Starting phenix.real_space_refine on Sat Jul 20 01:33:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/07_2024/8ubr_42101_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/07_2024/8ubr_42101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/07_2024/8ubr_42101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/07_2024/8ubr_42101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/07_2024/8ubr_42101_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/07_2024/8ubr_42101_neut.cif" } resolution = 2.7 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= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 6180 2.51 5 N 1547 2.21 5 O 1653 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 873": "OE1" <-> "OE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1152": "OD1" <-> "OD2" Residue "A ASP 1154": "OD1" <-> "OD2" Residue "A GLU 1228": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A ASP 1275": "OD1" <-> "OD2" Residue "A GLU 1308": "OE1" <-> "OE2" Residue "A GLU 1314": "OE1" <-> "OE2" Residue "A ASP 1341": "OD1" <-> "OD2" Residue "A ASP 1394": "OD1" <-> "OD2" Residue "A GLU 1401": "OE1" <-> "OE2" Residue "A GLU 1405": "OE1" <-> "OE2" Residue "A ASP 1425": "OD1" <-> "OD2" Residue "A PHE 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9440 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9265 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 30, 'TRANS': 1125} Chain breaks: 6 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 175 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 2, 'LBN': 2, 'WG5': 1} Classifications: {'undetermined': 9, 'water': 4} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'LBN:plan-2': 2, 'LBN:plan-3': 2, 'LBN:plan-1': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 7.44, per 1000 atoms: 0.79 Number of scatterers: 9440 At special positions: 0 Unit cell: (75.712, 87.204, 142.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1653 8.00 N 1547 7.00 C 6180 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: 3.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 71.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.611A pdb=" N ALA A 9 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 45 through 64 Processing helix chain 'A' and resid 68 through 109 removed outlier: 3.931A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 119 through 165 removed outlier: 3.737A pdb=" N PHE A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.539A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.718A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.602A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.871A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 199 through 220 Proline residue: A 205 - end of helix removed outlier: 4.032A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 4.453A pdb=" N GLY A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 277 through 308 removed outlier: 3.736A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.532A pdb=" N PHE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 329 removed outlier: 3.612A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.515A pdb=" N ILE A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 376 removed outlier: 3.575A pdb=" N TRP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.950A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.907A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 846 through 854 Processing helix chain 'A' and resid 856 through 886 removed outlier: 3.778A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 922 removed outlier: 4.038A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 934 through 959 Processing helix chain 'A' and resid 960 through 965 Processing helix chain 'A' and resid 968 through 985 removed outlier: 3.723A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1012 removed outlier: 4.447A pdb=" N LEU A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1047 removed outlier: 4.048A pdb=" N PHE A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.877A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 4.018A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1168 removed outlier: 3.962A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.608A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1284 Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1311 through 1322 Processing helix chain 'A' and resid 1324 through 1329 Processing helix chain 'A' and resid 1347 through 1362 Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 4.535A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1410 removed outlier: 3.848A pdb=" N CYS A1410 " --> pdb=" O MET A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.633A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1441 removed outlier: 3.722A pdb=" N ARG A1438 " --> pdb=" O ARG A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1450 