Starting phenix.real_space_refine on Thu Jan 18 23:38:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/01_2024/6o2p_0611_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/01_2024/6o2p_0611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/01_2024/6o2p_0611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/01_2024/6o2p_0611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/01_2024/6o2p_0611_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/01_2024/6o2p_0611_updated.pdb" } resolution = 3.3 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= 0.008 sd= 0.185 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 2 5.21 5 S 47 5.16 5 C 6387 2.51 5 N 1596 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 933": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 1158": "NH1" <-> "NH2" Residue "A ARG 1239": "NH1" <-> "NH2" Residue "A ARG 1259": "NH1" <-> "NH2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A ARG 1325": "NH1" <-> "NH2" Residue "A ARG 1358": "NH1" <-> "NH2" Residue "A ARG 1386": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9767 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9450 Classifications: {'peptide': 1179} Link IDs: {'PTRANS': 32, 'TRANS': 1146} Chain breaks: 4 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 232 Unusual residues: {' MG': 2, 'AJP': 1, 'ATP': 2, 'POV': 6, 'VX7': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 6.04, per 1000 atoms: 0.62 Number of scatterers: 9767 At special positions: 0 Unit cell: (102.942, 120.916, 111.929, 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 47 16.00 P 6 15.00 Mg 2 11.99 O 1729 8.00 N 1596 7.00 C 6387 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: 4.01 Conformation dependent library (CDL) restraints added in 1.8 seconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 6 sheets defined 64.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.593A pdb=" N ARG A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 46 through 63 removed outlier: 3.594A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.928A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 removed outlier: 3.680A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 4.086A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 166 removed outlier: 5.439A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.662A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 177 through 218 removed outlier: 3.726A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N PHE A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 3.670A pdb=" N GLY A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 267 removed outlier: 3.874A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 279 through 328 removed outlier: 3.613A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 333 through 351 removed outlier: 4.010A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 375 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.687A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 580 through 589 Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.534A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 846 through 853 removed outlier: 3.564A pdb=" N ILE A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 885 removed outlier: 3.529A pdb=" N ILE A 869 " --> pdb=" O TRP A 865 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 926 removed outlier: 3.908A pdb=" N SER A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 957 Proline residue: A 936 - end of helix removed outlier: 3.746A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 969 through 984 removed outlier: 3.801A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1011 removed outlier: 4.035A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1046 removed outlier: 3.950A pdb=" N VAL A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.863A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1060 removed outlier: 3.593A pdb=" N THR A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1068 Processing helix chain 'A' and resid 1071 through 1121 removed outlier: 3.536A pdb=" N THR A1076 " --> pdb=" O PRO A1072 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A1080 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1099 " --> pdb=" O THR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1167 removed outlier: 3.605A pdb=" N ALA A1136 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A1156 " --> pdb=" O ASP A1152 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A1161 " --> pdb=" O MET A1157 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.697A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1285 removed outlier: 3.927A pdb=" N LYS A1284 " --> pdb=" O GLN A1280 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A1285 " --> pdb=" O GLN