Starting phenix.real_space_refine on Fri May 10 03:33:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/05_2024/8ru2_19503_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/05_2024/8ru2_19503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/05_2024/8ru2_19503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/05_2024/8ru2_19503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/05_2024/8ru2_19503_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/05_2024/8ru2_19503_updated.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.043 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 9351 2.51 5 N 2494 2.21 5 O 2818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 856": "OE1" <-> "OE2" Residue "E TYR 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1140": "OE1" <-> "OE2" Residue "F ASP 774": "OD1" <-> "OD2" Residue "F ASP 1055": "OD1" <-> "OD2" Residue "F TYR 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1115": "OE1" <-> "OE2" Residue "F GLU 1140": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 14773 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2873 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3023 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 3 Chain: "F" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3023 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 3 Chain: "B" 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: "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} Time building chain proxies: 7.84, per 1000 atoms: 0.53 Number of scatterers: 14773 At special positions: 0 Unit cell: (110.88, 125.84, 155.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 101 16.00 P 6 15.00 Mg 3 11.99 O 2818 8.00 N 2494 7.00 C 9351 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: 5.67 Conformation dependent library (CDL) restraints added in 2.7 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3494 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 14 sheets defined 49.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 80 through 90 removed outlier: 4.072A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.581A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.538A pdb=" N ASP B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 215 removed outlier: 4.402A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.953A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.639A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.770A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 294 removed outlier: 3.690A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 335 through 348 removed outlier: 3.596A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 4.028A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.570A pdb=" N ASP B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 363' Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.842A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.539A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 80 through 91 removed outlier: 4.059A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.558A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 192 Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.708A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.775A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.031A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.837A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 261' Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.635A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.757A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.613A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.072A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 345 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 5.158A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.620A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.346A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.925A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.891A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.571A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.796A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 293 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.874A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 removed outlier: 4.032A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 353 removed outlier: 4.031A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 350 through 353' Processing helix chain 'D' and resid 359 through 