mm) REVERT: B 100 TRP cc_start: 0.8303 (t-100) cc_final: 0.7750 (t-100) REVERT: B 236 MET cc_start: 0.8918 (mmm) cc_final: 0.8580 (mmm) REVERT: B 281 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8938 (mm-30) REVERT: B 396 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8323 (ttm) REVERT: C 275 GLU cc_start: 0.9077 (mp0) cc_final: 0.8850 (mp0) REVERT: C 385 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7759 (ttp) REVERT: C 396 MET cc_start: 0.8777 (tpt) cc_final: 0.8549 (tpp) REVERT: K 36 MET cc_start: 0.9017 (mmm) cc_final: 0.8540 (mmm) REVERT: K 45 LYS cc_start: 0.9502 (mmtm) cc_final: 0.9041 (mmtm) REVERT: K 56 GLU cc_start: 0.9152 (pp20) cc_final: 0.8785 (pp20) REVERT: K 62 ASP cc_start: 0.8622 (t0) cc_final: 0.7967 (t0) REVERT: K 85 LEU cc_start: 0.9243 (tt) cc_final: 0.8906 (mt) outliers start: 37 outliers final: 19 residues processed: 207 average time/residue: 0.1295 time to fit residues: 39.4142 Evaluate side-chains 202 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 385 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [146, 59, 145, 164, 31, 104, 165, 77, 144, 79, 54] chunk 146 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 164 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 2 GLN I 2 GLN H 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.076197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051699 restraints weight = 53909.990| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.83 r_work: 0.2841 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15969 Z= 0.183 Angle : 0.603 9.940 21701 Z= 0.310 Chirality : 0.043 0.153 2355 Planarity : 0.004 0.045 2761 Dihedral : 4.651 21.070 2174 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.20 % Allowed : 16.06 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1970 helix: 1.05 (0.36), residues: 201 sheet: 0.04 (0.20), residues: 647 loop : 0.20 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 80 TYR 0.023 0.001 TYR C 98 PHE 0.016 0.001 PHE E 79 TRP 0.012 0.001 TRP G 35 HIS 0.004 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (15940) covalent geometry : angle 0.60278 / 0.31 (21643) SS BOND : bond 0.00205 / 0.11 ( 29) SS BOND : angle 0.72624 / 0.46 ( 58) hydrogen bonds : bond 0.03312 / 2.20 ( 507) hydrogen bonds : angle 5.17295 / 3.71 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.532 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: A 102 MET cc_start: 0.9469 (mmm) cc_final: 0.8731 (ptp) REVERT: A 134 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8380 (pt) REVERT: A 259 ASN cc_start: 0.7874 (t0) cc_final: 0.7418 (t0) REVERT: A 275 GLU cc_start: 0.9081 (mp0) cc_final: 0.8721 (pm20) REVERT: A 396 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7939 (ttp) REVERT: D 12 ASP cc_start: 0.8049 (t70) cc_final: 0.7723 (t0) REVERT: D 17 ARG cc_start: 0.8744 (ttt-90) cc_final: 0.8450 (ttp80) REVERT: D 50 TYR cc_start: 0.8377 (p90) cc_final: 0.8096 (p90) REVERT: J 31 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9016 (p) REVERT: J 39 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.7887 (p0) REVERT: J 42 GLN cc_start: 0.8536 (mp10) cc_final: 0.8140 (mp10) REVERT: E 76 LYS cc_start: 0.9499 (mtpt) cc_final: 0.9237 (mtpp) REVERT: I 28 ASP cc_start: 0.8890 (m-30) cc_final: 0.8616 (m-30) REVERT: I 65 LYS cc_start: 0.9076 (mttm) cc_final: 0.8799 (mmtt) REVERT: G 2 GLN cc_start: 0.7414 (pm20) cc_final: 0.7061 (pp30) REVERT: G 17 GLU cc_start: 0.9347 (mp0) cc_final: 0.9114 (mp0) REVERT: G 30 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8261 (mpt) REVERT: G 65 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8356 (mttp) REVERT: G 111 MET cc_start: 0.8753 (mtt) cc_final: 0.8322 (mtt) REVERT: F 50 TYR cc_start: 0.8077 (p90) cc_final: 0.7231 (p90) REVERT: F 79 LEU cc_start: 0.7958 (mp) cc_final: 0.7549 (tt) REVERT: H 17 ARG cc_start: 0.8066 (tmm-80) cc_final: 0.7392 (ttp80) REVERT: H 61 ASP cc_start: 0.9011 (p0) cc_final: 0.8391 (t0) REVERT: H 62 ARG cc_start: 0.8904 (ptp90) cc_final: 0.8587 (ptp90) REVERT: H 76 ILE cc_start: 0.8006 (mm) cc_final: 0.7496 (mm) REVERT: H 80 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.7684 (ptp90) REVERT: B 100 TRP cc_start: 0.8284 (t-100) cc_final: 0.7717 (t-100) REVERT: B 236 MET cc_start: 0.8949 (mmm) cc_final: 0.8607 (mmm) REVERT: B 281 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8931 (mm-30) REVERT: B 396 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8325 (ttm) REVERT: C 275 GLU cc_start: 0.9055 (mp0) cc_final: 0.8815 (mp0) REVERT: C 385 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7747 (ttp) REVERT: C 396 MET cc_start: 0.8822 (tpt) cc_final: 0.8558 (tpp) REVERT: K 36 MET cc_start: 0.9048 (mmm) cc_final: 0.8537 (mmm) REVERT: K 45 LYS cc_start: 0.9478 (mmtm) cc_final: 0.9025 (mmtm) REVERT: K 56 GLU cc_start: 0.9141 (pp20) cc_final: 0.8786 (pp20) REVERT: K 62 ASP cc_start: 0.8701 (t0) cc_final: 0.8139 (t0) REVERT: K 90 MET cc_start: 0.9407 (tmm) cc_final: 0.9196 (tmm) outliers start: 38 outliers final: 23 residues processed: 207 average time/residue: 0.1295 time to fit residues: 39.2403 Evaluate side-chains 207 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 385 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [138, 29, 47, 127, 28, 54, 9, 10, 190, 32, 60] chunk 138 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 47 optimal weight: 0.0370 chunk 127 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 GLN E 2 GLN I 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.078095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053688 restraints weight = 54212.147| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.84 r_work: 0.2891 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15969 Z= 0.103 Angle : 0.582 10.113 21701 Z= 0.295 Chirality : 0.043 0.184 2355 Planarity : 0.004 0.046 2761 Dihedral : 4.318 19.722 2174 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.91 % Allowed : 16.41 % Favored : 81.69 % 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: 0.27 (0.19), residues: 1970 helix: 1.00 (0.36), residues: 207 sheet: 0.10 (0.21), residues: 622 loop : 0.20 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 80 TYR 0.020 0.001 TYR C 98 PHE 0.013 0.001 PHE J 73 TRP 0.016 0.001 TRP B 14 HIS 0.004 0.000 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (15940) covalent geometry : angle 0.58155 / 0.30 (21643) SS BOND : bond 0.00203 / 0.12 ( 29) SS BOND : angle 0.64064 / 0.42 ( 58) hydrogen bonds : bond 0.03047 / 2.02 ( 507) hydrogen bonds : angle 4.96155 / 3.57 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.698 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: A 102 MET cc_start: 0.9456 (mmm) cc_final: 0.8711 (ptp) REVERT: A 134 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8248 (pt) REVERT: A 275 GLU cc_start: 0.9078 (mp0) cc_final: 0.8740 (pm20) REVERT: A 396 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8084 (ttp) REVERT: D 12 ASP cc_start: 0.7894 (t70) cc_final: 0.7581 (t0) REVERT: D 17 ARG cc_start: 0.8720 (ttt-90) cc_final: 0.8403 (ttp80) REVERT: D 50 TYR cc_start: 0.8290 (p90) cc_final: 0.8006 (p90) REVERT: J 39 