Starting phenix.real_space_refine on Tue Jun 10 11:30:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.cif" } resolution = 3.31 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= 0.002 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7349 2.51 5 N 1914 2.21 5 O 2210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11523 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1234, 9769 Classifications: {'peptide': 1234} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 9, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 1186} Chain breaks: 7 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 592 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 581 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 581 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU C 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU C 73 " occ=0.45 residue: pdb=" N ARG C 74 " occ=0.45 ... (3 atoms not shown) pdb=" CB ARG C 74 " occ=0.45 residue: pdb=" N GLY C 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY C 75 " occ=0.25 residue: pdb=" N GLY C 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY C 76 " occ=0.25 residue: pdb=" N LEU D 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU D 73 " occ=0.45 residue: pdb=" N ARG D 74 " occ=0.45 ... (3 atoms not shown) pdb=" CB ARG D 74 " occ=0.45 residue: pdb=" N LEU E 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU E 73 " occ=0.45 Time building chain proxies: 7.06, per 1000 atoms: 0.61 Number of scatterers: 11523 At special positions: 0 Unit cell: (109.548, 108.474, 132.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2210 8.00 N 1914 7.00 C 7349 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 - 3.00 Amino acid : True - 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: 2.77 Conformation dependent library (CDL) restraints added in 1.5 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 7 sheets defined 57.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 164 through 181 removed outlier: 3.995A pdb=" N GLU A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.912A pdb=" N GLU A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.866A pdb=" N ARG A 210 " --> pdb=" O MET A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 233 through 251 removed outlier: 3.505A pdb=" N MET A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.925A pdb=" N ILE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.559A pdb=" N GLY A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 292 removed outlier: 3.971A pdb=" N ALA A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.572A pdb=" N THR A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 316 through 330 removed outlier: 4.274A pdb=" N ILE A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 354 removed outlier: 3.605A pdb=" N ILE A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Proline residue: A 346 - end of helix Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 363 through 376 removed outlier: 3.597A pdb=" N MET A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 376 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.958A pdb=" N ARG A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.880A pdb=" N SER A 441 " --> pdb=" O MET A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 removed outlier: 4.282A pdb=" N ILE A 458 " --> pdb=" O HIS A 454 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.713A pdb=" N ILE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 521 removed outlier: 4.348A pdb=" N VAL A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Proline residue: A 513 - end of helix removed outlier: 4.488A pdb=" N GLU A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.855A pdb=" N LYS A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 3.987A pdb=" N LEU A 554 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.928A pdb=" N ALA A 568 " --> pdb=" O GLN A 564 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 564 through 569' Processing helix chain 'A' and resid 576 through 597 removed outlier: 3.735A pdb=" N GLY A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 609 Proline residue: A 603 - end of helix Processing helix chain 'A' and resid 610 through 624 Processing helix chain 'A' and resid 684 through 702 removed outlier: 3.910A pdb=" N LYS A 689 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 Processing helix chain 'A' and resid 733 through 749 removed outlier: 3.860A pdb=" N GLY A 739 " --> pdb=" O GLU A 735 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 763 removed outlier: 3.951A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 776 removed outlier: 3.503A pdb=" N ARG A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 791 removed outlier: 3.573A pdb=" N VAL