Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 12:53:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/08_2023/6o2p_0611_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/08_2023/6o2p_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_0611/08_2023/6o2p_0611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/08_2023/6o2p_0611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/08_2023/6o2p_0611_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2p_0611/08_2023/6o2p_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-1.21rc1-5044/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: 173 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: 5.68, per 1000 atoms: 0.58 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: 3.89 Conformation dependent library (CDL) restraints added in 1.3 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: 2.27 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: 3.39 Time building geometry restraints manager: 4.19 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 - 23.64: 5539 23.64 - 47.29: 278 47.29 - 70.93: 33 70.93 - 94.58: 5 94.58 - 118.22: 4 Dihedral angle restraints: 5859 sinusoidal: 2383 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=" C02 AJP A1511 " pdb=" C85 AJP A1511 " pdb=" O84 AJP A1511 " pdb=" C05 AJP A1511 " ideal model delta sinusoidal sigma weight residual -57.60 60.62 -118.22 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C16 AJP A1511 " pdb=" C17 AJP A1511 " pdb=" C18 AJP A1511 " pdb=" C19 AJP A1511 " ideal model delta sinusoidal sigma weight residual 54.20 -54.61 108.81 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 5856 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 12.290 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.670 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 46.690 ------------------------------------------------------------------------------- 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 : 14.483 118.221 3611 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 % 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 *********************** 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 : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 297 average time/residue: 0.2732 time to fit residues: 106.5049 Evaluate side-chains 163 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0877 time to fit residues: 2.0869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 290 GLN A 525 GLN A 552 GLN A1039 GLN A1238 GLN A1330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3164 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= 0.204 Angle : 0.965 34.168 13496 Z= 0.397 Chirality : 0.096 2.058 1562 Planarity : 0.004 0.032 1630 Dihedral : 5.395 56.532 1355 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1169 helix: 0.77 (0.18), residues: 757 sheet: -2.07 (0.53), residues: 79 loop : -1.55 (0.30), residues: 333 *********************** 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 219 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 215 average time/residue: 0.2278 time to fit residues: 68.8508 Evaluate side-chains 151 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1144 time to fit residues: 3.8610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 115 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 151 GLN A 199 HIS A 505 ASN A1079 HIS A1330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9973 Z= 0.190 Angle : 0.908 32.563 13496 Z= 0.365 Chirality : 0.093 2.007 1562 Planarity : 0.003 0.032 1630 Dihedral : 4.953 56.715 1355 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1169 helix: 1.46 (0.19), residues: 758 sheet: -1.81 (0.52), residues: 81 loop : -1.19 (0.32), residues: 330 *********************** 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 189 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 185 average time/residue: 0.2107 time to fit residues: 56.0493 Evaluate side-chains 158 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0956 time to fit residues: 4.6020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.3980 chunk 80 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 0.0470 chunk 30 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A1330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9973 Z= 0.165 Angle : 0.893 32.435 13496 Z= 0.354 Chirality : 0.093 2.000 1562 Planarity : 0.003 0.030 1630 Dihedral : 4.721 56.374 1355 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.25), residues: 1169 helix: 1.65 (0.19), residues: 768 sheet: -1.44 (0.54), residues: 81 loop : -0.93 (0.32), residues: 320 *********************** 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 168 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 158 average time/residue: 0.2108 time to fit residues: 47.5845 Evaluate side-chains 148 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0894 time to fit residues: 2.8263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A1100 GLN A1148 ASN A1330 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9973 Z= 0.250 Angle : 0.913 32.761 13496 Z= 0.370 Chirality : 0.093 1.999 1562 Planarity : 0.003 0.031 1630 Dihedral : 5.031 63.646 1355 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 2.13 % 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: 1.13 (0.25), residues: 1169 helix: 1.68 (0.19), residues: 766 sheet: -1.23 (0.54), residues: 87 loop : -0.91 (0.32), residues: 316 *********************** 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 167 