Starting phenix.real_space_refine on Sat Nov 18 01:13:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/11_2023/7p03_13142.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/11_2023/7p03_13142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/11_2023/7p03_13142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/11_2023/7p03_13142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/11_2023/7p03_13142.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/11_2023/7p03_13142.pdb" } resolution = 3.45 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= 0.001 sd= 0.159 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: 5 Type Number sf(0) Gaussians S 67 5.16 5 C 6900 2.51 5 N 1754 2.21 5 O 1930 1.98 5 H 10498 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 37": "OE1" <-> "OE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 630": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 739": "OE1" <-> "OE2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 866": "OE1" <-> "OE2" Residue "A ARG 872": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 953": "OD1" <-> "OD2" Residue "A PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A TYR 985": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "A PHE 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1035": "OD1" <-> "OD2" Residue "A TYR 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1127": "OE1" <-> "OE2" Residue "A ASP 1140": "OD1" <-> "OD2" Residue "A ARG 1146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1149": "OE1" <-> "OE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A ASP 1159": "OD1" <-> "OD2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A GLU 1179": "OE1" <-> "OE2" Residue "A TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1267": "OE1" <-> "OE2" Residue "A GLU 1270": "OE1" <-> "OE2" Residue "A ARG 1274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1322": "OE1" <-> "OE2" Residue "A ARG 1323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1353": "OE1" <-> "OE2" Residue "A PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1415": "OE1" <-> "OE2" Residue "A PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1445": "OD1" <-> "OD2" Residue "A PHE 1470": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1473": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21149 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 21149 Classifications: {'peptide': 1333} Link IDs: {'PTRANS': 51, 'TRANS': 1281} Chain breaks: 5 Time building chain proxies: 9.40, per 1000 atoms: 0.44 Number of scatterers: 21149 At special positions: 0 Unit cell: (80.52, 106.14, 152.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 O 1930 8.00 N 1754 7.00 C 6900 6.00 H 10498 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1411 " - pdb=" SG CYS A1455 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.87 Conformation dependent library (CDL) restraints added in 2.3 seconds 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 62.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 103 through 117 Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 198 through 207 removed outlier: 3.516A pdb=" N SER A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.628A pdb=" N LYS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.937A pdb=" N THR A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 291 removed outlier: 4.036A pdb=" N TYR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 325 removed outlier: 3.581A pdb=" N SER A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 358 removed outlier: 3.682A pdb=" N LEU A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.703A pdb=" N GLY A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 422 through 427 removed outlier: 6.845A pdb=" N SER A 425 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 427 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 454 through 469 removed outlier: 3.918A pdb=" N LYS A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 519 Processing helix chain 'A' and resid 519 through 540 removed outlier: 4.234A pdb=" N THR A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 542 No H-bonds generated for 'chain 'A' and resid 541 through 542' Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.541A pdb=" N LYS A 547 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.742A pdb=" N MET A 560 " --> pdb=" O ARG A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 574 removed outlier: 4.820A pdb=" N LEU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.578A pdb=" N ALA A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 595 through 607 removed outlier: 3.844A pdb=" N GLU A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 627 removed outlier: 4.159A pdb=" N VAL A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 removed outlier: 4.450A pdb=" N PHE A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 removed outlier: 4.823A pdb=" N VAL A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Proline residue: A 669 - end of helix Processing helix chain 'A' and resid 686 through 690 removed outlier: 3.606A pdb=" N ILE A 690 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 693 No H-bonds generated for 'chain 'A' and resid 691 through 693' Processing helix chain 'A' and resid 694 through 700 removed outlier: 3.669A pdb=" N TRP A 698 " --> pdb=" O SER A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 removed outlier: 3.624A pdb=" N TYR A 705 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 736 through 740 removed outlier: 3.846A pdb=" N SER A 740 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 764 Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'A' and resid 772 through 796 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.564A pdb=" N LEU A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 945 Processing helix chain 'A' and resid 960 through 973 removed outlier: 3.588A pdb=" N SER A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 993 removed outlier: 3.868A pdb=" N ASN A 983 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 removed outlier: 3.808A pdb=" N GLU A1023 " --> pdb=" O THR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1060 removed outlier: 3.514A pdb=" N GLY A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1076 removed outlier: 4.040A pdb=" N GLN A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1100 through 1110 Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 4.125A pdb=" N LEU A1126 " --> pdb=" O ALA A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 3.758A pdb=" N VAL A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1162 removed outlier: 3.652A pdb=" N ARG A1152 " --> pdb=" O SER A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1200 Processing helix chain 'A' and resid 1202 through 1224 removed outlier: 3.500A pdb=" N LEU A1206 " --> pdb=" O SER A1202 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A1212 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1218 " --> pdb=" O ILE A1214 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A1224 " --> pdb=" O ILE A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1244 Processing helix chain 'A' and resid 1247 through 1270 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1277 through 1306 removed outlier: 3.639A pdb=" N VAL A1290 " --> pdb=" O ILE A1286 " (cutoff:3.500A) Proline residue: A1291 - end of helix removed outlier: 3.720A pdb=" N LEU A1295 " --> pdb=" O PRO A1291 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR A1306 " --> pdb=" O PHE A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1318 removed outlier: 3.559A pdb=" N ASN A1313 " --> pdb=" O GLY A1309 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A1317 " --> pdb=" O ASN A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1348 removed outlier: 3.879A pdb=" N PHE A1327 " --> pdb=" O ARG A1323 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A1346 " --> pdb=" O GLY A1342 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE A1348 " --> pdb=" O LEU A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1369 removed outlier: 3.646A pdb=" N ALA A1355 " --> pdb=" O VAL A1351 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A1369 " --> pdb=" O MET A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1390 Processing helix chain 'A' and resid 1390 through 1405 removed outlier: 4.513A pdb=" N TYR A1394 " --> pdb=" O SER A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1432 Processing helix chain 'A' and resid 1433 through 1438 Processing helix chain 'A' and resid 1459 through 1468 removed outlier: 3.666A pdb=" N TYR A1463 " --> pdb=" O THR A1459 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A1465 " --> pdb=" O ASN A1461 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A1466 " --> pdb=" O ASP A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1472 No H-bonds generated for 'chain 'A' and resid 1470 through 1472' Processing helix chain 'A' and resid 1473 through 1500 removed outlier: 3.820A pdb=" N ASN A1477 " --> pdb=" O GLU A1473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 183 removed outlier: 5.004A pdb=" N PHE A 173 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ALA A 139 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE A 175 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER A 137 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LYS A 177 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER A 135 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET A 179 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 183 removed outlier: 5.004A pdb=" N PHE A 173 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ALA A 139 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE A 175 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER A 137 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LYS A 177 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER A 135 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET A 179 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 226 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 364 removed outlier: 6.306A pdb=" N LEU A 189 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 392 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 390 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASP A 384 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLN A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 719 through 721 Processing sheet with id=AA5, first strand: chain 'A' and resid 926 through 932 removed outlier: 7.208A pdb=" N VAL A 926 " --> pdb=" O TYR A 876 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 876 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 928 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 874 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP A 930 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 872 " --> pdb=" O ASP A 930 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL A 891 " --> pdb=" O ASN A 873 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS A 875 " --> pdb=" O ASN A 889 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN A 889 " --> pdb=" O CYS A 875 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLU A 877 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 887 " --> pdb=" O GLU A 877 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR A1090 " --> pdb=" O ASN A 889 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 891 " --> pdb=" O THR A1090 " (cutoff:3.500A) removed outlier: 11.676A pdb=" N TYR A1092 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N GLY A 893 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 10.290A pdb=" N GLY A1094 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE A1083 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A1093 " --> pdb=" O LEU A1081 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A1081 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A 900 " --> pdb=" O ARG A1080 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LEU A1082 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA A 902 " --> pdb=" O LEU A1082 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N MET A1084 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N MET A 904 " --> pdb=" O MET A1084 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 901 " --> pdb=" O CYS A1065 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A1064 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A1066 " --> pdb=" O LEU A1034 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1417 through 1419 removed outlier: 3.604A pdb=" N PHE A1419 " --> pdb=" O CYS A1452 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1611 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: 8.11 Time building geometry restraints manager: 16.