372 removed outlier: 3.551A pdb=" N ASP D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Proline residue: D 367 - end of helix removed outlier: 5.149A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 789 No H-bonds generated for 'chain 'E' and resid 786 through 789' Processing helix chain 'E' and resid 792 through 801 removed outlier: 3.551A pdb=" N LEU E 800 " --> pdb=" O ALA E 796 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 801 " --> pdb=" O LYS E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 847 removed outlier: 3.741A pdb=" N GLN E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 854 through 863 Processing helix chain 'E' and resid 871 through 878 removed outlier: 3.627A pdb=" N ILE E 878 " --> pdb=" O ILE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 884 through 887 Processing helix chain 'E' and resid 889 through 892 No H-bonds generated for 'chain 'E' and resid 889 through 892' Processing helix chain 'E' and resid 902 through 912 Processing helix chain 'E' and resid 916 through 923 Processing helix chain 'E' and resid 926 through 951 removed outlier: 4.229A pdb=" N SER E 930 " --> pdb=" O LYS E 926 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU E 931 " --> pdb=" O LEU E 927 " (cutoff:3.500A) Proline residue: E 938 - end of helix removed outlier: 3.528A pdb=" N SER E 942 " --> pdb=" O PRO E 938 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL E 943 " --> pdb=" O GLU E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 970 Processing helix chain 'E' and resid 987 through 989 No H-bonds generated for 'chain 'E' and resid 987 through 989' Processing helix chain 'E' and resid 1002 through 1013 removed outlier: 3.533A pdb=" N ALA E1007 " --> pdb=" O LEU E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1018 through 1023 Proline residue: E1021 - end of helix No H-bonds generated for 'chain 'E' and resid 1018 through 1023' Processing helix chain 'E' and resid 1027 through 1032 Processing helix chain 'E' and resid 1035 through 1058 removed outlier: 3.525A pdb=" N VAL E1052 " --> pdb=" O GLN E1048 " (cutoff:3.500A) Processing helix chain 'E' and resid 1070 through 1105 removed outlier: 4.492A pdb=" N THR E1074 " --> pdb=" O VAL E1070 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE E1076 " --> pdb=" O LYS E1072 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS E1078 " --> pdb=" O THR E1074 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS E1086 " --> pdb=" O GLU E1082 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET E1094 " --> pdb=" O MET E1090 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU E1095 " --> pdb=" O HIS E1091 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU E1100 " --> pdb=" O THR E1096 " (cutoff:3.500A) Processing helix chain 'E' and resid 1114 through 1147 Processing helix chain 'F' and resid 792 through 801 removed outlier: 3.533A pdb=" N LEU F 800 " --> pdb=" O ALA F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 850 removed outlier: 3.745A pdb=" N GLN F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE F 850 " --> pdb=" O PHE F 846 " (cutoff:3.500A) Processing helix chain 'F' and resid 854 through 863 Processing helix chain 'F' and resid 871 through 880 removed outlier: 3.879A pdb=" N ASN F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 879 " --> pdb=" O GLN F 875 " (cutoff:3.500A) Processing helix chain 'F' and resid 886 through 892 removed outlier: 4.248A pdb=" N LEU F 890 " --> pdb=" O GLN F 886 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER F 891 " --> pdb=" O LEU F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 902 through 912 Processing helix chain 'F' and resid 916 through 923 Processing helix chain 'F' and resid 926 through 951 removed outlier: 3.611A pdb=" N SER F 930 " --> pdb=" O LYS F 926 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU F 931 " --> pdb=" O LEU F 927 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 934 " --> pdb=" O SER F 930 " (cutoff:3.500A) Proline residue: F 938 - end of helix removed outlier: 3.503A pdb=" N VAL F 943 " --> pdb=" O GLU F 939 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR F 944 " --> pdb=" O ILE F 940 " (cutoff:3.500A) Processing helix chain 'F' and resid 954 through 970 Processing helix chain 'F' and resid 988 through 990 No H-bonds generated for 'chain 'F' and resid 988 through 990' Processing helix chain 'F' and resid 1002 through 1013 Processing helix chain 'F' and resid 1020 through 1023 No H-bonds generated for 'chain 'F' and resid 1020 