Processing sheet with id=AA1, first strand: chain 'A' and resid 441 through 448 removed outlier: 6.585A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 396 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 446 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N MET A 394 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LYS A 483 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN A 396 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS A 481 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.224A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASP A 572 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS A 491 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 454 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1234 removed outlier: 5.694A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE A1232 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS A1213 " --> pdb=" O PHE A1232 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE A1234 " --> pdb=" O THR A1211 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR A1211 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A1215 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU A1264 " --> pdb=" O LEU A1215 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA A1217 " --> pdb=" O ASN A1262 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A1262 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.569A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N CYS A1400 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A1369 " --> pdb=" O CYS A1400 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A1240 " --> pdb=" O LEU A1399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1298 through 1299 585 hydrogen bonds defined for protein. 1707 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: 3.29 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1592 1.32 - 1.45: 2466 1.45 - 1.57: 5490 1.57 - 1.69: 11 1.69 - 1.81: 81 Bond restraints: 9640 Sorted by residual: bond pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N PHE A 77 " pdb=" CA PHE A 77 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.12e+01 bond pdb=" N LEU A 987 " pdb=" CA LEU A 987 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.04e-02 9.25e+03 1.12e+01 bond pdb=" N VAL A1017 " pdb=" CA VAL A1017 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" N ILE A 106 " pdb=" CA ILE A 106 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.39e+00 ... (remaining 9635 not shown) Histogram of bond angle deviations from ideal: 92.94 - 101.37: 35 101.37 - 109.80: 1090 109.80 - 118.23: 6527 118.23 - 126.66: 5257 126.66 - 135.09: 143 Bond angle restraints: 13052 Sorted by residual: angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 133.72 6.15 1.00e+00 1.00e+00 3.79e+01 angle pdb=" PB ATP A1502 " pdb=" O3B ATP A1502 " pdb=" PG ATP A1502 " ideal model delta sigma weight residual 139.87 135.09 4.78 1.00e+00 1.00e+00 2.29e+01 angle pdb=" N VAL A 922 " pdb=" CA VAL A 922 " pdb=" C VAL A 922 " ideal model delta sigma weight residual 112.29 108.59 3.70 9.40e-01 1.13e+00 1.55e+01 angle pdb=" O VAL A1007 " pdb=" C VAL A1007 " pdb=" N VAL A1008 " ideal model delta sigma weight residual 121.83 117.96 3.87 1.03e+00 9.43e-01 1.41e+01 angle pdb=" CA VAL A1010 " pdb=" C VAL A1010 " pdb=" O VAL A1010 " ideal model delta sigma weight residual 120.85 116.93 3.92 1.06e+00 8.90e-01 1.37e+01 ... (remaining 13047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.47: 5116 19.47 - 38.93: 558 38.93 - 58.40: 152 58.40 - 77.86: 28 77.86 - 97.33: 11 Dihedral angle restraints: 5865 sinusoidal: 2506 harmonic: 3359 Sorted by residual: dihedral pdb=" C32 LBN A1505 " pdb=" C33 LBN A1505 " pdb=" C4 LBN A1505 " pdb=" C7 LBN A1505 " ideal model delta sinusoidal sigma weight residual 179.89 -82.78 -97.33 1 3.00e+01 1.11e-03 1.20e+01 dihedral pdb=" CB GLU A1228 " pdb=" CG GLU A1228 " pdb=" CD GLU A1228 " pdb=" OE1 GLU A1228 " ideal model delta sinusoidal sigma weight residual 0.00 89.01 -89.01 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASP A 579 " pdb=" CB ASP A 579 " pdb=" CG ASP A 579 " pdb=" OD1 ASP A 579 " ideal model delta sinusoidal sigma weight residual -30.00 -85.48 55.48 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 5862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1206 0.062 - 0.123: 227 0.123 - 0.185: 59 0.185 - 0.246: 14 0.246 - 0.308: 1 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA ILE A 906 " pdb=" N ILE A 906 " pdb=" C ILE A 906 " pdb=" CB ILE A 906 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LYS A 329 " pdb=" N LYS A 329 " pdb=" C LYS A 329 " pdb=" CB LYS A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA CYS A1344 " pdb=" N CYS A1344 " pdb=" C CYS A1344 " pdb=" CB CYS A1344 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1504 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1009 