A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1322 removed outlier: 4.867A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 removed outlier: 3.508A pdb=" N GLU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1325 through 1329' Processing helix chain 'A' and resid 1348 through 1361 removed outlier: 3.671A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1390 removed outlier: 3.779A pdb=" N GLN A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1408 removed outlier: 3.562A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1405 through 1408' Processing helix chain 'A' and resid 1427 through 1433 removed outlier: 3.636A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1440 Processing helix chain 'A' and resid 1443 through 1449 removed outlier: 4.310A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.652A pdb=" N UNK B 13 " --> pdb=" O UNK B 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK B 14 " --> pdb=" O UNK B 10 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 481 through 483 removed outlier: 3.586A pdb=" N LYS A 481 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 395 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 483 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 393 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 599 through 603 removed outlier: 6.979A pdb=" N GLN A 452 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 602 " --> pdb=" O GLN A 452 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU A 454 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS A 615 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA A 457 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 617 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= D, first strand: chain 'A' and resid 1210 through 1213 removed outlier: 3.575A pdb=" N GLU A1266 " --> pdb=" O LYS A1213 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1420 through 1424 removed outlier: 3.734A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A1397 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU A1242 " --> pdb=" O VAL A1397 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A1399 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N GLY A1244 " --> pdb=" O LEU A1399 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1215 through 1217 removed outlier: 7.458A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1431 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: 3.17 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1884 1.34 - 1.46: 2314 1.46 - 1.58: 5686 1.58 - 1.70: 10 1.70 - 1.82: 79 Bond restraints: 9973 Sorted by residual: bond pdb=" C29 POV A1508 " pdb="C210 POV A1508 " ideal model delta sigma weight residual 1.333 1.510 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N ILE A1289 " pdb=" CA ILE A1289 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.60e-03 1.35e+04 2.19e+01 bond pdb=" C02 VX7 A1512 " pdb=" C05 VX7 A1512 " ideal model delta sigma weight residual 1.535 1.454 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" N LEU A 935 " pdb=" CA LEU A 935 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.60e+01 bond pdb=" C15 VX7 A1512 " pdb=" N16 VX7 A1512 " ideal model delta sigma weight residual 1.329 1.409 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 9968 not shown) Histogram of bond angle deviations from ideal: 96.27 - 103.91: 101 103.91 - 111.55: 3972 111.55 - 119.19: 5345 119.19 - 126.83: 3958 126.83 - 134.46: 120 Bond angle restraints: 13496 Sorted by residual: angle pdb=" PB ATP A1504 " pdb=" O3B ATP A1504 " pdb=" PG ATP A1504 " ideal model delta sigma weight residual 139.87 132.08 7.79 1.00e+00 1.00e+00 6.06e+01 angle pdb=" PA ATP A1503 " pdb=" O3A ATP A1503 " pdb=" PB ATP A1503 " ideal model delta sigma weight residual 136.83 129.74 7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 133.14 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" PA ATP A1504 " pdb=" O3A ATP A1504 " pdb=" PB ATP A1504 " ideal model delta sigma weight residual 136.83 130.54 6.29 1.00e+00 1.00e+00 3.95e+01 angle pdb=" CA GLY A 480 " pdb=" C GLY A 480 " pdb=" O GLY A 480 " ideal model delta sigma weight residual 122.37 118.19 4.18 7.30e-01 1.88e+00 3.28e+01 ... (remaining 13491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 5850 34.87 - 69.75: 162 69.75 - 104.62: 26 104.62 - 139.49: 53 139.49 - 174.36: 12 Dihedral angle restraints: 6103 sinusoidal: 2627 harmonic: 3476 Sorted by residual: dihedral pdb=" CA VAL A1288 " pdb=" C VAL A1288 " pdb=" N ILE A1289 " pdb=" CA ILE A1289 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" C12 AJP A1511 " pdb=" C10 AJP A1511 " pdb=" C11 AJP A1511 " pdb=" O82 AJP A1511 " ideal model delta sinusoidal sigma weight residual 287.38 113.02 174.36 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C06 AJP A1511 " pdb=" C07 AJP A1511 " pdb=" C12 AJP A1511 " pdb=" C13 AJP A1511 " ideal model delta sinusoidal sigma weight residual 109.15 -82.00 -168.85 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 6100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.183: 1537 1.183 - 2.367: 0 2.367 - 3.550: 0 3.550 - 4.733: 4 4.733 - 5.916: 21 Chirality restraints: 1562 Sorted by residual: chirality pdb=" C12 AJP A1511 " pdb=" C07 AJP A1511 " pdb=" C11 AJP A1511 " pdb=" C13 AJP A1511 " both_signs ideal model delta sigma weight residual False 3.01 -2.91 5.92 2.00e-01 2.50e+01 8.75e+02 chirality pdb=" C20 AJP A1511 " pdb=" C15 AJP A1511 " pdb=" C19 AJP A1511 " pdb=" C21 AJP A1511 " both_signs ideal model delta sigma weight residual False 2.96 -2.86 5.82 2.00e-01 2.50e+01 8.46e+02 chirality pdb=" C07 AJP A1511 " pdb=" C06 AJP A1511 " pdb=" C08 AJP A1511 " pdb=" C12 AJP A1511 " both_signs ideal model delta sigma weight residual False -2.73 2.75 -5.48 2.00e-01 2.50e+01 7.50e+02 ... (remaining 1559 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1508 " -0.029 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C29 POV A1508 " 0.029 2.00e-02 2.50e+03 pdb="C210 POV A1508 " 0.030 2.00e-02 2.50e+03 pdb="C211 POV A1508 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 161 " -0.020 2.00e-02 2.50e+03 1.18e-02 2.77e+00 pdb=" CG TYR A 161 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 161 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 161 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 161 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 161 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 161 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 161 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 VX7 A1512 " -0.011 2.00e-02 2.50e+03 1.43e-02 2.56e+00 pdb=" C12 VX7 A1512 " 0.025 2.00e-02 2.50e+03 pdb=" C14 VX7 A1512 " -0.015 2.00e-02 2.50e+03 pdb=" N11 VX7 A1512 " 0.006 2.00e-02 2.50e+03 pdb=" O13 VX7 A1512 " -0.006 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 12 2.51 - 3.11: 5900 3.11 - 3.70: 14584 3.70 - 4.30: 19988 4.30 - 4.90: 34778 Nonbonded interactions: 75262 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O2B ATP A1504 " model vdw 1.908 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.029 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 2.051 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.111 2.170 nonbonded pdb="MG MG A1501 " pdb=" O2B ATP A1503 " model vdw 2.115 2.170 ... (remaining 75257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.030 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.310 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 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 : 0.014 0.177 9973 Z= 0.895 Angle : 1.830 13.896 13496 Z= 1.376 Chirality : 0.642 5.916 1562 Planarity : 0.003 0.029 1630 Dihedral : 22.920 174.362 3855 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.16 % Allowed : 5.51 % Favored : 93.33 % 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: -3.17 (0.20), residues: 1169 helix: -1.71 (0.16), residues: 723 sheet: -2.53 (0.53), residues: 74 loop : -2.47 (0.25), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1274 HIS 0.006 0.002 HIS A 146 PHE 0.019 0.002 PHE A 337 TYR 0.026 0.002 TYR A 161 ARG 0.003 0.001 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 287 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8640 (tt0) cc_final: 0.8383 (mm-30) REVERT: A 26 LYS cc_start: 0.7520 (tptp) cc_final: 0.6881 (tppt) REVERT: A 29 ARG cc_start: 0.7606 (ptp-170) cc_final: 0.7260 (ttm-80) REVERT: A 51 GLU cc_start: 0.8792 (tp30) cc_final: 0.8334 (pt0) REVERT: A 82 MET cc_start: 0.7882 (mmt) cc_final: 0.7377 (mpp) REVERT: A 216 TRP cc_start: 0.8128 (t60) cc_final: 0.7899 (t60) REVERT: A 220 GLN cc_start: 0.6695 (mm-40) cc_final: 0.6174 (mm-40) REVERT: A 257 GLU cc_start: 0.7928 (tt0) cc_final: 0.7293 (tp30) REVERT: A 267 GLU cc_start: 0.8391 (tt0) cc_final: 0.8146 (tp30) REVERT: A 369 ASN cc_start: 0.7730 (m-40) cc_final: 0.7500 (m-40) REVERT: A 373 ASP cc_start: 0.8464 (t0) cc_final: 0.8120 (m-30) REVERT: A 443 ASP cc_start: 0.8463 (m-30) cc_final: 0.7665 (p0) REVERT: A 448 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7571 (mt) REVERT: A 476 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8810 (mm-30) REVERT: A 487 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7636 (mtp180) REVERT: A 504 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7905 (mp0) REVERT: A 529 ASP cc_start: 0.9059 (m-30) cc_final: 0.8765 (m-30) REVERT: A 572 ASP cc_start: 0.8084 (t0) cc_final: 0.7795 (t0) REVERT: A 597 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7324 (m-40) REVERT: A 968 LYS cc_start: 0.7803 (mttm) cc_final: 0.7404 (mtmm) REVERT: A 1044 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 1046 GLU cc_start: 0.8008 (tt0) cc_final: 0.7549 (tp30) REVERT: A 1104 GLU cc_start: 0.8486 (tt0) cc_final: 0.8259 (tt0) REVERT: A 1128 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.7657 (ptt180) REVERT: A 1279 LEU cc_start: 0.7876 (tp) cc_final: 0.7663 (tt) REVERT: A 1284 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8718 (tptp) REVERT: A 1308 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8525 (mm-30) REVERT: A 1317 LYS cc_start: 0.8576 (tptp) cc_final: 0.8376 (tptp) REVERT: A 1320 ASP cc_start: 0.8503 (p0) cc_final: 0.8211 (p0) REVERT: A 1340 VAL cc_start: 0.7465 (m) cc_final: 0.7153 (p) REVERT: A 1341 ASP cc_start: 0.8212 (t70) cc_final: 0.7557 (t0) REVERT: A 1394 ASP cc_start: 0.8802 (m-30) cc_final: 0.7906 (t0) REVERT: A 1419 ASN cc_start: 0.8622 (m110) cc_final: 0.8259 (p0) REVERT: A 1437 PHE cc_start: 0.8307 (t80) cc_final: 0.7791 (t80) outliers start: 12 outliers final: 3 residues processed: 297 average time/residue: 0.2624 time to fit residues: 102.5415 Evaluate side-chains 181 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 176 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 92 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 68 optimal weight: 0.0970 chunk 107 optimal weight: 0.6980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 525 GLN A 552 GLN A1039 GLN A1238 GLN A1330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9973 Z= 0.171 Angle : 0.966 35.887 13496 Z= 0.391 Chirality : 0.090 2.011 1562 Planarity : 0.003 0.032 1630 Dihedral : 18.215 178.771 1607 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.74 % Allowed : 14.20 % Favored : 84.06 % 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: -0.13 (0.23), residues: 1169 helix: 0.85 (0.18), residues: 751 sheet: -1.96 (0.53), residues: 79 loop : -1.65 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1204 HIS 0.008 0.001 HIS A 199 PHE 0.017 0.001 PHE A 83 TYR 0.019 0.001 TYR A 517 ARG 0.006 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 228 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7467 (tptp) cc_final: 0.7158 (tptt) REVERT: A 33 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6353 (mt-10) REVERT: A 51 GLU cc_start: 0.8618 (tp30) cc_final: 0.8303 (mt-10) REVERT: A 56 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8601 (mm-30) REVERT: A 60 GLU cc_start: 0.8348 (tp30) cc_final: 0.8005 (tp30) REVERT: A 220 GLN cc_start: 0.6318 (mm-40) cc_final: 0.6014 (mm-40) REVERT: A 257 GLU cc_start: 0.7983 (tt0) cc_final: 0.7500 (tp30) REVERT: A 267 GLU cc_start: 0.8464 (tt0) cc_final: 0.8213 (tp30) REVERT: A 476 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8789 (mm-30) REVERT: A 487 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7683 (mmm-85) REVERT: A 504 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7917 (mp0) REVERT: A 600 ARG cc_start: 0.7436 (ptt-90) cc_final: 0.7145 (ptp90) REVERT: A 968 LYS cc_start: 0.7317 (mttm) cc_final: 0.6954 (mtmm) REVERT: A 1028 MET cc_start: 0.7970 (mmp) cc_final: 0.7634 (mtm) REVERT: A 1046 GLU cc_start: 0.7929 (tt0) cc_final: 0.7505 (tp30) REVERT: A 1128 ARG cc_start: 0.8438 (ttt-90) cc_final: 0.7497 (ptt90) REVERT: A 1264 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8486 (mt-10) REVERT: A 1308 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8432 (mm-30) REVERT: A 1320 ASP cc_start: 0.8233 (p0) cc_final: 0.8032 (p0) REVERT: A 1321 GLU cc_start: 0.8274 (mp0) cc_final: 0.8070 (mm-30) REVERT: A 1340 VAL cc_start: 0.7397 (m) cc_final: 0.7146 (p) REVERT: A 1341 ASP cc_start: 0.8013 (t70) cc_final: 0.7509 (t0) REVERT: A 1363 LYS cc_start: 0.9403 (tptm) cc_final: 0.9160 (tptp) REVERT: A 1394 ASP cc_start: 0.8921 (m-30) cc_final: 0.8490 (m-30) REVERT: A 1437 PHE cc_start: 0.8240 (t80) cc_final: 0.7903 (t80) outliers start: 18 outliers final: 10 residues processed: 242 average time/residue: 0.2188 time to fit residues: 73.8847 Evaluate side-chains 176 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 147 HIS A 151 GLN A 199 HIS A 505 ASN A1079 HIS A1330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9973 Z= 0.305 Angle : 0.963 34.357 13496 Z= 0.393 Chirality : 0.090 2.005 1562 Planarity : 0.004 0.035 1630 Dihedral : 17.478 179.013 1602 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.67 % Allowed : 16.04 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1169 helix: 1.33 (0.19), residues: 755 sheet: -2.05 (0.53), residues: 67 loop : -1.26 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 882 HIS 0.005 0.001 HIS A1085 PHE 0.017 0.002 PHE A 81 TYR 0.018 0.002 TYR A 38 ARG 0.006 0.001 ARG A1283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6694 (mt-10) REVERT: A 56 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8522 (mm-30) REVERT: A 60 GLU cc_start: 0.8516 (tp30) cc_final: 0.8283 (tp30) REVERT: A 92 GLU cc_start: 0.8537 (tp30) cc_final: 