through 1023' Processing helix chain 'F' and resid 1027 through 1031 Processing helix chain 'F' and resid 1035 through 1058 removed outlier: 3.930A pdb=" N VAL F1052 " --> pdb=" O GLN F1048 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F1053 " --> pdb=" O ILE F1049 " (cutoff:3.500A) Processing helix chain 'F' and resid 1070 through 1104 removed outlier: 4.139A pdb=" N THR F1074 " --> pdb=" O VAL F1070 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE F1076 " --> pdb=" O LYS F1072 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET F1089 " --> pdb=" O ASN F1085 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET F1090 " --> pdb=" O LYS F1086 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS F1091 " --> pdb=" O LEU F1087 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F1095 " --> pdb=" O HIS F1091 " (cutoff:3.500A) Processing helix chain 'F' and resid 1114 through 1147 removed outlier: 3.646A pdb=" N ASP F1120 " --> pdb=" O GLU F1116 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.522A pdb=" N CYS B 17 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.849A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.539A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= F, first strand: chain 'C' and resid 132 through 136 removed outlier: 7.106A pdb=" N VAL C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ALA C 135 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'C' and resid 298 through 300 removed outlier: 3.526A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 162 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= J, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.680A pdb=" N PHE D 31 " --> pdb=" O CYS D 17 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 35 through 38 removed outlier: 3.772A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= M, first strand: chain 'D' and resid 297 through 299 removed outlier: 6.013A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 176 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 239 through 241 530 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4838 1.35 - 1.46: 3314 1.46 - 1.58: 6728 1.58 - 1.70: 9 1.70 - 1.82: 179 Bond restraints: 15068 Sorted by residual: bond pdb=" CB GLN F 855 " pdb=" CG GLN F 855 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" CB MET C 153 " pdb=" CG MET C 153 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.55e-01 ... (remaining 15063 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.72: 497 106.72 - 114.11: 8609 114.11 - 121.50: 7876 121.50 - 128.88: 3286 128.88 - 136.27: 83 Bond angle restraints: 20351 Sorted by residual: angle pdb=" CA GLU D 276 " pdb=" CB GLU D 276 " pdb=" CG GLU D 276 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CB MET E1045 " pdb=" CG MET E1045 " pdb=" SD MET E1045 " ideal model delta sigma weight residual 112.70 122.92 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C PHE F1069 " pdb=" N VAL F1070 " pdb=" CA VAL F1070 " ideal model delta sigma weight residual 121.97 127.77 -5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CB MET C 325 " pdb=" CG MET C 325 " pdb=" SD MET C 325 " ideal model delta sigma weight residual 112.70 121.89 -9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" CA MET E1045 " pdb=" CB MET E1045 " pdb=" CG MET E1045 " ideal model delta sigma weight residual 114.10 119.70 -5.60 2.00e+00 2.50e-01 7.84e+00 ... (remaining 20346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 8799 34.54 - 69.09: 366 69.09 - 103.63: 22 103.63 - 138.17: 5 138.17 - 172.72: 2 Dihedral angle restraints: 9194 sinusoidal: 3803 harmonic: 5391 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.72 -172.72 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 84.42 -144.42 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.27 -120.28 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 9191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1481 0.032 - 0.064: 535 0.064 - 0.095: 149 0.095 - 0.127: 76 0.127 - 0.159: 6 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA PHE E1020 " pdb=" N PHE E1020 " pdb=" C PHE E1020 " pdb=" CB PHE E1020 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PHE F1020 " pdb=" N PHE F1020 " pdb=" C PHE F1020 " pdb=" CB PHE F1020 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2244 not shown) Planarity restraints: 2617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E1108 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO E1109 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO E1109 