Starting phenix.real_space_refine (version: dev) on Wed Feb 22 19:19:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/02_2023/7yzp_14393_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/02_2023/7yzp_14393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/02_2023/7yzp_14393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/02_2023/7yzp_14393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/02_2023/7yzp_14393_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/02_2023/7yzp_14393_updated.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4320 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B GLU 248": "OE1" <-> "OE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 935": "OE1" <-> "OE2" Residue "C GLU 1018": "OE1" <-> "OE2" Residue "D GLU 180": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14107 Number of models: 1 Model: "" Number of chains: 9 Chain: "F" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1211 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain: "A" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3013 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 20, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2819 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 4 Chain: "C" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3502 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 8, 'TRANS': 439} Chain breaks: 1 Chain: "D" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3502 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 8, 'TRANS': 439} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 residue: pdb=" N ALA A 287 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 287 " occ=0.60 residue: pdb=" N THR A 290 " occ=0.70 ... (5 atoms not shown) pdb=" CG2 THR A 290 " occ=0.70 residue: pdb=" N ALA A 291 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 291 " occ=0.60 residue: pdb=" N GLN A 292 " occ=0.70 ... (7 atoms not shown) pdb=" NE2 GLN A 292 " occ=0.70 residue: pdb=" N LEU A 293 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 293 " occ=0.80 residue: pdb=" N PRO A 303 " occ=0.61 ... (5 atoms not shown) pdb=" CD PRO A 303 " occ=0.61 residue: pdb=" N PRO A 304 " occ=0.68 ... (5 atoms not shown) pdb=" CD PRO A 304 " occ=0.68 residue: pdb=" N VAL A 305 " occ=0.88 ... (5 atoms not shown) pdb=" CG2 VAL A 305 " occ=0.88 residue: pdb=" N TRP A 306 " occ=0.97 ... (12 atoms not shown) pdb=" CH2 TRP A 306 " occ=0.97 residue: pdb=" N LEU A 307 " occ=0.87 ... (6 atoms not shown) pdb=" CD2 LEU A 307 " occ=0.87 residue: pdb=" N ILE A 309 " occ=0.89 ... (6 atoms not shown) pdb=" CD1 ILE A 309 " occ=0.89 ... (remaining 9 not shown) Time building chain proxies: 8.27, per 1000 atoms: 0.59 Number of scatterers: 14107 At special positions: 0 Unit cell: (100.605, 140.847, 139.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 38 16.00 P 63 15.00 Mg 2 11.99 O 2851 8.00 N 2499 7.00 C 8650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.95 Conformation dependent library (CDL) restraints added in 1.9 seconds 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 12 sheets defined 41.5% alpha, 13.9% beta 27 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 21 through 38 Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.618A pdb=" N GLN A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 4.450A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 137 No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 148 through 172 Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.759A pdb=" N GLN A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TRP A 296 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ARG A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.848A pdb=" N GLN A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 362 through 372 removed outlier: 3.609A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 394 removed outlier: 4.180A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 38 Processing helix chain 'B' and resid 57 through 73 removed outlier: 3.690A pdb=" N GLN B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 99 removed outlier: 3.621A pdb=" N GLU B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 172 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.574A pdb=" N GLU B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP B 296 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 removed outlier: 4.091A pdb=" N ARG B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 362 through 372 removed outlier: 4.648A pdb=" N LEU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 394 Processing helix chain 'C' and resid 45 through 55 removed outlier: 4.461A pdb=" N ILE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 129 through 140 removed outlier: 4.247A pdb=" N GLU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 150 removed outlier: 3.913A pdb=" N ARG C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 200 removed outlier: 3.691A pdb=" N PHE C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 215 through 234 removed outlier: 4.108A pdb=" N GLU C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 886 removed outlier: 3.588A pdb=" N GLN C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP C 879 " --> pdb=" O GLN C 875 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP C 880 " --> pdb=" O GLN C 876 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 882 " --> pdb=" O GLU C 878 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU C 883 " --> pdb=" O ASP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 916 removed outlier: 3.908A pdb=" N GLY C 901 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 971 removed outlier: 3.982A pdb=" N VAL C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 991 through 1006 Processing helix chain 'C' and resid 1018 through 1023 Processing helix chain 'D' and resid 25 through 28 No H-bonds generated for 'chain 'D' and resid 25 through 28' Processing helix chain 'D' and resid 45 through 55 removed outlier: 4.908A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 144 through 150 removed outlier: 4.544A pdb=" N ARG D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 