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.7931 (p0) REVERT: J 42 GLN cc_start: 0.8489 (mp10) cc_final: 0.8134 (mp10) REVERT: E 76 LYS cc_start: 0.9485 (mtpt) cc_final: 0.9221 (mtpp) REVERT: I 28 ASP cc_start: 0.8790 (m-30) cc_final: 0.8547 (m-30) REVERT: I 65 LYS cc_start: 0.9035 (mttm) cc_final: 0.8509 (mmtt) REVERT: G 2 GLN cc_start: 0.7707 (pm20) cc_final: 0.7386 (pp30) REVERT: G 65 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8295 (mttm) REVERT: F 50 TYR cc_start: 0.7926 (p90) cc_final: 0.6994 (p90) REVERT: F 61 ASP cc_start: 0.8539 (t0) cc_final: 0.8313 (t0) REVERT: F 62 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8784 (mtm-85) REVERT: F 79 LEU cc_start: 0.7945 (mp) cc_final: 0.7454 (tt) REVERT: F 80 ARG cc_start: 0.8073 (mmp80) cc_final: 0.7274 (mmp80) REVERT: F 83 ASP cc_start: 0.8204 (t0) cc_final: 0.7776 (t0) REVERT: F 106 LYS cc_start: 0.9200 (tppp) cc_final: 0.8854 (tppt) REVERT: H 17 ARG cc_start: 0.7992 (tmm-80) cc_final: 0.7284 (tmm-80) REVERT: H 50 TYR cc_start: 0.8306 (p90) cc_final: 0.7713 (p90) REVERT: H 76 ILE cc_start: 0.7692 (mm) cc_final: 0.7332 (mm) REVERT: H 80 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.7658 (ptp90) REVERT: B 100 TRP cc_start: 0.8341 (t-100) cc_final: 0.7756 (t-100) REVERT: B 236 MET cc_start: 0.8861 (mmm) cc_final: 0.8542 (mmm) REVERT: B 281 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8930 (mm-30) REVERT: B 396 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8426 (ttm) REVERT: C 275 GLU cc_start: 0.9083 (mp0) cc_final: 0.8828 (mp0) REVERT: C 385 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7611 (ttp) REVERT: C 396 MET cc_start: 0.8845 (tpt) cc_final: 0.8635 (tpp) REVERT: K 36 MET cc_start: 0.9035 (mmm) cc_final: 0.8562 (mmm) REVERT: K 45 LYS cc_start: 0.9490 (mmtm) cc_final: 0.9023 (mmtm) REVERT: K 56 GLU cc_start: 0.9129 (pp20) cc_final: 0.8778 (pp20) REVERT: K 62 ASP cc_start: 0.8714 (t0) cc_final: 0.8124 (t0) outliers start: 33 outliers final: 21 residues processed: 214 average time/residue: 0.1270 time to fit residues: 40.0836 Evaluate side-chains 203 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [164, 8, 15, 76, 93, 154, 187, 110, 68, 142, 188] chunk 164 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN E 2 GLN I 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.075052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.050342 restraints weight = 54510.378| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.84 r_work: 0.2805 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 15969 Z= 0.301 Angle : 0.689 14.271 21701 Z= 0.354 Chirality : 0.045 0.170 2355 Planarity : 0.005 0.047 2761 Dihedral : 4.926 21.624 2174 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.37 % Allowed : 16.46 % Favored : 81.17 % 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: 0.04 (0.19), residues: 1970 helix: 0.94 (0.36), residues: 201 sheet: -0.01 (0.21), residues: 594 loop : -0.02 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 80 TYR 0.027 0.002 TYR C 98 PHE 0.022 0.002 PHE E 79 TRP 0.018 0.002 TRP G 35 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.30 (15940) covalent geometry : angle 0.68847 / 0.35 (21643) SS BOND : bond 0.00231 / 0.13 ( 29) SS BOND : angle 0.86882 / 0.56 ( 58) hydrogen bonds : bond 0.03580 / 2.38 ( 507) hydrogen bonds : angle 5.24751 / 3.75 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.518 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: A 134 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8323 (pt) REVERT: A 259 ASN cc_start: 0.7987 (t0) cc_final: 0.7475 (t0) REVERT: A 275 GLU cc_start: 0.9085 (mp0) cc_final: 0.8731 (pm20) REVERT: A 396 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7973 (ttp) REVERT: D 12 ASP cc_start: 0.8156 (t70) cc_final: 0.7873 (t0) REVERT: D 17 ARG cc_start: 0.8806 (ttt-90) cc_final: 0.8495 (ttp80) REVERT: D 54 LYS cc_start: 0.9274 (mttm) cc_final: 0.8785 (mttt) REVERT: J 31 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.8947 (p) REVERT: J 39 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.7911 (p0) REVERT: J 42 GLN cc_start: 0.8625 (mp10) cc_final: 0.8244 (mp10) REVERT: E 76 LYS cc_start: 0.9489 (mtpt) cc_final: 0.9234 (mtpp) REVERT: I 28 ASP cc_start: 0.8866 (m-30) cc_final: 0.8507 (m-30) REVERT: G 2 GLN cc_start: 0.7642 (pm20) cc_final: 0.7232 (pp30) REVERT: G 28 ASP cc_start: 0.7781 (t0) cc_final: 0.7464 (t0) REVERT: G 30 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8296 (mpt) REVERT: G 65 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8384 (mttm) REVERT: F 16 GLN cc_start: 0.8134 (pm20) cc_final: 0.7798 (pm20) REVERT: F 50 TYR cc_start: 0.8205 (p90) cc_final: 0.7473 (p90) REVERT: F 79 LEU cc_start: 0.8052 (mp) cc_final: 0.7593 (tt) REVERT: H 17 ARG cc_start: 0.7927 (tmm-80) cc_final: 0.7225 (ttp80) REVERT: H 61 ASP cc_start: 0.8972 (p0) cc_final: 0.8357 (t0) REVERT: H 76 ILE cc_start: 0.7758 (mm) cc_final: 0.7072 (mm) REVERT: B 100 TRP cc_start: 0.8271 (t-100) cc_final: 0.7700 (t-100) REVERT: B 236 MET cc_start: 0.8963 (mmm) cc_final: 0.8625 (mmm) REVERT: B 281 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8986 (mm-30) REVERT: B 396 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8283 (ttm) REVERT: B 399 LEU cc_start: 0.8561 (pt) cc_final: 0.8242 (tp) REVERT: C 385 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7976 (ttp) REVERT: C 396 MET cc_start: 0.8810 (tpt) cc_final: 0.8563 (tpp) REVERT: K 36 MET cc_start: 0.9087 (mmm) cc_final: 0.8519 (mmm) REVERT: K 45 LYS cc_start: 0.9479 (mmtm) cc_final: 0.9018 (mmtm) REVERT: K 56 GLU cc_start: 0.9132 (pp20) cc_final: 0.8775 (pp20) REVERT: K 62 ASP cc_start: 0.8846 (t0) cc_final: 0.8467 (t0) REVERT: K 85 LEU cc_start: 0.9220 (tt) cc_final: 0.8944 (mt) outliers start: 41 outliers final: 26 residues processed: 204 average time/residue: 0.1237 time to fit residues: 37.5520 Evaluate side-chains 206 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [24, 73, 112, 177, 9, 13, 26, 140, 155, 34, 154] chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 2 GLN I 2 GLN C 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.077297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052508 restraints weight = 54485.267| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.95 r_work: 0.2859 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15969 Z= 0.127 Angle : 0.627 10.794 21701 Z= 0.318 Chirality : 0.044 0.174 2355 Planarity : 0.004 0.074 2761 Dihedral : 4.583 20.360 2174 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.56 % Allowed : 17.39 % Favored : 81.05 % 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: 0.09 (0.19), residues: 1970 helix: 0.97 (0.36), residues: 207 sheet: -0.06 (0.21), residues: 626 loop : 0.07 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 62 TYR 0.021 0.001 TYR C 98 PHE 0.013 0.001 PHE J 73 TRP 0.011 0.001 TRP K 46 HIS 0.004 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (15940) covalent geometry : angle 0.62694 / 0.32 (21643) SS BOND : bond 0.00202 / 0.11 ( 29) SS BOND : angle 0.73198 / 0.48 ( 58) hydrogen bonds : bond 0.03137 / 2.08 ( 507) hydrogen bonds : angle 5.03790 / 3.60 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.596 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: A 134 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8352 (pt) REVERT: A 275 GLU cc_start: 0.9088 (mp0) cc_final: 0.8745 (pm20) REVERT: A 396 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8104 (ttp) REVERT: D 12 ASP cc_start: 0.7972 (t70) cc_final: 0.7699 (t0) REVERT: D 17 ARG cc_start: 0.8738 (ttt-90) cc_final: 0.8441 (ttp80) REVERT: J 39 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8048 (p0) REVERT: J 42 GLN cc_start: 0.8567 (mp10) cc_final: 0.8288 (mp10) REVERT: E 76 LYS cc_start: 0.9478 (mtpt) cc_final: 0.9216 (mtpp) REVERT: G 2 GLN cc_start: 0.7760 (pm20) cc_final: 0.7283 (pp30) REVERT: G 65 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8289 (mttm) REVERT: G 111 MET cc_start: 0.8622 (mtt) cc_final: 0.8388 (mtt) REVERT: F 50 TYR cc_start: 0.8013 (p90) cc_final: 0.7107 (p90) REVERT: H 17 ARG cc_start: 0.7803 (tmm-80) cc_final: 0.7128 (tmm-80) REVERT: H 50 TYR cc_start: 0.8363 (p90) cc_final: 0.7823 (p90) REVERT: H 61 ASP cc_start: 0.8981 (p0) cc_final: 0.8365 (t0) REVERT: H 76 ILE cc_start: 0.7719 (mm) cc_final: 0.7310 (mm) REVERT: B 100 TRP cc_start: 0.8317 (t-100) cc_final: 0.7742 (t-100) REVERT: B 236 MET cc_start: 0.8900 (mmm) cc_final: 0.8553 (mmm) REVERT: B 281 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8941 (mm-30) REVERT: B 396 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8348 (ttm) REVERT: B 399 LEU cc_start: 0.8524 (pt) cc_final: 0.8154 (tp) REVERT: C 275 GLU cc_start: 0.9098 (mp0) cc_final: 0.8842 (mp0) REVERT: C 385 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7655 (ttp) REVERT: C 396 MET cc_start: 0.8834 (tpt) cc_final: 0.8618 (tpp) REVERT: K 36 MET cc_start: 0.9070 (mmm) cc_final: 0.8530 (mmm) REVERT: K 45 LYS cc_start: 0.9488 (mmtm) cc_final: 0.9013 (mmtm) REVERT: K 56 GLU cc_start: 0.9090 (pp20) cc_final: 0.8749 (pp20) REVERT: K 85 LEU cc_start: 0.9201 (tt) cc_final: 0.8897 (mt) outliers start: 27 outliers final: 19 residues processed: 198 average time/residue: 0.1295 time to fit residues: 38.0864 Evaluate side-chains 197 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: [66, 164, 147, 110, 142, 165, 153, 146, 180, 116, 74] chunk 66 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 2 GLN I 2 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.076706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.052072 restraints weight = 53749.878| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.85 r_work: 0.2852 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15969 Z= 0.161 Angle : 0.640 10.571 21701 Z= 0.323 Chirality : 0.044 0.177 2355 Planarity : 0.004 0.048 2761 Dihedral : 4.576 21.243 2174 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.91 % Allowed : 16.93 % Favored : 81.17 % 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: 0.05 (0.19), residues: 1970 helix: 0.96 (0.36), residues: 207 sheet: -0.06 (0.21), residues: 621 loop : 0.02 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 80 TYR 0.022 0.001 TYR C 98 PHE 0.015 0.001 PHE E 79 TRP 0.012 0.001 TRP G 35 HIS 0.004 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (15940) covalent geometry : angle 0.63973 / 0.32 (21643) SS BOND : bond 0.00181 / 0.11 ( 29) SS BOND : angle 0.73925 / 0.47 ( 58) hydrogen bonds : bond 0.03183 / 2.10 ( 507) hydrogen bonds : angle 5.04710 / 3.61 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3739.37 seconds wall clock time: 64 minutes 55.50 seconds (3895.50 seconds total)