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E1109 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 276 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" CD GLU D 276 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU D 276 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU D 276 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1106 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C VAL E1106 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL E1106 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE E1107 " -0.010 2.00e-02 2.50e+03 ... (remaining 2614 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 109 2.56 - 3.14: 11950 3.14 - 3.73: 23214 3.73 - 4.31: 31477 4.31 - 4.90: 51714 Nonbonded interactions: 118464 Sorted by model distance: nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.974 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.011 2.170 nonbonded pdb=" O GLU C 117 " pdb=" OG1 THR C 120 " model vdw 2.219 2.440 nonbonded pdb=" OG SER B 358 " pdb=" OE1 GLN B 360 " model vdw 2.220 2.440 nonbonded pdb=" O THR C 304 " pdb=" NH1 ARG C 335 " model vdw 2.235 2.520 ... (remaining 118459 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 'B' and (resid 6 through 374 or resid 401 through 402)) selection = chain 'C' selection = (chain 'D' and (resid 6 through 374 or resid 401 through 402)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 7.860 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: 23.080 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.800 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.002 0.040 15068 Z= 0.161 Angle : 0.552 10.217 20351 Z= 0.272 Chirality : 0.039 0.159 2247 Planarity : 0.003 0.067 2617 Dihedral : 18.072 172.716 5700 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.37 % Rotamer: Outliers : 0.37 % Allowed : 26.24 % Favored : 73.38 % 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: -0.23 (0.20), residues: 1818 helix: 0.09 (0.18), residues: 818 sheet: 0.06 (0.48), residues: 140 loop : -0.28 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 340 HIS 0.002 0.000 HIS B 161 PHE 0.022 0.001 PHE D 279 TYR 0.023 0.001 TYR B 240 ARG 0.002 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: B 225 GLN cc_start: 0.7862 (pp30) cc_final: 0.7603 (pp30) REVERT: D 82 MET cc_start: 0.7410 (tpp) cc_final: 0.7209 (tpp) REVERT: E 925 PHE cc_start: 0.8007 (m-80) cc_final: 0.7701 (m-80) outliers start: 6 outliers final: 4 residues processed: 162 average time/residue: 0.2154 time to fit residues: 56.2829 Evaluate side-chains 157 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain F residue 1084 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 0.0010 chunk 167 optimal weight: 30.0000 overall best weight: 1.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 880 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15068 Z= 0.230 Angle : 0.586 7.739 20351 Z= 0.292 Chirality : 0.042 0.161 2247 Planarity : 0.004 0.056 2617 Dihedral : 8.540 166.728 2034 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.82 % Rotamer: Outliers : 3.48 % Allowed : 24.32 % Favored : 72.20 % 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: -0.17 (0.20), residues: 1818 helix: 0.26 (0.18), residues: 830 sheet: -0.29 (0.48), residues: 135 loop : -0.32 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 340 HIS 0.004 0.001 HIS D 371 PHE 0.016 0.002 PHE E1020 TYR 0.020 0.001 TYR C 143 ARG 0.003 0.000 ARG F 917 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 159 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: C 10 VAL cc_start: 0.8720 (t) cc_final: 0.8451 (m) REVERT: C 16 MET cc_start: 0.7387 (ttt) cc_final: 0.6992 (ttp) REVERT: F 775 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7049 (tt) REVERT: F 1082 GLU cc_start: 0.3162 (OUTLIER) cc_final: 0.2271 (mt-10) outliers start: 56 outliers final: 31 residues processed: 204 average time/residue: 0.2110 time to fit residues: 69.5962 Evaluate side-chains 184 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain F residue 775 LEU Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 944 THR Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 167 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 149 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 865 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15068 Z= 0.372 Angle : 0.677 8.044 20351 Z= 0.337 Chirality : 0.046 0.192 2247 Planarity : 0.005 0.062 2617 Dihedral : 8.085 142.783 2027 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.39 % Rotamer: Outliers : 5.78 % Allowed : 23.88 % Favored : 70.34 % 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: -0.62 (0.20), residues: 1818 helix: 0.03 (0.18), residues: 836 sheet: -0.86 (0.43), residues: 156 loop : -0.65 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 86 HIS 0.005 0.001 HIS D 371 PHE 0.037 0.002 PHE D 279 TYR 0.028 0.002 TYR C 143 ARG 0.003 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 150 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 355 MET cc_start: 0.7542 (tpp) cc_final: 0.7330 (tpp) REVERT: C 10 VAL cc_start: 0.8821 (t) cc_final: 0.8533 (m) REVERT: C 16 MET cc_start: 0.7748 (ttt) cc_final: 0.7442 (ttp) REVERT: C 82 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6929 (tpp) REVERT: C 313 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7492 (mtp) REVERT: D 136 ILE cc_start: 0.8749 (mm) cc_final: 0.8412 (mt) REVERT: E 1022 ASP cc_start: 0.7760 (m-30) cc_final: 0.7483 (p0) outliers start: 93 outliers final: 60 residues processed: 227 average time/residue: 0.2246 time to fit residues: 80.9269 Evaluate side-chains 203 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 141 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 764 ARG Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 852 MET Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 874 ILE Chi-restraints excluded: chain E residue 920 LEU Chi-restraints excluded: chain E residue 926 LYS Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1108 ASP Chi-restraints excluded: chain F residue 770 PHE Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 964 LEU Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15068 Z= 0.199 Angle : 0.571 9.017 20351 Z= 0.276 Chirality : 0.041 0.160 2247 Planarity : 0.004 0.054 2617 Dihedral : 7.421 132.824 2025 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 4.23 % Allowed : 24.88 % Favored : 70.90 % 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: -0.33 (0.20), residues: 1818 helix: 0.24 (0.18), residues: 849 sheet: -0.59 (0.50), residues: 125 loop : -0.51 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 86 HIS 0.004 0.001 HIS D 371 PHE 0.027 0.001 PHE D 279 TYR 0.019 0.001 TYR C 143 ARG 0.002 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 155 time to evaluate : 1.742 Fit side-chains revert: symmetry clash REVERT: B 316 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6501 (mm-30) REVERT: B 355 MET cc_start: 0.7544 (tpp) cc_final: 0.7261 (tpp) REVERT: C 10 VAL cc_start: 0.8675 (t) cc_final: 0.8425 (m) REVERT: D 136 ILE cc_start: 0.8734 (mm) cc_final: 0.8396 (mt) REVERT: D 294 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8248 (t80) REVERT: E 1022 ASP cc_start: 0.7702 (m-30) cc_final: 0.7427 (p0) REVERT: F 775 LEU cc_start: 0.7410 (pt) cc_final: 0.6922 (tt) REVERT: F 1001 THR cc_start: 0.4839 (OUTLIER) cc_final: 0.4546 (p) REVERT: F 1082 GLU cc_start: 0.3343 (OUTLIER) cc_final: 0.2452 (mt-10) outliers start: 68 outliers final: 40 residues processed: 214 average time/residue: 0.2357 time to fit residues: 80.3153 Evaluate side-chains 188 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 874 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain F residue 770 PHE Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1038 LEU Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.0370 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15068 Z= 0.170 Angle : 0.564 11.135 20351 Z= 0.267 Chirality : 0.041 0.173 2247 Planarity : 0.004 0.060 2617 Dihedral : 7.045 127.730 2025 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 3.86 % Allowed : 25.37 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.21), residues: 1818 helix: 0.45 (0.18), residues: 850 sheet: -0.46 (0.50), residues: 125 loop : -0.42 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 340 HIS 0.003 0.001 HIS D 371 PHE 0.025 0.001 PHE D 279 TYR 0.015 0.001 TYR C 143 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 155 time to evaluate : 1.571 Fit side-chains REVERT: B 316 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6482 (mm-30) REVERT: B 355 MET cc_start: 0.7522 (tpp) cc_final: 0.7239 (tpp) REVERT: B 361 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: C 10 VAL cc_start: 0.8633 (t) cc_final: 0.8374 (m) REVERT: C 16 MET cc_start: 0.7450 (ttt) cc_final: 0.7064 (ttp) REVERT: C 82 MET cc_start: 0.7131 (tpp) cc_final: 0.6914 (tpp) REVERT: C 107 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: C 313 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7099 (mtp) REVERT: D 136 ILE