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" C ALA A1009 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA A1009 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL A1010 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 WG5 A1508 " -0.029 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" C12 WG5 A1508 " 0.014 2.00e-02 2.50e+03 pdb=" C13 WG5 A1508 " 0.012 2.00e-02 2.50e+03 pdb=" C14 WG5 A1508 " 0.005 2.00e-02 2.50e+03 pdb=" C15 WG5 A1508 " 0.001 2.00e-02 2.50e+03 pdb=" C16 WG5 A1508 " 0.005 2.00e-02 2.50e+03 pdb=" C17 WG5 A1508 " 0.011 2.00e-02 2.50e+03 pdb=" C18 WG5 A1508 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1007 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C VAL A1007 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL A1007 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A1008 " -0.010 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 13 2.49 - 3.09: 6324 3.09 - 3.69: 13741 3.69 - 4.30: 20712 4.30 - 4.90: 34105 Nonbonded interactions: 74895 Sorted by model distance: nonbonded pdb=" O3G ATP A1503 " pdb="MG MG A1509 " model vdw 1.887 2.170 nonbonded pdb="MG MG A1509 " pdb=" O HOH A1602 " model vdw 1.904 2.170 nonbonded pdb="MG MG A1509 " pdb=" O HOH A1601 " model vdw 1.926 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1509 " model vdw 2.009 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.045 2.170 ... (remaining 74890 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: 7.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 31.300 Find NCS groups from input model: 0.100 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.006 0.043 9640 Z= 0.399 Angle : 0.831 6.554 13052 Z= 0.566 Chirality : 0.056 0.308 1507 Planarity : 0.004 0.031 1574 Dihedral : 17.606 97.329 3693 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.10 % Allowed : 19.82 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1142 helix: 1.32 (0.19), residues: 757 sheet: -1.22 (0.44), residues: 88 loop : -0.95 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1063 HIS 0.005 0.001 HIS A 939 PHE 0.019 0.002 PHE A 446 TYR 0.024 0.002 TYR A 38 ARG 0.007 0.001 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.058 Fit side-chains REVERT: A 536 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7329 (mppt) REVERT: A 1010 VAL cc_start: 0.6843 (t) cc_final: 0.6636 (t) REVERT: A 1109 ILE cc_start: 0.7663 (mt) cc_final: 0.7325 (tt) REVERT: A 1341 ASP cc_start: 0.7051 (t0) cc_final: 0.6699 (t70) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 1.3011 time to fit residues: 191.6733 Evaluate side-chains 108 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1166 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN A1224 ASN A1423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9640 Z= 0.162 Angle : 0.496 6.019 13052 Z= 0.269 Chirality : 0.039 0.136 1507 Planarity : 0.004 0.032 1574 Dihedral : 8.620 63.707 1491 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.16 % Allowed : 19.92 % Favored : 76.92 % 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: 1.89 (0.24), residues: 1142 helix: 2.20 (0.19), residues: 763 sheet: -0.29 (0.49), residues: 92 loop : -0.84 (0.31), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 865 HIS 0.004 0.001 HIS A 949 PHE 0.013 0.001 PHE A1257 TYR 0.013 0.001 TYR A1073 ARG 0.004 0.001 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.982 Fit side-chains REVERT: A 47 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6685 (p0) REVERT: A 279 GLU cc_start: 0.6937 (mp0) cc_final: 0.6653 (mp0) REVERT: A 286 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7281 (mm-30) REVERT: A 373 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6728 (t0) REVERT: A 476 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 536 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7387 (mppt) REVERT: A 920 VAL cc_start: 0.7244 (t) cc_final: 0.6958 (p) REVERT: A 1010 VAL cc_start: 0.6820 (t) cc_final: 0.6555 (t) REVERT: A 1091 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8367 (tt) REVERT: A 1109 ILE cc_start: 0.7661 (mt) cc_final: 0.7309 (tt) REVERT: A 1317 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7222 (tttp) REVERT: A 1341 ASP cc_start: 0.7240 (t0) cc_final: 0.6848 (t70) outliers start: 32 outliers final: 10 residues processed: 137 average time/residue: 1.1832 time to fit residues: 174.0195 Evaluate side-chains 121 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1390 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 187 ASN A1224 ASN A1375 HIS A1402 HIS ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1428 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9640 Z= 0.417 Angle : 0.740 10.530 13052 Z= 0.391 Chirality : 0.049 0.158 1507 Planarity : 0.006 0.050 1574 Dihedral : 9.106 75.394 1491 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.83 % Allowed : 18.64 % Favored : 76.53 % 