4.292A pdb=" N GLU D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 209 removed outlier: 3.998A pdb=" N LEU D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 233 Processing helix chain 'D' and resid 836 through 887 removed outlier: 3.760A pdb=" N ARG D 840 " --> pdb=" O HIS D 836 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 875 " --> pdb=" O ALA D 871 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN D 876 " --> pdb=" O GLN D 872 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP D 879 " --> pdb=" O GLN D 875 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU D 886 " --> pdb=" O TYR D 882 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 918 removed outlier: 4.733A pdb=" N LEU D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 913 " --> pdb=" O HIS D 909 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 950 No H-bonds generated for 'chain 'D' and resid 948 through 950' Processing helix chain 'D' and resid 953 through 972 removed outlier: 3.762A pdb=" N VAL D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER D 972 " --> pdb=" O SER D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 1005 removed outlier: 3.528A pdb=" N ASP D 995 " --> pdb=" O SER D 991 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1020 No H-bonds generated for 'chain 'D' and resid 1018 through 1020' Processing helix chain 'D' and resid 1043 through 1045 No H-bonds generated for 'chain 'D' and resid 1043 through 1045' Processing sheet with id= A, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.208A pdb=" N LEU A 77 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 42 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 4 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 6 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 3 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 267 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER A 261 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.808A pdb=" N ILE A 218 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 115 " --> pdb=" O GLY A 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 279 through 283 removed outlier: 6.556A pdb=" N TRP A 306 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU A 282 " --> pdb=" O TRP A 306 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP A 308 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 336 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 309 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 264 through 271 removed outlier: 6.748A pdb=" N THR B 259 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 268 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B 257 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN B 270 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 255 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 256 " --> pdb=" O HIS B 5 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA B 42 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N THR B 6 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 44 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N HIS B 76 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL B 45 " --> pdb=" O HIS B 76 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 78 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 235 through 237 removed outlier: 6.677A pdb=" N ILE B 218 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 115 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL B 125 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN B 113 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.533A pdb=" N TRP B 306 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU B 282 " --> pdb=" O TRP B 306 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP B 308 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY B 284 " --> pdb=" O ASP B 308 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU B 310 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE B 309 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B 338 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 311 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG B 340 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 17 through 21 removed outlier: 4.066A pdb=" N GLU C 84 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 80 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 115 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.580A pdb=" N PHE C 33 " --> pdb=" O ILE C1011 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 35 " --> pdb=" O VAL C1013 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 980 " --> pdb=" O THR C1010 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 922 through 926 Processing sheet with id= J, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.556A pdb=" N GLU D 84 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU D 6 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU D 82 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU D 8 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU D 80 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 1039 through 1041 removed outlier: 7.611A pdb=" N ALA D 34 " --> pdb=" O ILE D1028 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL D1030 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 36 " --> pdb=" O VAL D1030 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LYS D1032 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 922 through 926 removed outlier: 3.510A pdb=" N ARG D 946 " --> pdb=" O VAL D 936 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 5.22 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4471 1.34 - 1.46: 2318 1.46 - 1.58: 7491 1.58 - 1.70: 123 1.70 - 1.82: 60 Bond restraints: 14463 Sorted by residual: bond pdb=" C4 ADP D1101 " pdb=" C5 ADP D1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP C1101 " pdb=" C5 ADP C1101 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C5 ADP D1101 " pdb=" C6 ADP D1101 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C5 ADP C1101 " pdb=" C6 ADP C1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N ASP A 85 " pdb=" CA ASP A 