cc_start: 0.8730 (mm) cc_final: 0.8407 (mt) REVERT: D 294 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8248 (t80) REVERT: E 1022 ASP cc_start: 0.7704 (m-30) cc_final: 0.7397 (p0) REVERT: E 1118 PHE cc_start: 0.7003 (m-80) cc_final: 0.6699 (m-80) REVERT: F 775 LEU cc_start: 0.7396 (pt) cc_final: 0.6964 (tt) REVERT: F 1001 THR cc_start: 0.4835 (OUTLIER) cc_final: 0.4534 (p) REVERT: F 1082 GLU cc_start: 0.3218 (OUTLIER) cc_final: 0.2373 (mt-10) outliers start: 62 outliers final: 43 residues processed: 206 average time/residue: 0.2207 time to fit residues: 72.7867 Evaluate side-chains 198 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 149 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1108 ASP Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1038 LEU Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15068 Z= 0.179 Angle : 0.562 8.451 20351 Z= 0.266 Chirality : 0.041 0.160 2247 Planarity : 0.004 0.062 2617 Dihedral : 6.836 124.796 2025 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 4.54 % Allowed : 25.31 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.21), residues: 1818 helix: 0.48 (0.18), residues: 850 sheet: -0.37 (0.48), residues: 135 loop : -0.39 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 340 HIS 0.003 0.001 HIS D 371 PHE 0.015 0.001 PHE E1020 TYR 0.019 0.001 TYR E1084 ARG 0.002 0.000 ARG F 917 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 154 time to evaluate : 1.731 Fit side-chains revert: symmetry clash REVERT: B 16 MET cc_start: 0.8090 (tpp) cc_final: 0.7602 (ttm) REVERT: B 237 GLU cc_start: 0.7692 (pp20) cc_final: 0.7483 (pp20) REVERT: B 316 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6506 (mm-30) REVERT: B 355 MET cc_start: 0.7427 (tpp) cc_final: 0.7112 (tpp) REVERT: B 361 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: C 10 VAL cc_start: 0.8637 (t) cc_final: 0.8355 (m) REVERT: C 16 MET cc_start: 0.7533 (ttt) cc_final: 0.7122 (ttp) REVERT: C 82 MET cc_start: 0.7362 (tpp) cc_final: 0.7112 (tpp) REVERT: C 107 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: C 313 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7102 (mtp) REVERT: D 136 ILE cc_start: 0.8736 (mm) cc_final: 0.8405 (mt) REVERT: D 294 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8126 (t80) REVERT: E 1022 ASP cc_start: 0.7699 (m-30) cc_final: 0.7386 (p0) REVERT: E 1083 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: E 1118 PHE cc_start: 0.6989 (m-80) cc_final: 0.6694 (m-80) REVERT: F 775 LEU cc_start: 0.7349 (pt) cc_final: 0.6922 (tt) REVERT: F 1001 THR cc_start: 0.4869 (OUTLIER) cc_final: 0.4543 (p) REVERT: F 1082 GLU cc_start: 0.3255 (OUTLIER) cc_final: 0.2399 (mt-10) REVERT: F 1118 PHE cc_start: -0.3444 (OUTLIER) cc_final: -0.3658 (t80) outliers start: 73 outliers final: 51 residues processed: 217 average time/residue: 0.2239 time to fit residues: 77.8840 Evaluate side-chains 208 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 149 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1083 GLN Chi-restraints excluded: chain E residue 1108 ASP Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 964 LEU Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1038 LEU Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 0.0060 chunk 130 optimal weight: 0.0670 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 108 optimal weight: 0.0020 chunk 81 optimal weight: 0.9980 overall best weight: 0.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1130 GLN F 905 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15068 Z= 0.143 Angle : 0.551 8.622 20351 Z= 0.259 Chirality : 0.040 0.159 2247 Planarity : 0.003 0.057 2617 Dihedral : 6.444 117.413 2025 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Rotamer: Outliers : 3.23 % Allowed : 26.62 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.21), residues: 1818 helix: 0.62 (0.19), residues: 849 sheet: -0.16 (0.45), residues: 155 loop : -0.24 (0.24), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 340 HIS 0.003 0.000 HIS C 161 PHE 0.025 0.001 PHE D 279 TYR 0.024 0.001 TYR E1084 ARG 0.002 0.000 ARG F 917 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 165 time to evaluate : 1.802 Fit side-chains revert: symmetry clash REVERT: B 213 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7603 (ttpp) REVERT: B 316 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6497 (mm-30) REVERT: B 355 MET cc_start: 0.7375 (tpp) cc_final: 0.7098 (tpp) REVERT: B 361 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: C 10 VAL cc_start: 