0.8041 (tp30) REVERT: A 257 GLU cc_start: 0.7929 (tt0) cc_final: 0.7531 (tp30) REVERT: A 267 GLU cc_start: 0.8398 (tt0) cc_final: 0.8187 (tp30) REVERT: A 385 TYR cc_start: 0.7785 (t80) cc_final: 0.7524 (t80) REVERT: A 476 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8906 (mm-30) REVERT: A 485 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8407 (t) REVERT: A 487 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7663 (mtp180) REVERT: A 504 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7946 (mp0) REVERT: A 600 ARG cc_start: 0.7501 (ptt-90) cc_final: 0.7187 (ptp90) REVERT: A 871 LEU cc_start: 0.8819 (mt) cc_final: 0.8552 (mm) REVERT: A 968 LYS cc_start: 0.7000 (mttm) cc_final: 0.6656 (mtmm) REVERT: A 1028 MET cc_start: 0.7949 (mmp) cc_final: 0.7613 (mtm) REVERT: A 1046 GLU cc_start: 0.7892 (tt0) cc_final: 0.7607 (tp30) REVERT: A 1128 ARG cc_start: 0.8463 (ttt-90) cc_final: 0.7651 (ptt90) REVERT: A 1308 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8483 (mm-30) REVERT: A 1320 ASP cc_start: 0.8331 (p0) cc_final: 0.7650 (p0) REVERT: A 1321 GLU cc_start: 0.8110 (mp0) cc_final: 0.7847 (mp0) REVERT: A 1340 VAL cc_start: 0.7362 (m) cc_final: 0.7128 (p) REVERT: A 1341 ASP cc_start: 0.8110 (t70) cc_final: 0.7683 (t0) REVERT: A 1363 LYS cc_start: 0.9332 (tptm) cc_final: 0.9012 (tptp) REVERT: A 1370 ASP cc_start: 0.7915 (t0) cc_final: 0.7496 (t70) REVERT: A 1394 ASP cc_start: 0.8830 (m-30) cc_final: 0.8339 (m-30) REVERT: A 1419 ASN cc_start: 0.8981 (m110) cc_final: 0.7921 (t0) REVERT: A 1437 PHE cc_start: 0.8084 (t80) cc_final: 0.7884 (t80) outliers start: 38 outliers final: 26 residues processed: 195 average time/residue: 0.2090 time to fit residues: 57.2295 Evaluate side-chains 174 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1430 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9973 Z= 0.190 Angle : 0.910 34.088 13496 Z= 0.362 Chirality : 0.089 1.995 1562 Planarity : 0.003 0.031 1630 Dihedral : 16.977 176.234 1602 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.71 % Allowed : 17.87 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1169 helix: 1.52 (0.19), residues: 765 sheet: -1.81 (0.52), residues: 76 loop : -1.11 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 882 HIS 0.003 0.001 HIS A 199 PHE 0.014 0.001 PHE A 81 TYR 0.012 0.001 TYR A 517 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6806 (mt-10) REVERT: A 56 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8544 (mm-30) REVERT: A 92 GLU cc_start: 0.8563 (tp30) cc_final: 0.8079 (tp30) REVERT: A 257 GLU cc_start: 0.8019 (tt0) cc_final: 0.7668 (tp30) REVERT: A 267 GLU cc_start: 0.8466 (tt0) cc_final: 0.8221 (tp30) REVERT: A 331 ILE cc_start: 0.9263 (tp) cc_final: 0.9056 (tp) REVERT: A 476 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8881 (mm-30) REVERT: A 485 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8368 (t) REVERT: A 487 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7645 (mtp180) REVERT: A 504 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7992 (mp0) REVERT: A 600 ARG cc_start: 0.7398 (ptt-90) cc_final: 0.7043 (ptp90) REVERT: A 1028 MET cc_start: 0.7926 (mmp) cc_final: 0.7598 (mtm) REVERT: A 1046 GLU cc_start: 0.7849 (tt0) cc_final: 0.7596 (tp30) REVERT: A 1128 ARG cc_start: 0.8502 (ttt-90) cc_final: 0.7398 (ptt90) REVERT: A 1308 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8472 (mm-30) REVERT: A 1317 LYS cc_start: 0.7831 (tppt) cc_final: 0.7527 (tptp) REVERT: A 1320 ASP cc_start: 0.8065 (p0) cc_final: 0.7800 (p0) REVERT: A 1341 ASP cc_start: 0.7941 (t70) cc_final: 0.7405 (t0) REVERT: A 1363 LYS cc_start: 0.9317 (tptm) cc_final: 0.9064 (tptp) REVERT: A 1370 ASP cc_start: 0.7908 (t0) cc_final: 0.7613 (t0) REVERT: A 1394 ASP cc_start: 0.8738 (m-30) cc_final: 0.8246 (m-30) REVERT: A 1419 ASN cc_start: 0.8976 (m110) cc_final: 0.7929 (t0) outliers start: 28 outliers final: 17 residues processed: 183 average time/residue: 0.2121 time to fit residues: 55.5296 Evaluate side-chains 164 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1326 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 0.0170 chunk 28 optimal weight: 0.8980 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9973 Z= 0.233 Angle : 0.918 34.218 13496 Z= 0.369 Chirality : 0.089 2.001 1562 Planarity : 0.003 0.031 1630 Dihedral : 16.846 177.205 1600 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.35 % Allowed : 17.97 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1169 helix: 1.58 (0.19), residues: 765 sheet: -1.69 (0.51), residues: 77 loop : -0.93 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 216 HIS 0.004 0.001 HIS A1085 PHE 0.013 0.001 PHE A 81 TYR 0.012 0.001 TYR A 38 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 151 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7662 (tptp) cc_final: 0.7250 (tptt) REVERT: A 33 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6863 (mt-10) REVERT: A 56 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8517 (mm-30) REVERT: A 92 GLU cc_start: 0.8595 (tp30) cc_final: 0.8105 (tp30) REVERT: A 111 PRO cc_start: 0.8384 (Cg_endo) cc_final: 0.8129 (Cg_exo) REVERT: A 257 GLU cc_start: 0.7980 (tt0) cc_final: 0.7653 (tp30) REVERT: A 267 GLU cc_start: 0.8452 (tt0) cc_final: 0.8219 (tp30) REVERT: A 331 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9084 (tp) REVERT: A 476 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8879 (mm-30) REVERT: A 485 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8506 (t) REVERT: A 487 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7616 (mtp180) REVERT: A 504 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7900 (mp0) REVERT: A 600 ARG cc_start: 0.7440 (ptt-90) cc_final: 0.7117 (ptp90) REVERT: A 1028 MET cc_start: 0.7918 (mmp) cc_final: 0.7587 (mtm) REVERT: A 1046 GLU cc_start: 0.7824 (tt0) cc_final: 0.7623 (tp30) REVERT: A 1128 ARG cc_start: 0.8472 (ttt-90) cc_final: 0.7455 (ptt90) REVERT: A 1284 LYS cc_start: 0.8845 (tppt) cc_final: 0.8234 (tptp) REVERT: A 1308 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8537 (mm-30) REVERT: A 1309 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8832 (pm20) REVERT: A 1341 ASP cc_start: 0.8099 (t70) cc_final: 0.7559 (t0) REVERT: A 1363 LYS cc_start: 0.9343 (tptm) cc_final: 0.9008 (tptp) REVERT: A 1370 ASP cc_start: 0.7894 (t0) cc_final: 0.7542 (t0) REVERT: A 1394 ASP cc_start: 0.8698 (m-30) cc_final: 0.8175 (m-30) REVERT: A 1419 ASN cc_start: 0.9019 (m110) cc_final: 0.7973 (t0) outliers start: 45 outliers final: 22 residues processed: 188 average time/residue: 0.2015 time to fit residues: 54.2927 Evaluate side-chains 165 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1326 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A1330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9973 Z= 0.185 Angle : 0.906 34.066 13496 Z= 0.360 Chirality : 0.089 2.003 1562 Planarity : 0.003 0.031 1630 Dihedral : 16.720 176.708 1600 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.48 % Allowed : 19.32 % Favored : 77.20 % 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: 1.12 (0.25), residues: 1169 helix: 1.65 (0.19), residues: 765 sheet: -1.33 (0.53), residues: 75 loop : -0.83 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 216 HIS 0.003 0.001 HIS A1085 PHE 0.011 0.001 PHE A 81 TYR 0.017 0.001 TYR A 385 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7571 (mm-30) cc_final: 0.6940 (mt-10) REVERT: A 56 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8527 (mm-30) REVERT: A 92 GLU cc_start: 0.8600 (tp30) cc_final: 0.8112 (tp30) REVERT: A 111 PRO cc_start: 0.8287 (Cg_endo) cc_final: 0.8077 (Cg_exo) REVERT: A 257 GLU cc_start: 0.7961 (tt0) cc_final: 0.7677 (tp30) REVERT: A 267 GLU cc_start: 0.8490 (tt0) cc_final: 0.8233 (tp30) REVERT: A 331 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9060 (tp) REVERT: A 476 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8861 (mm-30) REVERT: A 485 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8452 (t) REVERT: A 487 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7616 (mtp180) REVERT: A 504 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7850 (mp0) REVERT: A 600 ARG cc_start: 0.7461 (ptt-90) cc_final: 0.7156 (ptp90) REVERT: A 1012 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7444 (tm-30) REVERT: A 1028 MET cc_start: 0.7921 (mmp) cc_final: 0.7607 (mtm) REVERT: A 1128 ARG cc_start: 0.8426 (ttt-90) cc_final: 0.7336 (ptt90) REVERT: A 1166 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7630 (t80) REVERT: A 1284 LYS cc_start: 0.8768 (tppt) cc_final: 0.8170 (tptp) REVERT: A 1308 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8515 (mm-30) REVERT: A 1309 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8830 (pm20) REVERT: A 1341 ASP cc_start: 0.7947 (t70) cc_final: 0.7386 (t0) REVERT: A 1363 LYS cc_start: 0.9330 (tptm) cc_final: 0.8976 (tptp) REVERT: A 1370 ASP cc_start: 0.7867 (t0) cc_final: 0.7560 (t0) REVERT: A 1394 ASP cc_start: 0.8654 (m-30) cc_final: 0.8127 (m-30) REVERT: A 1419 ASN cc_start: 0.9007 (m110) cc_final: 0.7974 (t0) outliers start: 36 outliers final: 25 residues processed: 184 average time/residue: 0.2186 time to fit residues: 57.3598 Evaluate side-chains 171 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1395 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A1330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9973 Z= 0.211 Angle : 0.917 34.083 13496 Z= 0.366 Chirality : 0.089 2.003 1562 Planarity : 0.003 0.031 1630 Dihedral : 16.696 177.046 1600 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.29 % Allowed : 20.10 