A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 810 removed outlier: 3.830A pdb=" N ILE A 801 " --> pdb=" O ARG A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 863 through 876 removed outlier: 3.732A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 928 through 938 Processing helix chain 'A' and resid 941 through 948 removed outlier: 3.700A pdb=" N LEU A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 947 " --> pdb=" O LYS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 removed outlier: 4.181A pdb=" N TYR A 981 " --> pdb=" O ARG A 978 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 982 " --> pdb=" O ASP A 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 982' Processing helix chain 'A' and resid 991 through 993 No H-bonds generated for 'chain 'A' and resid 991 through 993' Processing helix chain 'A' and resid 994 through 1006 Processing helix chain 'A' and resid 1016 through 1028 Processing helix chain 'A' and resid 1029 through 1034 Processing helix chain 'A' and resid 1039 through 1049 Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1068 through 1072 Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1109 through 1122 removed outlier: 3.526A pdb=" N GLY A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1154 removed outlier: 3.873A pdb=" N THR A1143 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A1147 " --> pdb=" O THR A1143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 removed outlier: 6.663A pdb=" N SER A1158 " --> pdb=" O ALA A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1217 removed outlier: 3.634A pdb=" N THR A1209 " --> pdb=" O GLY A1205 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A1217 " --> pdb=" O ARG A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1238 removed outlier: 3.658A pdb=" N PHE A1230 " --> pdb=" O SER A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1256 Processing helix chain 'A' and resid 1259 through 1272 Processing helix chain 'A' and resid 1275 through 1283 removed outlier: 3.604A pdb=" N LEU A1282 " --> pdb=" O THR A1278 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A1283 " --> pdb=" O LEU A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1322 Processing helix chain 'A' and resid 1326 through 1341 removed outlier: 3.596A pdb=" N LEU A1330 " --> pdb=" O ILE A1326 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A1332 " --> pdb=" O LYS A1328 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A1339 " --> pdb=" O GLU A1335 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A1340 " --> pdb=" O GLY A1336 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A1341 " --> pdb=" O PHE A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.534A pdb=" N LEU A1347 " --> pdb=" O GLU A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1353 Processing helix chain 'A' and resid 1354 through 1359 Processing helix chain 'A' and resid 1366 through 1372 removed outlier: 3.773A pdb=" N LEU A1370 " --> pdb=" O SER A1366 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR A1371 " --> pdb=" O MET A1367 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A1372 " --> pdb=" O ALA A1368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1366 through 1372' Processing helix chain 'A' and resid 1387 through 1395 removed outlier: 3.676A pdb=" N ILE A1394 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A1395 " --> pdb=" O ILE A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1410 removed outlier: 3.710A pdb=" N ARG A1403 " --> pdb=" O LYS A1399 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A1408 " --> pdb=" O LEU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1423 removed outlier: 3.559A pdb=" N SER A1422 " --> pdb=" O GLY A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1477 Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'D' and resid 23 through 34 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'E' and resid 24 through 34 Processing helix chain 'E' and resid 37 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 831 through 835 removed outlier: 3.739A pdb=" N VAL A 856 " --> pdb=" O ILE A 834 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 837 through 838 removed outlier: 6.523A pdb=" N VAL A 837 " --> pdb=" O PHE A 954 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1100 through 1105 removed outlier: 5.988A pdb=" N ARG A1101 " --> pdb=" O GLU A1129 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU A1131 " --> pdb=" O ARG A1101 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU A1103 " --> pdb=" O GLU A1131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1429 through 1432 removed outlier: 6.035A pdb=" N VAL A1430 " --> pdb=" O LEU A1456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.683A pdb=" N