0.8488 (t) cc_final: 0.8232 (m) REVERT: C 16 MET cc_start: 0.7455 (ttt) cc_final: 0.7043 (ttp) REVERT: C 82 MET cc_start: 0.7451 (tpp) cc_final: 0.7190 (tpp) REVERT: C 196 ARG cc_start: 0.7192 (ttm-80) cc_final: 0.6389 (ttm-80) REVERT: C 313 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7071 (mtp) REVERT: D 136 ILE cc_start: 0.8715 (mm) cc_final: 0.8394 (mt) REVERT: D 294 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8151 (t80) REVERT: E 1022 ASP cc_start: 0.7685 (m-30) cc_final: 0.7344 (p0) REVERT: E 1118 PHE cc_start: 0.6902 (m-80) cc_final: 0.6657 (m-80) REVERT: F 775 LEU cc_start: 0.7348 (pt) cc_final: 0.7004 (tt) REVERT: F 1001 THR cc_start: 0.4965 (OUTLIER) cc_final: 0.4689 (p) REVERT: F 1082 GLU cc_start: 0.3234 (OUTLIER) cc_final: 0.2395 (mt-10) REVERT: F 1118 PHE cc_start: -0.3463 (OUTLIER) cc_final: -0.3690 (t80) outliers start: 52 outliers final: 36 residues processed: 208 average time/residue: 0.2182 time to fit residues: 72.7785 Evaluate side-chains 196 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain E residue 1108 ASP Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 889 MET Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 112 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.4280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15068 Z= 0.256 Angle : 0.617 8.605 20351 Z= 0.296 Chirality : 0.043 0.161 2247 Planarity : 0.004 0.066 2617 Dihedral : 6.625 118.860 2025 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.73 % Favored : 95.10 % Rotamer: Outliers : 4.04 % Allowed : 26.74 % Favored : 69.22 % 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: -0.06 (0.21), residues: 1818 helix: 0.52 (0.18), residues: 843 sheet: -0.75 (0.46), residues: 152 loop : -0.36 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 340 HIS 0.003 0.001 HIS B 87 PHE 0.019 0.002 PHE D 223 TYR 0.017 0.001 TYR C 143 ARG 0.002 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 148 time to evaluate : 2.033 Fit side-chains revert: symmetry clash REVERT: B 16 MET cc_start: 0.8126 (tpp) cc_final: 0.7708 (ttm) REVERT: B 316 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6568 (mm-30) REVERT: B 355 MET cc_start: 0.7495 (tpp) cc_final: 0.7224 (tpp) REVERT: B 361 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: C 16 MET cc_start: 0.7681 (ttt) cc_final: 0.7305 (ttp) REVERT: C 82 MET cc_start: 0.7546 (tpp) cc_final: 0.7234 (tpp) REVERT: C 313 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7365 (mtp) REVERT: D 294 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8244 (t80) REVERT: E 1022 ASP cc_start: 0.7660 (m-30) cc_final: 0.7346 (p0) REVERT: E 1118 PHE cc_start: 0.6994 (m-80) cc_final: 0.6735 (m-80) REVERT: F 775 LEU cc_start: 0.7336 (pt) cc_final: 0.6897 (tt) REVERT: F 1001 THR cc_start: 0.4980 (OUTLIER) cc_final: 0.4640 (p) REVERT: F 1082 GLU cc_start: 0.3364 (OUTLIER) cc_final: 0.2496 (mt-10) REVERT: F 1118 PHE cc_start: -0.3317 (OUTLIER) cc_final: -0.3642 (t80) outliers start: 65 outliers final: 45 residues processed: 198 average time/residue: 0.2212 time to fit residues: 70.6098 Evaluate side-chains 196 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 874 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1108 ASP Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 889 MET Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 964 LEU Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 30.0000 chunk 155 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 0.1980 chunk 156 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15068 Z= 0.252 Angle : 0.619 9.124 20351 Z= 0.295 Chirality : 0.042 0.161 2247 Planarity : 0.004 0.062 2617 Dihedral : 6.646 115.464 2025 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.73 % Favored : 95.10 % Rotamer: Outliers : 3.73 % Allowed : 27.24 % Favored : 69.03 % 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: -0.14 (0.21), residues: 1818 helix: 0.44 (0.18), residues: 852 sheet: -0.41 (0.48), residues: 135 loop : -0.49 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 340 HIS 0.003 0.001 HIS D 371 PHE 0.016 0.002 PHE D 279 TYR 0.019 0.001 TYR C 143 ARG 0.002 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 150 time to evaluate : 1.708 Fit side-chains REVERT: B 16 MET cc_start: 0.8104 (tpp) cc_final: 0.7691 (ttm) REVERT: B 316 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6518 (mm-30) REVERT: B 355 MET cc_start: 0.7464 (tpp) cc_final: 0.7254 (tpp) REVERT: B 361 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: C 10 VAL cc_start: 