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1169 helix: 1.68 (0.19), residues: 767 sheet: -1.25 (0.54), residues: 75 loop : -0.78 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 216 HIS 0.003 0.001 HIS A1085 PHE 0.011 0.001 PHE A 81 TYR 0.019 0.001 TYR A 385 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7714 (tptp) cc_final: 0.7259 (tptt) REVERT: A 33 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6935 (mt-10) REVERT: A 56 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8509 (mm-30) REVERT: A 92 GLU cc_start: 0.8624 (tp30) cc_final: 0.8125 (tp30) REVERT: A 111 PRO cc_start: 0.8254 (Cg_endo) cc_final: 0.8051 (Cg_exo) REVERT: A 257 GLU cc_start: 0.8006 (tt0) cc_final: 0.7718 (tp30) REVERT: A 267 GLU cc_start: 0.8490 (tt0) cc_final: 0.8239 (tp30) REVERT: A 331 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9054 (tp) REVERT: A 476 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8864 (mm-30) REVERT: A 485 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8514 (t) REVERT: A 487 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7598 (mtp180) REVERT: A 504 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7841 (mp0) REVERT: A 600 ARG cc_start: 0.7490 (ptt-90) cc_final: 0.7192 (ptp90) REVERT: A 1012 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 1028 MET cc_start: 0.7913 (mmp) cc_final: 0.7598 (mtm) REVERT: A 1128 ARG cc_start: 0.8388 (ttt-90) cc_final: 0.7264 (ptt90) REVERT: A 1166 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7690 (t80) REVERT: A 1284 LYS cc_start: 0.8760 (tppt) cc_final: 0.8155 (tptp) REVERT: A 1308 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8520 (mm-30) REVERT: A 1309 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8878 (pm20) REVERT: A 1341 ASP cc_start: 0.8084 (t70) cc_final: 0.7551 (t0) REVERT: A 1363 LYS cc_start: 0.9316 (tptm) cc_final: 0.8959 (tptp) REVERT: A 1370 ASP cc_start: 0.7896 (t0) cc_final: 0.7583 (t0) REVERT: A 1394 ASP cc_start: 0.8673 (m-30) cc_final: 0.8149 (m-30) REVERT: A 1419 ASN cc_start: 0.9009 (m110) cc_final: 0.7974 (t0) outliers start: 34 outliers final: 23 residues processed: 168 average time/residue: 0.2091 time to fit residues: 49.9987 Evaluate side-chains 164 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1395 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 0.0170 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9973 Z= 0.215 Angle : 0.918 34.113 13496 Z= 0.367 Chirality : 0.089 2.002 1562 Planarity : 0.003 0.031 1630 Dihedral : 16.673 177.368 1600 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.67 % Allowed : 19.71 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1169 helix: 1.62 (0.19), residues: 768 sheet: -1.15 (0.54), residues: 75 loop : -0.74 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 216 HIS 0.003 0.001 HIS A1085 PHE 0.015 0.001 PHE A 319 TYR 0.025 0.001 TYR A 517 ARG 0.003 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7725 (tptp) cc_final: 0.7358 (tptt) REVERT: A 33 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7007 (mt-10) REVERT: A 92 GLU cc_start: 0.8610 (tp30) cc_final: 0.8120 (tp30) REVERT: A 111 PRO cc_start: 0.8109 (Cg_endo) cc_final: 0.7901 (Cg_exo) REVERT: A 114 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7851 (pttt) REVERT: A 257 GLU cc_start: 0.8014 (tt0) cc_final: 0.7731 (tp30) REVERT: A 267 GLU cc_start: 0.8390 (tt0) cc_final: 0.8152 (tp30) REVERT: A 331 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9062 (tp) REVERT: A 476 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8872 (mm-30) REVERT: A 485 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8519 (t) REVERT: A 487 ARG cc_start: 0.8240 (mtt180) cc_final: 0.7640 (mtp180) REVERT: A 504 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7843 (mp0) REVERT: A 600 ARG cc_start: 0.7512 (ptt-90) cc_final: 0.7173 (ptp90) REVERT: A 1012 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 1028 MET cc_start: 0.7909 (mmp) cc_final: 0.7595 (mtm) REVERT: A 1128 ARG cc_start: 0.8406 (ttt-90) cc_final: 0.7258 (ptt90) REVERT: A 1166 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7673 (t80) REVERT: A 1308 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8511 (mm-30) REVERT: A 1309 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8866 (pm20) REVERT: A 1341 ASP cc_start: 0.8088 (t70) cc_final: 0.7548 (t0) REVERT: A 1363 LYS cc_start: 0.9303 (tptm) cc_final: 0.8994 (tptp) REVERT: A 1370 ASP cc_start: 0.7905 (t0) cc_final: 0.7592 (t0) REVERT: A 1394 ASP cc_start: 0.8560 (m-30) cc_final: 0.8145 (m-30) REVERT: A 1419 ASN cc_start: 0.9004 (m110) cc_final: 0.7962 (t0) REVERT: A 1439 GLN cc_start: 0.8861 (mm110) cc_final: 0.8415 (tt0) outliers start: 38 outliers final: 28 residues processed: 171 average time/residue: 0.2172 time to fit residues: 52.8166 Evaluate side-chains 170 