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: 1.03 (0.23), residues: 1142 helix: 1.49 (0.18), residues: 758 sheet: 0.01 (0.51), residues: 85 loop : -1.14 (0.29), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1063 HIS 0.006 0.002 HIS A 949 PHE 0.020 0.003 PHE A 131 TYR 0.017 0.003 TYR A 304 ARG 0.007 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 108 time to evaluate : 1.069 Fit side-chains REVERT: A 47 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6847 (p0) REVERT: A 476 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: A 536 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7461 (mmmm) REVERT: A 907 ILE cc_start: 0.5322 (OUTLIER) cc_final: 0.5101 (mt) REVERT: A 1091 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8278 (tt) REVERT: A 1109 ILE cc_start: 0.7862 (mt) cc_final: 0.7533 (tt) REVERT: A 1165 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7893 (mmtm) REVERT: A 1341 ASP cc_start: 0.7365 (t0) cc_final: 0.6957 (t70) outliers start: 49 outliers final: 18 residues processed: 146 average time/residue: 1.2527 time to fit residues: 196.1587 Evaluate side-chains 129 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1415 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0030 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1224 ASN A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9640 Z= 0.256 Angle : 0.597 7.161 13052 Z= 0.318 Chirality : 0.042 0.136 1507 Planarity : 0.004 0.035 1574 Dihedral : 8.831 72.341 1491 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.54 % Allowed : 20.41 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.24), residues: 1142 helix: 1.72 (0.18), residues: 758 sheet: 0.17 (0.53), residues: 85 loop : -1.15 (0.29), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 865 HIS 0.005 0.001 HIS A 939 PHE 0.014 0.002 PHE A1296 TYR 0.014 0.002 TYR A 917 ARG 0.004 0.001 ARG A 975 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 108 time to evaluate : 1.047 Fit side-chains REVERT: A 47 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6790 (p0) REVERT: A 279 GLU cc_start: 0.7077 (mp0) cc_final: 0.6782 (mp0) REVERT: A 384 GLU cc_start: 0.3565 (OUTLIER) cc_final: 0.2346 (pm20) REVERT: A 476 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: A 536 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7528 (mmmm) REVERT: A 598 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7764 (mmtt) REVERT: A 920 VAL cc_start: 0.7445 (t) cc_final: 0.7133 (p) REVERT: A 1091 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8294 (tt) REVERT: A 1109 ILE cc_start: 0.7845 (mt) cc_final: 0.7455 (tp) REVERT: A 1165 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7820 (mmtm) REVERT: A 1341 ASP cc_start: 0.7350 (t0) cc_final: 0.6958 (t70) REVERT: A 1351 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8190 (mttm) outliers start: 46 outliers final: 20 residues processed: 148 average time/residue: 1.2505 time to fit residues: 198.3497 Evaluate side-chains 129 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1351 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.0060 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1224 ASN A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9640 Z= 0.162 Angle : 0.492 6.287 13052 Z= 0.265 Chirality : 0.039 0.131 1507 Planarity : 0.003 0.031 1574 Dihedral : 8.218 67.742 1491 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.75 % Allowed : 21.99 % Favored : 74.26 % 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: 1.93 (0.24), residues: 1142 helix: 2.20 (0.19), residues: 759 sheet: 0.47 (0.55), residues: 85 loop : -0.95 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 865 HIS 0.004 0.001 HIS A 939 PHE 0.011 0.001 PHE A1257 TYR 0.013 0.001 TYR A1073 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 1.153 Fit side-chains REVERT: A 47 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6745 (p0) REVERT: A 286 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 373 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6768 (t0) REVERT: A 384 GLU cc_start: 0.3627 (OUTLIER) cc_final: 0.2855 (pm20) REVERT: A 476 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 535 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: A 543 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6414 (tt0) REVERT: A 1091 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 1109 ILE cc_start: 0.7717 (mt) cc_final: 0.7374 (tt) REVERT: A 1165 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7717 (mmtm) REVERT: A 1317 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7205 (tttp) REVERT: A 1341 ASP cc_start: 0.7357 (t0) cc_final: 0.6983 (t70) REVERT: A 1405 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6652 (mp0) outliers start: 38 outliers final: 15 residues processed: 133 average time/residue: 1.2328 time to fit residues: 175.9320 Evaluate side-chains 130 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9640 