85 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.14e-02 7.69e+03 9.25e+00 ... (remaining 14458 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.65: 703 106.65 - 113.61: 8092 113.61 - 120.57: 5797 120.57 - 127.53: 5063 127.53 - 134.49: 206 Bond angle restraints: 19861 Sorted by residual: angle pdb=" PA ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sigma weight residual 120.50 134.49 -13.99 3.00e+00 1.11e-01 2.17e+01 angle pdb=" C ASN D 12 " pdb=" CA ASN D 12 " pdb=" CB ASN D 12 " ideal model delta sigma weight residual 116.63 111.67 4.96 1.16e+00 7.43e-01 1.83e+01 angle pdb=" N ASN A 83 " pdb=" CA ASN A 83 " pdb=" C ASN A 83 " ideal model delta sigma weight residual 113.12 107.86 5.26 1.25e+00 6.40e-01 1.77e+01 angle pdb=" N VAL C 971 " pdb=" CA VAL C 971 " pdb=" C VAL C 971 " ideal model delta sigma weight residual 112.29 108.37 3.92 9.40e-01 1.13e+00 1.74e+01 angle pdb=" PA ADP C1101 " pdb=" O3A ADP C1101 " pdb=" PB ADP C1101 " ideal model delta sigma weight residual 120.50 131.68 -11.18 3.00e+00 1.11e-01 1.39e+01 ... (remaining 19856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.90: 7943 28.90 - 57.80: 551 57.80 - 86.70: 46 86.70 - 115.60: 3 115.60 - 144.50: 1 Dihedral angle restraints: 8544 sinusoidal: 3808 harmonic: 4736 Sorted by residual: dihedral pdb=" C ASP B 376 " pdb=" N ASP B 376 " pdb=" CA ASP B 376 " pdb=" CB ASP B 376 " ideal model delta harmonic sigma weight residual -122.60 -135.45 12.85 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N ASP B 376 " pdb=" C ASP B 376 " pdb=" CA ASP B 376 " pdb=" CB ASP B 376 " ideal model delta harmonic sigma weight residual 122.80 133.54 -10.74 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C4' DG F 34 " pdb=" C3' DG F 34 " pdb=" O3' DG F 34 " pdb=" P DT F 35 " ideal model delta sinusoidal sigma weight residual 220.00 75.50 144.50 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 8541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2128 0.079 - 0.159: 160 0.159 - 0.238: 5 0.238 - 0.318: 0 0.318 - 0.397: 1 Chirality restraints: 2294 Sorted by residual: chirality pdb=" CA ASP B 376 " pdb=" N ASP B 376 " pdb=" C ASP B 376 " pdb=" CB ASP B 376 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C3' ADP D1101 " pdb=" C2' ADP D1101 " pdb=" C4' ADP D1101 " pdb=" O3' ADP D1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ASP A 85 " pdb=" N ASP A 85 " pdb=" C ASP A 85 " pdb=" CB ASP A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 2291 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 895 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C PHE D 895 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE D 895 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG D 896 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C1034 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C ASN C1034 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN C1034 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY C1035 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 87 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C VAL D 87 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL D 87 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS D 88 " 0.009 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 20 2.25 - 2.92: 5576 2.92 - 3.58: 21330 3.58 - 4.24: 32084 4.24 - 4.90: 52751 Nonbonded interactions: 111761 Sorted by model distance: nonbonded pdb=" OD1 ASN A 83 " pdb="MN MN A 502 " model vdw 1.593 2.320 nonbonded pdb=" N ASN B 83 " pdb="MN MN B 502 " model vdw 2.004 2.400 nonbonded pdb=" OD1 ASP B 8 " pdb="MN MN B 501 " model vdw 2.006 2.320 nonbonded pdb=" OD1 ASN B 83 " pdb="MN MN B 502 " model vdw 2.023 2.320 nonbonded pdb=" CD2 HIS A 222 " pdb="MN MN A 502 " model vdw 2.051 2.540 ... (remaining 111756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 105 or resid 109 through 137 or resid 151 throug \ h 188 or resid 205 through 342 or resid 354 through 395 or resid 501 through 502 \ )) selection = (chain 'B' and (resid 1 through 188 or resid 205 through 395 or resid 501 throug \ h 502)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 63 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 8650 2.51 5 N 2499 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.28 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 6.980 Check model and map are aligned: 0.200 Process input model: 41.650 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 0.109 14463 Z= 0.213 Angle : 0.619 13.986 19861 Z= 0.316 Chirality : 0.040 0.397 2294 Planarity : 0.003 0.036 2364 Dihedral : 17.628 144.499 5464 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1611 helix: 1.67 (0.21), residues: 686 sheet: 0.15 (0.35), residues: 225 loop : -0.56 (0.25), residues: 700 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.601 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2105 time to fit residues: 49.2089 Evaluate side-chains 93 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1027 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 14463 Z= 0.287 Angle : 0.622 7.366 19861 Z= 0.315 Chirality : 0.041 0.169 2294 Planarity : 0.003 0.039 2364 Dihedral : 17.490 145.449 2357 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1611 helix: 1.66 (0.21), residues: 674 sheet: 0.14 (0.33), residues: 255 loop : -0.47 (0.26), residues: 682 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 1.624 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 102 average time/residue: 0.2169 time to fit residues: 35.9340 Evaluate side-chains 96 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1502 time to fit residues: 5.0413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 0.0980 chunk 163 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 121 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 864 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 14463 Z= 0.143 Angle : 0.546 9.324 19861 Z= 0.270 Chirality : 0.038 0.150 2294 Planarity : 0.003 0.029 2364 Dihedral : 17.444 145.011 2357 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1611 helix: 1.85 (0.21), residues: 672 sheet: 0.17 (0.33), residues: 265 loop : -0.47 (0.26), residues: 