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1395 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 0.0010 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS A1330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9973 Z= 0.177 Angle : 0.907 33.913 13496 Z= 0.361 Chirality : 0.089 2.002 1562 Planarity : 0.003 0.031 1630 Dihedral : 16.610 177.101 1600 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.71 % Allowed : 21.06 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1169 helix: 1.66 (0.19), residues: 768 sheet: -0.95 (0.55), residues: 75 loop : -0.70 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 216 HIS 0.017 0.001 HIS A 856 PHE 0.022 0.001 PHE A 83 TYR 0.030 0.001 TYR A 517 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7002 (mt-10) REVERT: A 92 GLU cc_start: 0.8606 (tp30) cc_final: 0.8117 (tp30) REVERT: A 257 GLU cc_start: 0.8004 (tt0) cc_final: 0.7697 (tp30) REVERT: A 267 GLU cc_start: 0.8384 (tt0) cc_final: 0.8150 (tp30) REVERT: A 331 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9007 (tp) REVERT: A 476 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8879 (mm-30) REVERT: A 485 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8507 (t) REVERT: A 487 ARG cc_start: 0.8261 (mtt180) cc_final: 0.7654 (mtp180) REVERT: A 504 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7853 (mp0) REVERT: A 600 ARG cc_start: 0.7546 (ptt-90) cc_final: 0.7220 (ptp90) REVERT: A 1012 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 1028 MET cc_start: 0.7879 (mmp) cc_final: 0.7584 (mtm) REVERT: A 1128 ARG cc_start: 0.8411 (ttt-90) cc_final: 0.7238 (ptt90) REVERT: A 1166 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7613 (t80) REVERT: A 1284 LYS cc_start: 0.8790 (tppt) cc_final: 0.8156 (tptp) REVERT: A 1305 ASP cc_start: 0.8162 (p0) cc_final: 0.7609 (p0) REVERT: A 1308 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8336 (mm-30) REVERT: A 1309 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8867 (pm20) REVERT: A 1341 ASP cc_start: 0.7948 (t70) cc_final: 0.7359 (t0) REVERT: A 1363 LYS cc_start: 0.9292 (tptm) cc_final: 0.8927 (tptp) REVERT: A 1370 ASP cc_start: 0.7870 (t0) cc_final: 0.7567 (t0) REVERT: A 1394 ASP cc_start: 0.8515 (m-30) cc_final: 0.8084 (m-30) REVERT: A 1419 ASN cc_start: 0.8985 (m110) cc_final: 0.7956 (t0) REVERT: A 1439 GLN cc_start: 0.8868 (mm110) cc_final: 0.8428 (tt0) outliers start: 28 outliers final: 21 residues processed: 165 average time/residue: 0.2175 time to fit residues: 51.4702 Evaluate side-chains 163 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.5012 > 50: distance: 74 - 97: 24.977 distance: 79 - 82: 14.692 distance: 82 - 83: 18.358 distance: 83 - 84: 21.436 distance: 83 - 86: 15.111 distance: 84 - 85: 26.458 distance: 84 - 90: 28.909 distance: 86 - 87: 11.464 distance: 87 - 88: 9.724 distance: 87 - 89: 26.281 distance: 90 - 91: 4.693 distance: 91 - 94: 15.221 distance: 92 - 93: 21.705 distance: 92 - 97: 16.913 distance: 94 - 95: 30.126 distance: 94 - 96: 40.910 distance: 97 - 98: 15.723 distance: 98 - 99: 27.356 distance: 98 - 101: 29.692 distance: 99 - 100: 26.590 distance: 99 - 105: 17.201 distance: 101 - 102: 6.579 distance: 102 - 103: 40.146 distance: 102 - 104: 45.802 distance: 105 - 106: 22.071 distance: 106 - 107: 40.950 distance: 106 - 109: 9.046 distance: 107 - 108: 20.337 distance: 107 - 113: 37.790 distance: 109 - 110: 8.733 distance: 110 - 111: 21.077 distance: 110 - 112: 3.972 distance: 113 - 114: 11.059 distance: 114 - 115: 11.013 distance: 114 - 117: 11.003 distance: 115 - 116: 14.636 distance: 115 - 118: 23.400 distance: 118 - 119: 15.048 distance: 119 - 120: 9.015 distance: 120 - 121: 23.083 distance: 120 - 126: 16.711 distance: 122 - 123: 8.062 distance: 123 - 124: 7.114 distance: 124 - 125: 6.813 distance: 126 - 127: 22.920 distance: 127 - 128: 8.007 distance: 128 - 130: 44.073 distance: 130 - 131: 26.442 distance: 131 - 132: 29.567 distance: 131 - 134: 25.911 distance: 132 - 133: 23.880 distance: 132 - 141: 18.980 distance: 133 - 167: 6.832 distance: 134 - 135: 31.087 distance: 135 - 136: 25.142 distance: 135 - 137: 19.737 distance: 136 - 138: 9.125 distance: 137 - 139: 3.203 distance: 138 - 140: 7.577 distance: 139 - 140: 5.627 distance: 141 - 142: 10.373 distance: 142 - 143: 17.667 distance: 142 - 145: 19.308 distance: 143 - 144: 16.401 distance: 143 - 152: 12.583 distance: 145 - 146: 8.214 distance: 146 - 147: 13.435 distance: 146 - 148: 16.951 distance: 147 - 149: 22.754 distance: 148 - 150: 9.861 distance: 149 - 151: 17.825 distance: 150 - 151: 29.732 distance: 152 - 153: 10.992 distance: 153 - 154: 20.389 distance: 153 - 156: 6.645 distance: 154 - 155: 8.842 distance: 154 - 163: 24.650 distance: 156 - 157: 7.064 distance: 157 - 158: 5.445 distance: 158 - 159: 6.930 distance: 160 - 161: 6.066 distance: 160 - 162: 5.773