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 161 average time/residue: 0.2155 time to fit residues: 50.2526 Evaluate side-chains 137 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0954 time to fit residues: 2.8249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7126 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9973 Z= 0.213 Angle : 0.901 32.803 13496 Z= 0.362 Chirality : 0.092 1.998 1562 Planarity : 0.003 0.031 1630 Dihedral : 4.952 64.878 1355 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.45 % 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: 1.18 (0.25), residues: 1169 helix: 1.70 (0.19), residues: 765 sheet: -1.10 (0.54), residues: 87 loop : -0.87 (0.32), residues: 317 *********************** 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 158 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.107 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 152 average time/residue: 0.2104 time to fit residues: 46.4354 Evaluate side-chains 135 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0935 time to fit residues: 2.5296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0010 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1100 GLN A1148 ASN A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4743 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= 0.180 Angle : 0.902 32.544 13496 Z= 0.362 Chirality : 0.092 1.997 1562 Planarity : 0.003 0.030 1630 Dihedral : 4.844 65.062 1355 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.87 % 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: 1.72 (0.19), residues: 763 sheet: -0.91 (0.56), residues: 88 loop : -0.81 (0.32), residues: 318 *********************** 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 152 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 1.201 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 149 average time/residue: 0.2247 time to fit residues: 47.9507 Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1108 time to fit residues: 1.9408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 103 optimal weight: 0.0980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 856 HIS A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4898 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= 0.172 Angle : 0.898 32.379 13496 Z= 0.358 Chirality : 0.093 1.999 1562 Planarity : 0.003 0.045 1630 Dihedral : 4.710 64.240 1355 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.77 % 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: 1.39 (0.25), residues: 1169 helix: 1.82 (0.19), residues: 762 sheet: -0.75 (0.56), residues: 88 loop : -0.74 (0.33), residues: 319 *********************** 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 150 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.126 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 147 average time/residue: 0.2147 time to fit residues: 45.6054 Evaluate side-chains 135 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0966 time to fit residues: 2.2619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7109 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 9973 Z= 0.199 Angle : 0.909 32.460 13496 Z= 0.366 Chirality : 0.092 1.999 1562 Planarity : 0.003 0.044 1630 Dihedral : 4.742 65.514 1355 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.68 % 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: 1.40 (0.25), residues: 1169 helix: 1.81 (0.19), residues: 763 sheet: -0.66 (0.57), residues: 88 loop : -0.71 (0.33), residues: 318 *********************** 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 141 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.069 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 140 average time/residue: 0.2122 time to fit residues: 42.7757 Evaluate side-chains 133 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0910 time to fit residues: 2.2534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7122 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 9973 Z= 0.222 Angle : 0.921 32.577 13496 Z= 0.375 Chirality : 0.092 1.997 1562 Planarity : 0.003 0.031 1630 Dihedral : 4.839 66.925 1355 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1169 helix: 1.72 (0.19), residues: 769 sheet: -0.59 (0.58), residues: 84 loop : -0.77 (0.33), residues: 316 ********************** REFINEMENT MACRO_CYCLE 10 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 140 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.216 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 138 average time/residue: 0.2150 time to fit residues: 43.0773 Evaluate side-chains 131 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0963 time to fit residues: 1.9506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 5 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: A1330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.093391 restraints weight = 20296.151| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.05 r_work: 0.3056 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 9973 Z= 0.207 Angle : 0.919 32.540 13496 Z= 0.371 Chirality : 0.092 1.997 1562 Planarity : 0.003 0.031 1630 Dihedral : 4.790 66.762 1355 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.39 % 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: 1.36 (0.25), residues: 1169 helix: 1.76 (0.19), residues: 762 sheet: -0.47 (0.59), residues: 84 loop : -0.75 (0.32), residues: 323 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.95 seconds wall clock time: 41 minutes 4.67 seconds (2464.67 seconds total)