ILE C 13 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE C 4 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C 69 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS C 6 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'E' and resid 12 through 16 removed outlier: 9.851A pdb=" N LEU E 67 " --> pdb=" O GLN E 2 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE E 4 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU E 69 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS E 6 " --> pdb=" O LEU E 69 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1353 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: 3.28 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: 3761 1.34 - 1.46: 2475 1.46 - 1.58: 5396 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 11709 Sorted by residual: bond pdb=" CA THR E 9 " pdb=" CB THR E 9 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.46e-02 4.69e+03 2.61e+00 bond pdb=" CG LEU A 643 " pdb=" CD1 LEU A 643 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" N ASN A1452 " pdb=" CA ASN A1452 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.15e+00 bond pdb=" C LEU A1444 " pdb=" N PRO A1445 " ideal model delta sigma weight residual 1.332 1.348 -0.016 1.12e-02 7.97e+03 2.09e+00 bond pdb=" CG1 ILE A 176 " pdb=" CD1 ILE A 176 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.04e+00 ... (remaining 11704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 15608 2.80 - 5.60: 173 5.60 - 8.40: 21 8.40 - 11.19: 12 11.19 - 13.99: 3 Bond angle restraints: 15817 Sorted by residual: angle pdb=" N ILE A1386 " pdb=" CA ILE A1386 " pdb=" C ILE A1386 " ideal model delta sigma weight residual 113.47 106.67 6.80 1.01e+00 9.80e-01 4.54e+01 angle pdb=" C THR D 22 " pdb=" CA THR D 22 " pdb=" CB THR D 22 " ideal model delta sigma weight residual 115.79 108.46 7.33 1.19e+00 7.06e-01 3.79e+01 angle pdb=" N ILE D 23 " pdb=" CA ILE D 23 " pdb=" C ILE D 23 " ideal model delta sigma weight residual 112.12 107.29 4.83 8.40e-01 1.42e+00 3.31e+01 angle pdb=" C ALA A1451 " pdb=" N ASN A1452 " pdb=" CA ASN A1452 " ideal model delta sigma weight residual 121.70 130.95 -9.25 1.80e+00 3.09e-01 2.64e+01 angle pdb=" N ASN A1452 " pdb=" CA ASN A1452 " pdb=" C ASN A1452 " ideal model delta sigma weight residual 111.00 124.99 -13.99 2.80e+00 1.28e-01 2.50e+01 ... (remaining 15812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 6508 16.49 - 32.99: 530 32.99 - 49.48: 93 49.48 - 65.98: 10 65.98 - 82.47: 8 Dihedral angle restraints: 7149 sinusoidal: 2901 harmonic: 4248 Sorted by residual: dihedral pdb=" CA LEU A 643 " pdb=" C LEU A 643 " pdb=" N HIS A 644 " pdb=" CA HIS A 644 " ideal model delta harmonic sigma weight residual 180.00 134.82 45.18 0 5.00e+00 4.00e-02 8.16e+01 dihedral pdb=" CA GLN A1074 " pdb=" C GLN A1074 " pdb=" N LEU A1075 " pdb=" CA LEU A1075 " ideal model delta harmonic sigma weight residual 180.00 -148.89 -31.11 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA HIS A 644 " pdb=" C HIS A 644 " pdb=" N SER A 645 " pdb=" CA SER A 645 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 7146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1493 0.055 - 0.110: 334 0.110 - 0.165: 28 0.165 - 0.220: 7 0.220 - 0.274: 2 Chirality restraints: 1864 Sorted by residual: chirality pdb=" CA ASN A1452 " pdb=" N ASN A1452 " pdb=" C ASN A1452 " pdb=" CB ASN A1452 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA LEU A 643 " pdb=" N LEU A 643 " pdb=" C LEU A 643 " pdb=" CB LEU A 643 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE A 855 " pdb=" CA ILE A 855 " pdb=" CG1 ILE A 855 " pdb=" CG2 ILE A 855 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1861 not shown) Planarity restraints: 2011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 36 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO D 37 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 37 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 37 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1424 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A1425 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1425 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1425 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 18 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.08e+00 pdb=" N PRO D 19 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 19 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 19 " 0.024 5.00e-02 4.00e+02 ... (remaining 2008 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 383 2.71 - 3.25: 12507 3.25 - 3.80: 18599 3.80 - 4.35: 24277 4.35 - 4.90: 38504 Nonbonded interactions: 94270 Sorted by model distance: nonbonded pdb=" O ASP A 625 " pdb=" NZ LYS A 689 " model vdw 2.158 3.120 nonbonded