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10476 1.03 - 1.23: 52 1.23 - 1.42: 4726 1.42 - 1.62: 6064 1.62 - 1.81: 106 Bond restraints: 21424 Sorted by residual: bond pdb=" CB PRO A 97 " pdb=" CG PRO A 97 " ideal model delta sigma weight residual 1.492 1.609 -0.117 5.00e-02 4.00e+02 5.50e+00 bond pdb=" CA GLU A1036 " pdb=" C GLU A1036 " ideal model delta sigma weight residual 1.532 1.521 0.011 6.50e-03 2.37e+04 3.02e+00 bond pdb=" CB GLN A1085 " pdb=" CG GLN A1085 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CB VAL A1091 " pdb=" CG2 VAL A1091 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.16e+00 bond pdb=" N PRO A 97 " pdb=" CA PRO A 97 " ideal model delta sigma weight residual 1.473 1.454 0.019 1.33e-02 5.65e+03 2.01e+00 ... (remaining 21419 not shown) Histogram of bond angle deviations from ideal: 74.05 - 86.05: 6 86.05 - 98.04: 1 98.04 - 110.04: 18753 110.04 - 122.03: 16667 122.03 - 134.03: 3133 Bond angle restraints: 38560 Sorted by residual: angle pdb=" C ASP A 120 " pdb=" CA ASP A 120 " pdb=" HA ASP A 120 " ideal model delta sigma weight residual 109.00 74.05 34.95 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 110.00 75.31 34.69 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N ASP A 120 " pdb=" CA ASP A 120 " pdb=" HA ASP A 120 " ideal model delta sigma weight residual 110.00 75.49 34.51 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 109.00 74.78 34.22 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 109.00 75.46 33.54 3.00e+00 1.11e-01 1.25e+02 ... (remaining 38555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8024 17.92 - 35.84: 574 35.84 - 53.76: 91 53.76 - 71.68: 18 71.68 - 89.60: 14 Dihedral angle restraints: 8721 sinusoidal: 3884 harmonic: 4837 Sorted by residual: dihedral pdb=" CA TYR A1199 " pdb=" C TYR A1199 " pdb=" N TRP A1200 " pdb=" CA TRP A1200 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA LEU A 249 " pdb=" C LEU A 249 " pdb=" N PRO A 250 " pdb=" CA PRO A 250 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ASN A 334 " pdb=" C ASN A 334 " pdb=" N ALA A 335 " pdb=" CA ALA A 335 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 8718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1519 0.080 - 0.160: 95 0.160 - 0.240: 0 0.240 - 0.320: 0 0.320 - 0.399: 2 Chirality restraints: 1616 Sorted by residual: chirality pdb=" CA ARG A 517 " pdb=" N ARG A 517 " pdb=" C ARG A 517 " pdb=" CB ARG A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA ASP A 120 " pdb=" N ASP A 120 " pdb=" C ASP A 120 " pdb=" CB ASP A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PRO A 250 " pdb=" N PRO A 250 " pdb=" C PRO A 250 " pdb=" CB PRO A 250 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 1613 not shown) Planarity restraints: 3149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 96 " 0.100 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO A 97 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1215 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C PHE A1215 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE A1215 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A1216 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1290 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A1291 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1291 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1291 " 0.025 5.00e-02 4.00e+02 ... (remaining 3146 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 201 2.03 - 2.67: 31348 2.67 - 3.31: 61394 3.31 - 3.96: 76628 3.96 - 4.60: 122689 Nonbonded interactions: 292260 Sorted by model distance: nonbonded pdb=" OE1 GLN A1350 " pdb="HH12 ARG A1500 " model vdw 1.387 1.850 nonbonded pdb="HH22 ARG A 872 " pdb=" OD1 ASP A1159 " model vdw 1.553 1.850 nonbonded pdb=" H ASP A 120 " pdb=" HA ASP A 120 " model vdw 1.583 1.816 nonbonded pdb=" OD1 ASN A 303 " pdb=" H ASP A 304 " model vdw 1.588 1.850 nonbonded pdb=" OD1 ASP A1204 " pdb=" H TYR A1205 " model vdw 1.611 1.850 ... (remaining 292255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.330 Extract box with map and model: 5.120 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 65.120 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 10926 Z= 0.389 Angle : 0.681 13.882 14809 Z= 0.407 Chirality : 0.043 0.399 1616 Planarity : 0.005 0.140 1872 Dihedral : 13.857 89.596 3919 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1321 helix: 0.40 (0.19), residues: 737 sheet: -1.77 (0.61), residues: 67 loop : -1.49 (0.26), residues: 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.799 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: symmetry clash 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.5040 time to fit residues: 218.0190 Evaluate side-chains 176 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 0.0770 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 470 ASN A 530 ASN A 619 ASN A1061 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10926 Z= 0.190 Angle : 0.558 7.010 14809 Z= 0.299 Chirality : 0.041 0.376 1616 Planarity : 0.004 0.070 1872 Dihedral : 4.824 22.344 1460 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.83 % Allowed : 9.08 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1321 helix: 0.70 (0.19), residues: 756 sheet: -1.60 (0.59), residues: 67 loop : -1.21 (0.27), residues: 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.726 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 208 average time/residue: 0.4963 time to fit residues: 152.4478 Evaluate side-chains 191 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.590 