Z= 0.132 Angle : 0.451 5.972 13052 Z= 0.241 Chirality : 0.037 0.132 1507 Planarity : 0.003 0.029 1574 Dihedral : 7.487 69.116 1491 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.96 % Allowed : 23.37 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.36 (0.25), residues: 1142 helix: 2.51 (0.19), residues: 760 sheet: 0.63 (0.56), residues: 85 loop : -0.73 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1063 HIS 0.003 0.001 HIS A 939 PHE 0.010 0.001 PHE A1257 TYR 0.011 0.001 TYR A1073 ARG 0.004 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 1.061 Fit side-chains REVERT: A 47 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6718 (p0) REVERT: A 286 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7298 (mm-30) REVERT: A 443 ASP cc_start: 0.7272 (t70) cc_final: 0.6961 (t0) REVERT: A 476 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 535 GLU cc_start: 0.6982 (mp0) cc_final: 0.6619 (mp0) REVERT: A 536 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7389 (mmtm) REVERT: A 543 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6373 (tt0) REVERT: A 1091 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8275 (tt) REVERT: A 1109 ILE cc_start: 0.7608 (mt) cc_final: 0.7223 (tt) REVERT: A 1317 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7016 (tttp) REVERT: A 1341 ASP cc_start: 0.7316 (t0) cc_final: 0.6959 (t70) REVERT: A 1405 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6635 (mp0) outliers start: 30 outliers final: 8 residues processed: 129 average time/residue: 1.2523 time to fit residues: 173.1388 Evaluate side-chains 113 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9640 Z= 0.133 Angle : 0.455 6.718 13052 Z= 0.241 Chirality : 0.037 0.129 1507 Planarity : 0.003 0.029 1574 Dihedral : 7.307 72.048 1491 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.35 % Allowed : 22.78 % Favored : 73.87 % 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: 2.51 (0.25), residues: 1142 helix: 2.62 (0.19), residues: 758 sheet: 0.69 (0.57), residues: 85 loop : -0.62 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1063 HIS 0.004 0.001 HIS A 939 PHE 0.010 0.001 PHE A1257 TYR 0.013 0.001 TYR A1073 ARG 0.006 0.000 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 1.083 Fit side-chains REVERT: A 47 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6702 (p0) REVERT: A 279 GLU cc_start: 0.6828 (mp0) cc_final: 0.6510 (mp0) REVERT: A 286 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7278 (mm-30) REVERT: A 373 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6782 (t0) REVERT: A 384 GLU cc_start: 0.3581 (OUTLIER) cc_final: 0.2367 (pm20) REVERT: A 443 ASP cc_start: 0.7267 (t70) cc_final: 0.6911 (t0) REVERT: A 476 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: A 536 LYS cc_start: 0.7636 (mmmm) cc_final: 0.7410 (mmtp) REVERT: A 543 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: A 1091 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 1109 ILE cc_start: 0.7597 (mt) cc_final: 0.7215 (tt) REVERT: A 1317 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7048 (tttp) REVERT: A 1341 ASP cc_start: 0.7313 (t0) cc_final: 0.6954 (t70) REVERT: A 1389 LYS cc_start: 0.7369 (mtpt) cc_final: 0.7120 (ttpt) REVERT: A 1405 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6651 (mp0) outliers start: 34 outliers final: 15 residues processed: 124 average time/residue: 1.3197 time to fit residues: 175.2653 Evaluate side-chains 120 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A1224 ASN A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9640 Z= 0.166 Angle : 0.500 8.559 13052 Z= 0.266 Chirality : 0.039 0.171 1507 Planarity : 0.003 0.028 1574 Dihedral : 7.423 66.901 1491 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.45 % Allowed : 22.78 % Favored : 73.77 % 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: 2.36 (0.25), residues: 1142 helix: 2.50 (0.19), residues: 759 sheet: 0.69 (0.57), residues: 85 loop : -0.70 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1063 HIS 0.004 0.001 HIS A 939 PHE 0.012 0.001 PHE A 446 TYR 0.016 0.001 TYR A1073 ARG 0.005 0.000 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 1.097 Fit side-chains REVERT: A 47 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6709 (p0) REVERT: A 279 GLU cc_start: 0.6915 (mp0) cc_final: 0.6581 (mp0) REVERT: A 286 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7301 (mm-30) REVERT: A 373 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6774 (t0) REVERT: A 384 GLU cc_start: 0.3573 (OUTLIER) cc_final: 0.2319 (pm20) REVERT: A 443 ASP cc_start: 0.7228 (t70) cc_final: 0.6812 (t0) REVERT: A 476 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: A 483 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7826 (mtmm) REVERT: A 543 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6388 (tt0) REVERT: A 598 