pdb=" O GLY A 824 " pdb=" OG SER A 827 " model vdw 2.173 3.040 nonbonded pdb=" O GLU A 391 " pdb=" NE2 GLN A 395 " model vdw 2.175 3.120 nonbonded pdb=" O ILE A 176 " pdb=" OG1 THR A 179 " model vdw 2.176 3.040 nonbonded pdb=" O ARG A 698 " pdb=" OG SER A 701 " model vdw 2.212 3.040 ... (remaining 94265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 28 or resid 30 through 71 or (resid 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 through 74)) selection = (chain 'D' and (resid 1 through 28 or resid 30 through 50 or (resid 51 and (name \ N or name CA or name C or name O or name CB )) or resid 52 through 71 or (resid \ 72 and (name N or name CA or name C or name O or name CB )) or resid 73 through \ 74)) selection = (chain 'E' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 28 or resid 30 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 74)) } 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=0.25 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: 0.690 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.400 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11709 Z= 0.159 Angle : 0.813 13.992 15817 Z= 0.444 Chirality : 0.045 0.274 1864 Planarity : 0.004 0.045 2011 Dihedral : 12.574 82.474 4381 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.52 (0.22), residues: 1436 helix: -0.73 (0.20), residues: 701 sheet: -0.99 (0.57), residues: 88 loop : -1.21 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 741 HIS 0.003 0.001 HIS A1234 PHE 0.024 0.002 PHE A 870 TYR 0.017 0.002 TYR A 369 ARG 0.005 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.20184 ( 475) hydrogen bonds : angle 6.94206 ( 1353) covalent geometry : bond 0.00326 (11709) covalent geometry : angle 0.81311 (15817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.7925 (t80) cc_final: 0.7234 (t80) REVERT: A 202 MET cc_start: 0.7780 (ppp) cc_final: 0.7530 (ppp) REVERT: A 1391 ILE cc_start: 0.7772 (mm) cc_final: 0.7431 (mt) REVERT: D 4 PHE cc_start: 0.7276 (m-80) cc_final: 0.7048 (m-80) REVERT: D 32 ASP cc_start: 0.8460 (m-30) cc_final: 0.8250 (m-30) REVERT: D 64 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7535 (tp30) REVERT: E 50 LEU cc_start: 0.6271 (mt) cc_final: 0.5745 (mt) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2343 time to fit residues: 66.1395 Evaluate side-chains 150 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 572 ASN A 939 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.142240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.112162 restraints weight = 27618.886| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 4.16 r_work: 0.3916 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11709 Z= 0.191 Angle : 0.762 14.727 15817 Z= 0.381 Chirality : 0.046 0.292 1864 Planarity : 0.005 0.053 2011 Dihedral : 5.661 36.364 1545 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 1.61 % Allowed : 10.55 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.70 (0.22), residues: 1436 helix: -0.70 (0.19), residues: 741 sheet: -1.14 (0.54), residues: 94 loop : -1.55 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 741 HIS 0.014 0.002 HIS A1234 PHE 0.023 0.002 PHE A 248 TYR 0.021 0.002 TYR A 489 ARG 0.005 0.001 ARG A1213 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 475) hydrogen bonds : angle 5.43648 ( 1353) covalent geometry : bond 0.00445 (11709) covalent geometry : angle 0.76225 (15817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8033 (ppp) cc_final: 0.7524 (ppp) REVERT: A 600 LEU cc_start: 0.8474 (tt) cc_final: 0.8240 (mt) REVERT: A 954 PHE cc_start: 0.7567 (p90) cc_final: 0.6676 (p90) REVERT: C 43 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7195 (mm) REVERT: D 4 PHE cc_start: 0.7510 (m-80) cc_final: 0.7202 (m-80) REVERT: D 32 ASP cc_start: 0.8421 (m-30) cc_final: 0.8171 (m-30) REVERT: D 44 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7342 (mm) outliers start: 21 outliers final: 14 residues processed: 174 average time/residue: 0.2597 time to fit residues: 66.5207 Evaluate side-chains 160 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 864 PHE Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN A 820 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1197 ASN A1373 ASN D 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.144142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.114258 restraints weight = 27678.069| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 4.20 r_work: 0.3960 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11709 Z= 0.130 Angle : 0.691 14.139 15817 Z= 0.342 Chirality : 0.043 0.254 1864 Planarity : 0.004 0.048 2011 Dihedral : 5.318 32.485 1545 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 1.91 % Allowed : 13.30 