0.8659 (t) cc_final: 0.8376 (m) REVERT: C 16 MET cc_start: 0.7823 (ttt) cc_final: 0.7473 (ttp) REVERT: C 82 MET cc_start: 0.7469 (tpp) cc_final: 0.7177 (tpp) REVERT: C 313 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7347 (mtp) REVERT: D 294 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8194 (t80) REVERT: D 346 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8086 (tt) REVERT: E 1022 ASP cc_start: 0.7707 (m-30) cc_final: 0.7350 (p0) REVERT: E 1118 PHE cc_start: 0.6983 (m-80) cc_final: 0.6716 (m-80) REVERT: F 1001 THR cc_start: 0.5003 (OUTLIER) cc_final: 0.4646 (p) REVERT: F 1082 GLU cc_start: 0.3393 (OUTLIER) cc_final: 0.2517 (mt-10) REVERT: F 1118 PHE cc_start: -0.3369 (OUTLIER) cc_final: -0.3610 (t80) outliers start: 60 outliers final: 49 residues processed: 198 average time/residue: 0.2194 time to fit residues: 70.0633 Evaluate side-chains 204 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 148 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 874 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1108 ASP Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 889 MET Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 121 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15068 Z= 0.178 Angle : 0.588 9.140 20351 Z= 0.276 Chirality : 0.041 0.158 2247 Planarity : 0.003 0.061 2617 Dihedral : 6.433 114.947 2025 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.35 % Favored : 95.49 % Rotamer: Outliers : 2.99 % Allowed : 27.92 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.21), residues: 1818 helix: 0.54 (0.19), residues: 848 sheet: -0.28 (0.47), residues: 145 loop : -0.34 (0.24), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 340 HIS 0.003 0.001 HIS D 371 PHE 0.015 0.001 PHE E1020 TYR 0.016 0.001 TYR C 143 ARG 0.001 0.000 ARG B 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 150 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: B 16 MET cc_start: 0.8097 (tpp) cc_final: 0.7658 (ttm) REVERT: B 316 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6464 (mm-30) REVERT: B 361 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: C 10 VAL cc_start: 0.8597 (t) cc_final: 0.8339 (m) REVERT: C 82 MET cc_start: 0.7478 (tpp) cc_final: 0.7202 (tpp) REVERT: C 196 ARG cc_start: 0.7259 (ttm-80) cc_final: 0.6424 (ttm-80) REVERT: C 313 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7246 (mtp) REVERT: D 283 MET cc_start: 0.8978 (mmm) cc_final: 0.8705 (mmm) REVERT: D 294 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8054 (t80) REVERT: D 346 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8029 (tt) REVERT: E 1022 ASP cc_start: 0.7695 (m-30) cc_final: 0.7354 (p0) REVERT: E 1118 PHE cc_start: 0.6968 (m-80) cc_final: 0.6757 (m-80) REVERT: F 775 LEU cc_start: 0.7263 (pt) cc_final: 0.6799 (tt) REVERT: F 1001 THR cc_start: 0.4976 (OUTLIER) cc_final: 0.4645 (p) REVERT: F 1082 GLU cc_start: 0.3232 (OUTLIER) cc_final: 0.2393 (mt-10) outliers start: 48 outliers final: 38 residues processed: 187 average time/residue: 0.2155 time to fit residues: 65.3848 Evaluate side-chains 193 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 149 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain E residue 1108 ASP Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 889 MET Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 44 optimal weight: 0.0010 chunk 134 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 128 optimal weight: 2.9990 overall best weight: 0.6966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1057 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.141109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.105630 restraints weight = 32061.810| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.99 r_work: 0.3574 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15068 Z= 0.176 Angle : 0.584 9.302 20351 Z= 0.275 Chirality : 0.041 0.156 2247 Planarity : 0.003 0.061 2617 Dihedral : 6.391 114.007 2025 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.38 % Rotamer: Outliers : 3.23 % Allowed : 27.80 % Favored : 68.97 % 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: 0.04 (0.21), residues: 1818 helix: 0.52 (0.18), residues: 861 sheet: -0.06 (0.45), residues: 152 loop : -0.37 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 340 HIS 0.003 0.001 HIS D 371 PHE 0.025 0.001 PHE D 279 TYR 0.015 0.001 TYR C 143 ARG 0.002 0.000 ARG F1146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3292.82 seconds wall clock time: 62 minutes 8.01 seconds (3728.01 seconds total)