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7704 (mmtt) REVERT: A 1091 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 1109 ILE cc_start: 0.7582 (mt) cc_final: 0.7214 (tt) REVERT: A 1317 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7126 (tptp) REVERT: A 1341 ASP cc_start: 0.7323 (t0) cc_final: 0.6942 (t70) REVERT: A 1405 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6702 (mp0) outliers start: 35 outliers final: 16 residues processed: 123 average time/residue: 1.2815 time to fit residues: 168.9933 Evaluate side-chains 122 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9640 Z= 0.204 Angle : 0.541 8.172 13052 Z= 0.287 Chirality : 0.040 0.155 1507 Planarity : 0.004 0.030 1574 Dihedral : 7.708 67.317 1491 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.25 % Allowed : 22.88 % Favored : 73.87 % 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: 2.12 (0.25), residues: 1142 helix: 2.31 (0.19), residues: 759 sheet: 0.61 (0.57), residues: 85 loop : -0.79 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A1063 HIS 0.005 0.001 HIS A 939 PHE 0.013 0.002 PHE A 446 TYR 0.015 0.002 TYR A1073 ARG 0.004 0.000 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 1.107 Fit side-chains REVERT: A 47 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6797 (p0) REVERT: A 279 GLU cc_start: 0.6986 (mp0) cc_final: 0.6685 (mp0) REVERT: A 373 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6772 (t0) REVERT: A 384 GLU cc_start: 0.3632 (OUTLIER) cc_final: 0.2674 (pm20) REVERT: A 476 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: A 483 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7850 (mtmm) REVERT: A 536 LYS cc_start: 0.7760 (mmtp) cc_final: 0.7544 (mmmm) REVERT: A 543 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6426 (tt0) REVERT: A 598 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7717 (mmtt) REVERT: A 1091 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 1109 ILE cc_start: 0.7609 (mt) cc_final: 0.7275 (tt) REVERT: A 1165 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7757 (mmtm) REVERT: A 1341 ASP cc_start: 0.7361 (t0) cc_final: 0.6958 (t70) REVERT: A 1405 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6715 (mp0) outliers start: 33 outliers final: 18 residues processed: 125 average time/residue: 1.3461 time to fit residues: 179.7246 Evaluate side-chains 123 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9640 Z= 0.153 Angle : 0.480 8.169 13052 Z= 0.258 Chirality : 0.038 0.140 1507 Planarity : 0.003 0.028 1574 Dihedral : 7.469 64.530 1491 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.66 % Allowed : 23.57 % Favored : 73.77 % 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: 2.32 (0.25), residues: 1142 helix: 2.47 (0.19), residues: 759 sheet: 0.71 (0.57), residues: 85 loop : -0.74 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A1063 HIS 0.004 0.001 HIS A 939 PHE 0.010 0.001 PHE A 446 TYR 0.014 0.001 TYR A1073 ARG 0.004 0.000 ARG A 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.944 Fit side-chains REVERT: A 47 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6727 (p0) REVERT: A 279 GLU cc_start: 0.6852 (mp0) cc_final: 0.6554 (mp0) REVERT: A 286 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 373 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6768 (t0) REVERT: A 543 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6365 (tt0) REVERT: A 598 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7717 (mmtt) REVERT: A 1091 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 1109 ILE cc_start: 0.7605 (mt) cc_final: 0.7240 (tt) REVERT: A 1120 LEU cc_start: 0.6660 (mt) cc_final: 0.6397 (mm) REVERT: A 1317 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7126 (tttp) REVERT: A 1341 ASP cc_start: 0.7324 (t0) cc_final: 0.6951 (t70) REVERT: A 1405 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6671 (mp0) outliers start: 27 outliers final: 15 residues processed: 115 average time/residue: 1.2875 time to fit residues: 158.5567 Evaluate side-chains 116 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111703 restraints weight = 11833.365| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.33 r_work: 0.3147 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9640 Z= 0.142 Angle : 0.471 9.194 13052 Z= 0.251 Chirality : 0.038 0.132 1507 Planarity : 0.003 0.028 1574 Dihedral : 7.311 68.053 1491 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.37 % Allowed : 23.96 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.41 (0.25), residues: 1142 helix: 2.53 (0.19), residues: 759 sheet: 0.78 (0.57), residues: 85 loop : -0.69 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A1063 HIS 0.004 0.001 HIS A 939 PHE 0.010 0.001 PHE A1110 TYR 0.013 0.001 TYR A1073 ARG 0.004 0.000 ARG A 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3756.01 seconds wall clock time: 66 minutes 29.07 seconds (3989.07 seconds total)