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1436 helix: -0.46 (0.19), residues: 741 sheet: -1.10 (0.57), residues: 82 loop : -1.36 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1076 HIS 0.006 0.001 HIS A1234 PHE 0.018 0.001 PHE A 248 TYR 0.012 0.001 TYR A1443 ARG 0.004 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 475) hydrogen bonds : angle 5.01428 ( 1353) covalent geometry : bond 0.00296 (11709) covalent geometry : angle 0.69081 (15817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8033 (ppp) cc_final: 0.7547 (ppp) REVERT: A 244 MET cc_start: 0.8073 (ppp) cc_final: 0.7801 (ppp) REVERT: A 369 TYR cc_start: 0.6593 (t80) cc_final: 0.6147 (t80) REVERT: A 600 LEU cc_start: 0.8465 (tt) cc_final: 0.8258 (mt) REVERT: A 954 PHE cc_start: 0.7579 (p90) cc_final: 0.6762 (p90) REVERT: A 1001 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7206 (mp) REVERT: A 1256 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: A 1267 LYS cc_start: 0.7804 (ptpp) cc_final: 0.7551 (ptpp) REVERT: A 1366 SER cc_start: 0.7761 (t) cc_final: 0.7431 (t) REVERT: A 1370 LEU cc_start: 0.7525 (pp) cc_final: 0.6659 (tt) REVERT: D 4 PHE cc_start: 0.7443 (m-80) cc_final: 0.7233 (m-80) REVERT: D 32 ASP cc_start: 0.8389 (m-30) cc_final: 0.8132 (m-30) REVERT: D 44 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7385 (mm) REVERT: E 50 LEU cc_start: 0.5646 (mm) cc_final: 0.5426 (mm) outliers start: 25 outliers final: 12 residues processed: 184 average time/residue: 0.2346 time to fit residues: 62.5772 Evaluate side-chains 164 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 864 PHE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1256 GLU Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 33 optimal weight: 0.0000 chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.144972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.113253 restraints weight = 27714.603| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 4.18 r_work: 0.3969 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11709 Z= 0.124 Angle : 0.677 14.479 15817 Z= 0.332 Chirality : 0.043 0.243 1864 Planarity : 0.004 0.048 2011 Dihedral : 5.170 33.964 1545 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 2.22 % Allowed : 15.29 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.31 (0.22), residues: 1436 helix: -0.37 (0.19), residues: 740 sheet: -1.18 (0.56), residues: 91 loop : -1.34 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1076 HIS 0.006 0.001 HIS A1234 PHE 0.018 0.001 PHE A1061 TYR 0.029 0.002 TYR A 489 ARG 0.004 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 475) hydrogen bonds : angle 4.88365 ( 1353) covalent geometry : bond 0.00288 (11709) covalent geometry : angle 0.67719 (15817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.8517 (t80) cc_final: 0.7540 (t80) REVERT: A 190 MET cc_start: 0.7087 (mmm) cc_final: 0.6683 (mmm) REVERT: A 202 MET cc_start: 0.7999 (ppp) cc_final: 0.7478 (ppp) REVERT: A 238 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5337 (ttp) REVERT: A 244 MET cc_start: 0.8151 (ppp) cc_final: 0.7840 (ppp) REVERT: A 304 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6503 (pp) REVERT: A 369 TYR cc_start: 0.6387 (t80) cc_final: 0.6094 (t80) REVERT: A 644 HIS cc_start: 0.5900 (OUTLIER) cc_final: 0.5354 (m90) REVERT: A 954 PHE cc_start: 0.7720 (p90) cc_final: 0.6926 (p90) REVERT: C 1 MET cc_start: 0.6897 (tmm) cc_final: 0.6071 (tmm) REVERT: D 4 PHE cc_start: 0.7481 (m-80) cc_final: 0.7195 (m-80) REVERT: D 32 ASP cc_start: 0.8369 (m-30) cc_final: 0.8111 (m-30) REVERT: D 44 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7413 (mm) REVERT: E 41 GLN cc_start: 0.6430 (mm110) cc_final: 0.5206 (tt0) outliers start: 29 outliers final: 16 residues processed: 178 average time/residue: 0.2444 time to fit residues: 63.2634 Evaluate side-chains 161 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 864 PHE Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1256 GLU Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 697 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.145031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.115286 restraints weight = 27578.639| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 4.18 r_work: 0.3976 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11709 Z= 0.128 Angle : 0.677 15.708 15817 Z= 0.330 Chirality : 0.043 0.213 1864 Planarity : 0.005 0.131 2011 Dihedral : 5.060 33.602 1545 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 3.06 % Allowed : 16.36 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1436 helix: -0.22 (0.20), residues: 733 sheet: -1.11 (0.57), residues: 91 loop : -1.24 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1076 HIS 0.004 0.001 HIS A1234 PHE 0.017 0.001 PHE A1061 TYR 0.021 0.001 TYR