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.2559 time to fit residues: 10.5358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A1061 GLN A1085 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10926 Z= 0.208 Angle : 0.540 7.314 14809 Z= 0.283 Chirality : 0.040 0.376 1616 Planarity : 0.004 0.055 1872 Dihedral : 4.518 20.100 1460 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.70 % Allowed : 10.57 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1321 helix: 1.04 (0.19), residues: 757 sheet: -1.26 (0.55), residues: 78 loop : -1.12 (0.28), residues: 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 193 average time/residue: 0.4199 time to fit residues: 123.7523 Evaluate side-chains 167 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2501 time to fit residues: 4.6414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10926 Z= 0.288 Angle : 0.605 7.696 14809 Z= 0.320 Chirality : 0.042 0.380 1616 Planarity : 0.004 0.054 1872 Dihedral : 4.620 18.652 1460 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.48 % Allowed : 11.79 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1321 helix: 0.96 (0.19), residues: 762 sheet: -1.10 (0.57), residues: 71 loop : -1.16 (0.28), residues: 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 181 average time/residue: 0.4208 time to fit residues: 115.8836 Evaluate side-chains 157 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2846 time to fit residues: 6.4854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 3.9990 chunk 72 optimal weight: 0.0030 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1456 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10926 Z= 0.300 Angle : 0.557 7.336 14809 Z= 0.297 Chirality : 0.040 0.384 1616 Planarity : 0.004 0.038 1872 Dihedral : 4.569 18.960 1460 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.57 % Allowed : 13.89 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1321 helix: 1.02 (0.19), residues: 763 sheet: -1.12 (0.56), residues: 72 loop : -1.31 (0.28), residues: 486 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 170 average time/residue: 0.4085 time to fit residues: 106.6565 Evaluate side-chains 154 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2453 time to fit residues: 6.9561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10926 Z= 0.184 Angle : 0.510 7.231 14809 Z= 0.266 Chirality : 0.039 0.378 1616 Planarity : 0.003 0.041 1872 Dihedral : 4.387 18.293 1460 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.17 % Allowed : 15.81 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1321 helix: 1.15 (0.19), residues: 771 sheet: -1.03 (0.55), residues: 78 loop : -1.28 (0.28), residues: 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 155 average time/residue: 0.4181 time to fit residues: 99.5880 Evaluate side-chains 146 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2311 time to fit residues: 2.5265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10926 Z= 0.192 Angle : 0.502 7.180 14809 Z= 0.263 Chirality : 0.039 0.380 1616 Planarity : 0.003 0.035 1872 Dihedral : 4.245 18.139 1460 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.44 % Allowed : 16.16 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1321 helix: 1.24 (0.19), residues: 770 sheet: -0.79 (0.57), residues: 78 loop : -1.27 (0.28), residues: 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 152 average time/residue: 0.4203 time to fit residues: 97.7724 Evaluate side-chains 146 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2547 time to fit residues: 3.9177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10926 Z= 0.146 Angle : 0.490 7.254 14809 Z= 0.255 Chirality : 0.038 0.398 1616 Planarity : 0.003 0.035 1872 Dihedral : 4.116 17.396 1460 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 16.51 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1321 helix: 1.39 (0.19), residues: 770 sheet: -0.74 (0.57), residues: 78 loop : -1.23 (0.28), residues: 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.4363 time to fit residues: 99.0043 Evaluate side-chains 142 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10926 Z= 0.176 Angle : 0.500 7.163 14809 Z= 0.261 Chirality : 0.038 0.388 1616 Planarity : 0.003 0.037 1872 Dihedral : 4.057 17.641 1460 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.17 % Allowed : 17.21 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1321 helix: 1.43 (0.19), residues: 773 sheet: -1.19 (0.50), residues: 97 loop : -1.16 (0.29), residues: 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 145 average time/residue: 0.4560 time to fit residues: 101.5606 Evaluate side-chains 141 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2411 time to fit residues: 2.4823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 81 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.6672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10926 Z= 0.182 Angle : 0.497 7.194 14809 Z= 0.260 Chirality : 0.039 0.389 1616 Planarity : 0.003 0.035 1872 Dihedral : 4.046 17.499 1460 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.09 % Allowed : 17.64 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1321 helix: 1.49 (0.19), residues: 771 sheet: -1.20 (0.51), residues: 97 loop : -1.14 (0.29), residues: 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.4259 time to fit residues: 96.1422 Evaluate side-chains 142 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108739 restraints weight = 45853.454| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.26 r_work: 0.3143 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10926 Z= 0.241 Angle : 0.519 7.278 14809 Z= 0.275 Chirality : 0.039 0.388 1616 Planarity : 0.003 0.035 1872 Dihedral : 4.107 17.963 1460 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.17 % Allowed : 17.47 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1321 helix: 1.41 (0.19), residues: 771 sheet: -1.34 (0.50), residues: 97 loop : -1.15 (0.29), residues: 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4723.57 seconds wall clock time: 84 minutes 43.46 seconds (5083.46 seconds total)