674 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.538 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 107 average time/residue: 0.2039 time to fit residues: 35.8560 Evaluate side-chains 93 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1452 time to fit residues: 2.7385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN C 872 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14463 Z= 0.245 Angle : 0.592 10.143 19861 Z= 0.296 Chirality : 0.040 0.160 2294 Planarity : 0.003 0.029 2364 Dihedral : 17.578 146.228 2357 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1611 helix: 1.63 (0.21), residues: 679 sheet: -0.04 (0.33), residues: 269 loop : -0.47 (0.26), residues: 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.459 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.2099 time to fit residues: 35.3583 Evaluate side-chains 93 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1347 time to fit residues: 4.3748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 144 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14463 Z= 0.179 Angle : 0.572 10.635 19861 Z= 0.280 Chirality : 0.039 0.155 2294 Planarity : 0.003 0.027 2364 Dihedral : 17.560 146.129 2357 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1611 helix: 1.70 (0.21), residues: 679 sheet: 0.00 (0.33), residues: 269 loop : -0.50 (0.26), residues: 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.530 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 106 average time/residue: 0.2101 time to fit residues: 36.8074 Evaluate side-chains 93 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1180 time to fit residues: 3.0164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 94 optimal weight: 0.0670 chunk 39 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 13 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14463 Z= 0.243 Angle : 0.606 13.174 19861 Z= 0.299 Chirality : 0.040 0.159 2294 Planarity : 0.003 0.029 2364 Dihedral : 17.652 146.820 2357 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1611 helix: 1.65 (0.21), residues: 679 sheet: 0.00 (0.34), residues: 261 loop : -0.58 (0.26), residues: 671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.540 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.2084 time to fit residues: 35.4775 Evaluate side-chains 98 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1422 time to fit residues: 5.3854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.0970 chunk 91 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14463 Z= 0.157 Angle : 0.577 14.993 19861 Z= 0.278 Chirality : 0.038 0.154 2294 Planarity : 0.003 0.027 2364 Dihedral : 17.599 146.176 2357 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1611 helix: 1.78 (0.21), residues: 675 sheet: -0.01 (0.33), residues: 269 loop : -0.59 (0.26), residues: 667 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.587 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 107 average time/residue: 0.2096 time to fit residues: 36.8684 Evaluate side-chains 92 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1211 time to fit residues: 2.6444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 145 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 GLN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 14463 Z= 0.152 Angle : 0.586 15.399 19861 Z= 0.281 Chirality : 0.038 0.151 2294 Planarity : 0.003 0.028 2364 Dihedral : 17.579 145.389 2357 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1611 helix: 1.74 (0.21), residues: 677 sheet: 0.05 (0.33), residues: 271 loop : -0.57 (0.26), residues: 663 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.580 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 99 average time/residue: 0.2171 time to fit residues: 35.5092 Evaluate side-chains 92 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.714 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1540 time to fit residues: 3.0782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 64 optimal weight: 0.0770 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 14463 Z= 0.157 Angle : 0.598 15.591 19861 Z= 0.286 Chirality : 0.039 0.152 2294 Planarity : 0.003 0.030 2364 Dihedral : 17.575 145.076 2357 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1611 helix: 1.75 (0.21), residues: 677 sheet: 0.05 (0.33), residues: 271 loop : -0.57 (0.26), residues: 663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.663 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.2110 time to fit residues: 33.2588 Evaluate side-chains 90 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14463 Z= 0.178 Angle : 0.609 15.426 19861 Z= 0.291 Chirality : 0.039 0.164 2294 Planarity : 0.003 0.034 2364 Dihedral : 17.606 145.160 2357 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1611 helix: 1.71 (0.21), residues: 677 sheet: 0.01 (0.33), residues: 271 loop : -0.57 (0.26), residues: 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.646 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.2153 time to fit residues: 33.1730 Evaluate side-chains 90 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1465 time to fit residues: 2.9425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 135 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.0070 chunk 115 optimal weight: 0.8980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.095615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079637 restraints weight = 40172.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080849 restraints weight = 29668.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081935 restraints weight = 21508.213| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 14463 Z= 0.135 Angle : 0.601 15.808 19861 Z= 0.284 Chirality : 0.038 0.164 2294 Planarity : 0.003 0.030 2364 Dihedral : 17.575 144.423 2357 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1611 helix: 1.71 (0.21), residues: 683 sheet: 0.08 (0.34), residues: 269 loop : -0.56 (0.26), residues: 659 =============================================================================== Job complete usr+sys time: 2051.20 seconds wall clock time: 38 minutes 38.48 seconds (2318.48 seconds total)