A 489 ARG 0.014 0.000 ARG A1224 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 475) hydrogen bonds : angle 4.79923 ( 1353) covalent geometry : bond 0.00300 (11709) covalent geometry : angle 0.67678 (15817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.8538 (t80) cc_final: 0.7668 (t80) REVERT: A 202 MET cc_start: 0.7974 (ppp) cc_final: 0.7498 (ppp) REVERT: A 238 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5511 (ttp) REVERT: A 244 MET cc_start: 0.8011 (ppp) cc_final: 0.7797 (ppp) REVERT: A 304 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6620 (pp) REVERT: A 954 PHE cc_start: 0.7757 (p90) cc_final: 0.6982 (p90) REVERT: A 1001 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7238 (mp) REVERT: A 1100 ARG cc_start: 0.6334 (mmp80) cc_final: 0.6044 (mmt180) REVERT: A 1224 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.6150 (tpm170) REVERT: A 1256 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: D 4 PHE cc_start: 0.7463 (m-80) cc_final: 0.7202 (m-80) REVERT: D 32 ASP cc_start: 0.8353 (m-30) cc_final: 0.8092 (m-30) REVERT: D 44 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7421 (mm) REVERT: E 41 GLN cc_start: 0.6414 (mm110) cc_final: 0.5230 (tt0) outliers start: 40 outliers final: 21 residues processed: 183 average time/residue: 0.2401 time to fit residues: 62.9138 Evaluate side-chains 173 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 864 PHE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1254 MET Chi-restraints excluded: chain A residue 1256 GLU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1366 SER Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 0.0980 chunk 61 optimal weight: 0.0770 chunk 131 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 939 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.145929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.116582 restraints weight = 27686.196| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 4.21 r_work: 0.3969 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11709 Z= 0.127 Angle : 0.683 15.909 15817 Z= 0.334 Chirality : 0.043 0.196 1864 Planarity : 0.004 0.102 2011 Dihedral : 4.988 38.134 1545 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 2.37 % Allowed : 18.35 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.10 (0.22), residues: 1436 helix: -0.20 (0.20), residues: 734 sheet: -1.10 (0.57), residues: 91 loop : -1.22 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1076 HIS 0.020 0.001 HIS A 644 PHE 0.031 0.001 PHE A 248 TYR 0.017 0.001 TYR A 245 ARG 0.011 0.000 ARG A1224 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 475) hydrogen bonds : angle 4.76303 ( 1353) covalent geometry : bond 0.00296 (11709) covalent geometry : angle 0.68257 (15817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.8609 (t80) cc_final: 0.7726 (t80) REVERT: A 202 MET cc_start: 0.8016 (ppp) cc_final: 0.7520 (ppp) REVERT: A 244 MET cc_start: 0.8106 (ppp) cc_final: 0.7852 (ppp) REVERT: A 304 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6724 (pp) REVERT: A 482 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7568 (mtm-85) REVERT: A 954 PHE cc_start: 0.7768 (p90) cc_final: 0.7038 (p90) REVERT: A 1001 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7133 (mp) REVERT: A 1256 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7789 (pm20) REVERT: A 1367 MET cc_start: 0.5160 (mmm) cc_final: 0.4896 (tpt) REVERT: C 6 LYS cc_start: 0.9226 (mmpt) cc_final: 0.8966 (mmmt) REVERT: D 4 PHE cc_start: 0.7478 (m-80) cc_final: 0.7196 (m-80) REVERT: D 32 ASP cc_start: 0.8191 (m-30) cc_final: 0.7973 (m-30) REVERT: D 44 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7426 (mm) REVERT: E 41 GLN cc_start: 0.6458 (mm110) cc_final: 0.5345 (tt0) outliers start: 31 outliers final: 21 residues processed: 176 average time/residue: 0.2804 time to fit residues: 71.1399 Evaluate side-chains 166 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 864 PHE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 ILE Chi-restraints excluded: chain A residue 1256 GLU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 139 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN A 939 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.146160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.116179 restraints weight = 28126.104| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 4.39 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4168 r_free = 0.4168 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4168 r_free = 0.4168 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11709 Z= 0.120 Angle : 0.679 16.126 15817 Z= 0.332 Chirality : 0.043 0.179 1864 Planarity : 0.004 0.053 2011 Dihedral : 4.841 34.357 1545 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 2.37 % Allowed : 19.27 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.00 (0.23), residues: 1436 helix: -0.13 (0.20), residues: 736 sheet: -1.06 (0.57), residues: 91 loop : -1.16 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1076 HIS 0.006 0.001 HIS A 644 PHE 0.032 0.001 PHE A 248 TYR 0.017 0.001 TYR A 245 ARG 0.008 0.000 ARG A1224 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 475) hydrogen bonds : angle 4.69255 ( 1353) covalent geometry : bond 0.00277 (11709) covalent geometry : angle 0.67852 (15817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.8466 (t80) cc_final: 0.7582 (t80) REVERT: A 202 MET cc_start: 0.7820 (ppp) cc_final: 0.7372 (ppp) REVERT: A 238 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4745 (ttp) REVERT: A 244 MET cc_start: 0.8019 (ppp) cc_final: 0.7770 (ppp) REVERT: A 256 SER cc_start: 0.8480 (m) cc_final: 0.8142 (p) REVERT: A 304 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6465 (pp) REVERT: A 482 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7123 (mtm-85) REVERT: A 954 PHE cc_start: 0.7449 (p90) cc_final: 0.6663 (p90) REVERT: A 1001 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7178 (mp) REVERT: A 1367 MET cc_start: 0.5201 (mmm) cc_final: 0.4902 (tpt) REVERT: C 6 LYS cc_start: 0.9148 (mmpt) cc_final: 0.8871 (mmmt) REVERT: D 4 PHE cc_start: 0.7412 (m-80) cc_final: 0.7163 (m-80) REVERT: D 32 ASP cc_start: 0.8104 (m-30) cc_final: 0.7873 (m-30) REVERT: D 44 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7377 (mm) REVERT: E 41 GLN cc_start: 0.6372 (mm110) cc_final: 0.5304 (tt0) outliers start: 31 outliers final: 22 residues processed: 175 average time/residue: 0.2420 time to fit residues: 61.0105 Evaluate side-chains 170 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 864 PHE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 ILE Chi-restraints excluded: chain A residue 1256 GLU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 117 optimal weight: 0.7980 chunk 103 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 50 optimal weight: 0.0060 chunk 52 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.0170 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.147517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.117573 restraints weight = 27907.284| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 4.43 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4189 r_free = 0.4189 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4189 r_free = 0.4189 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11709 Z= 0.116 Angle : 0.669 16.258 15817 Z= 0.326 Chirality : 0.042 0.178 1864 Planarity : 0.004 0.048 2011 Dihedral : 4.699 32.592 1545 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 2.14 % Allowed : 19.57 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.88 (0.23), residues: 1436 helix: -0.05 (0.20), residues: 736 sheet: -0.81 (0.60), residues: 82 loop : -1.11 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1076 HIS 0.006 0.001 HIS A 644 PHE 0.032 0.001 PHE A 248 TYR 0.016 0.001 TYR A 245 ARG 0.008 0.000 ARG A 938 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 475) hydrogen bonds : angle 4.60815 ( 1353) covalent geometry : bond 0.00259 (11709) covalent geometry : angle 0.66947 (15817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.8398 (t80) cc_final: 0.7570 (t80) REVERT: A 202 MET cc_start: 0.7802 (ppp) cc_final: 0.7385 (ppp) REVERT: A 238 MET cc_start: 0.5409 (OUTLIER) cc_final: 0.4709 (ttp) REVERT: A 244 MET cc_start: 0.8017 (ppp) cc_final: 0.7804 (ppp) REVERT: A 256 SER cc_start: 0.8449 (m) cc_final: 0.8112 (p) REVERT: A 304 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6379 (pp) REVERT: A 482 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7166 (mtm-85) REVERT: A 548 LYS cc_start: 0.7302 (mttt) cc_final: 0.6897 (mtmt) REVERT: A 954 PHE cc_start: 0.7256 (p90) cc_final: 0.6444 (p90) REVERT: A 1001 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7177 (mp) REVERT: A 1391 ILE cc_start: 0.7720 (mm) cc_final: 0.7308 (mt) REVERT: A 1424 ASN cc_start: 0.7858 (m-40) cc_final: 0.7497 (p0) REVERT: C 6 LYS cc_start: 0.9164 (mmpt) cc_final: 0.8843 (mmmt) REVERT: D 4 PHE cc_start: 0.7441 (m-80) cc_final: 0.7212 (m-80) REVERT: D 32 ASP cc_start: 0.8083 (m-30) cc_final: 0.7851 (m-30) REVERT: D 44 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7475 (mm) outliers start: 28 outliers final: 16 residues processed: 176 average time/residue: 0.2429 time to fit residues: 62.3199 Evaluate side-chains 165 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 864 PHE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 ILE Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1366 SER Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 88 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 141 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 3 optimal weight: 0.1980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 694 ASN A 939 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.147407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.117288 restraints weight = 28028.608| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 4.44 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4183 r_free = 0.4183 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4183 r_free = 0.4183 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11709 Z= 0.119 Angle : 0.683 16.148 15817 Z= 0.333 Chirality : 0.043 0.176 1864 Planarity : 0.004 0.047 2011 Dihedral : 4.681 29.279 1545 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 1.91 % Allowed : 20.34 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.71 % 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: -0.79 (0.23), residues: 1436 helix: 0.01 (0.20), residues: 736 sheet: -0.81 (0.60), residues: 82 loop : -1.03 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 741 HIS 0.005 0.001 HIS A 644 PHE 0.033 0.001 PHE A 248 TYR 0.022 0.001 TYR A 245 ARG 0.005 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 475) hydrogen bonds : angle 4.64017 ( 1353) covalent geometry : bond 0.00273 (11709) covalent geometry : angle 0.68264 (15817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.8393 (t80) cc_final: 0.7512 (t80) REVERT: A 202 MET cc_start: 0.7847 (ppp) cc_final: 0.7399 (ppp) REVERT: A 256 SER cc_start: 0.8495 (m) cc_final: 0.8157 (p) REVERT: A 304 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6358 (pp) REVERT: A 482 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.7192 (mtm-85) REVERT: A 548 LYS cc_start: 0.7365 (mttt) cc_final: 0.6944 (mtmt) REVERT: A 954 PHE cc_start: 0.7216 (p90) cc_final: 0.6640 (p90) REVERT: A 1001 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7200 (mp) REVERT: A 1391 ILE cc_start: 0.7639 (mm) cc_final: 0.7323 (mt) REVERT: A 1424 ASN cc_start: 0.7919 (m-40) cc_final: 0.7523 (p0) REVERT: C 6 LYS cc_start: 0.9165 (mmpt) cc_final: 0.8831 (mmmt) REVERT: D 4 PHE cc_start: 0.7428 (m-80) cc_final: 0.7203 (m-80) REVERT: D 32 ASP cc_start: 0.8102 (m-30) cc_final: 0.7881 (m-30) REVERT: D 44 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7465 (mm) outliers start: 25 outliers final: 18 residues processed: 170 average time/residue: 0.2336 time to fit residues: 58.5999 Evaluate side-chains 168 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 864 PHE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 ILE Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5344 > 50: distance: 13 - 36: 7.893 distance: 19 - 44: 9.709 distance: 23 - 51: 6.532 distance: 28 - 36: 4.138 distance: 29 - 60: 11.830 distance: 36 - 37: 5.112 distance: 37 - 38: 12.686 distance: 37 - 40: 10.542 distance: 38 - 39: 18.834 distance: 40 - 41: 13.488 distance: 40 - 42: 11.189 distance: 41 - 43: 7.375 distance: 44 - 45: 15.925 distance: 45 - 46: 11.131 distance: 45 - 48: 9.363 distance: 48 - 49: 5.095 distance: 48 - 50: 6.592 distance: 51 - 52: 27.482 distance: 52 - 53: 32.805 distance: 52 - 55: 52.340 distance: 53 - 54: 14.869 distance: 53 - 60: 22.885 distance: 55 - 56: 53.678 distance: 56 - 57: 53.439 distance: 57 - 58: 48.610 distance: 57 - 59: 35.714 distance: 60 - 61: 23.241 distance: 61 - 62: 26.154 distance: 61 - 64: 32.532 distance: 62 - 63: 32.302 distance: 62 - 68: 9.496 distance: 64 - 65: 21.765 distance: 65 - 66: 6.703 distance: 65 - 67: 7.152 distance: 68 - 69: 28.134 distance: 69 - 70: 17.799 distance: 69 - 72: 30.637 distance: 70 - 71: 22.282 distance: 70 - 75: 21.016 distance: 72 - 73: 26.742 distance: 72 - 74: 17.789 distance: 75 - 76: 33.864 distance: 76 - 77: 49.637 distance: 76 - 79: 32.921 distance: 77 - 78: 23.406 distance: 77 - 81: 44.496 distance: 79 - 80: 17.499 distance: 81 - 82: 34.102 distance: 82 - 83: 18.704 distance: 82 - 85: 16.024 distance: 83 - 84: 12.621 distance: 83 - 89: 20.885 distance: 85 - 86: 14.317 distance: 85 - 87: 13.860 distance: 86 - 88: 9.112 distance: 89 - 90: 45.509 distance: 90 - 91: 50.644 distance: 90 - 93: 51.655 distance: 91 - 92: 29.819 distance: 91 - 98: 22.182 distance: 93 - 94: 54.247 distance: 94 - 95: 56.534 distance: 95 - 96: 50.377 distance: 95 - 97: 31.750 distance: 98 - 99: 8.613 distance: 99 - 100: 13.857 distance: 99 - 102: 17.888 distance: 100 - 101: 16.778 distance: 100 - 106: 18.616 distance: 102 - 103: 6.625 distance: 103 - 104: 5.722 distance: 103 - 105: 4.962 distance: 106 - 107: 15.949 distance: 107 - 108: 6.236 distance: 107 - 110: 14.736 distance: 108 - 109: 11.135 distance: 108 - 113: 3.197 distance: 110 - 111: 14.071 distance: 110 - 112: 11.603