Starting phenix.real_space_refine on Thu Feb 5 02:43:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3a_72189/02_2026/9q3a_72189.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3a_72189/02_2026/9q3a_72189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q3a_72189/02_2026/9q3a_72189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3a_72189/02_2026/9q3a_72189.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q3a_72189/02_2026/9q3a_72189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3a_72189/02_2026/9q3a_72189.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 103 5.16 5 C 9086 2.51 5 N 2428 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14223 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 12506 Classifications: {'peptide': 1579} Link IDs: {'PTRANS': 82, 'TRANS': 1496} Chain breaks: 4 Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 320 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "B" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 554 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 420 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "E" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 422 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7637 SG CYS A 993 61.336 64.200 35.443 1.00 66.50 S ATOM 9199 SG CYS A1210 59.566 62.432 33.238 1.00 76.27 S ATOM 9221 SG CYS A1213 58.798 63.042 36.548 1.00 73.11 S Time building chain proxies: 2.80, per 1000 atoms: 0.20 Number of scatterers: 14223 At special positions: 0 Unit cell: (92.4, 132.72, 138.6, 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) Zn 1 29.99 S 103 16.00 O 2605 8.00 N 2428 7.00 C 9086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1557 " - pdb=" SG CYS A1579 " distance=2.03 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: 1.20 Conformation dependent library (CDL) restraints added in 482.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A1210 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 993 " pdb="ZN ZN A1801 " - pdb=" SG CYS A1213 " 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 10 sheets defined 62.7% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.632A pdb=" N GLY A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 54 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.704A pdb=" N LEU A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 104 through 118 Processing helix chain 'A' and resid 118 through 139 Processing helix chain 'A' and resid 176 through 202 removed outlier: 3.606A pdb=" N ALA A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 225 through 248 removed outlier: 4.711A pdb=" N SER A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 280 through 290 removed outlier: 3.621A pdb=" N VAL A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 318 through 346 removed outlier: 3.611A pdb=" N THR A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.525A pdb=" N LYS A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.854A pdb=" N ALA A 382 " --> pdb=" O GLN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.745A pdb=" N ILE A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.314A pdb=" N VAL A 415 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 416 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A 418 " --> pdb=" O VAL A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 468 through 471 Processing helix chain 'A' and resid 494 through 511 Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.598A pdb=" N MET A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 4.169A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.597A pdb=" N GLN A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 578 through 586 removed outlier: 4.055A pdb=" N GLY A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 627 through 643 removed outlier: 3.505A pdb=" N GLU A 639 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 689 Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.775A pdb=" N GLN A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 Processing helix chain 'A' and resid 759 through 779 removed outlier: 4.026A pdb=" N GLU A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 786 through 796 Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.647A pdb=" N VAL A 812 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 813 " --> pdb=" O PRO A 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 813' Processing helix chain 'A' and resid 819 through 835 removed outlier: 4.472A pdb=" N PHE A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 Processing helix chain 'A' and resid 855 through 862 removed outlier: 3.683A pdb=" N LEU A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 890 removed outlier: 3.676A pdb=" N ALA A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 905 through 915 removed outlier: 3.626A pdb=" N LEU A 909 " --> pdb=" O GLU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 932 through 947 removed outlier: 3.914A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 946 " --> pdb=" O ASP A 942 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 979 removed outlier: 3.704A pdb=" N ALA A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 removed outlier: 4.065A pdb=" N GLU A 991 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1031 through 1036 Processing helix chain 'A' and resid 1048 through 1053 Processing helix chain 'A' and resid 1088 through 1096 Processing helix chain 'A' and resid 1097 through 1101 Processing helix chain 'A' and resid 1104 through 1119 removed outlier: 3.934A pdb=" N LYS A1118 " --> pdb=" O PHE A1114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A1119 " --> pdb=" O LEU A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1143 Processing helix chain 'A' and resid 1148 through 1152 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1178 through 1195 Processing helix chain 'A' and resid 1210 through 1214 Processing helix chain 'A' and resid 1255 through 1278 removed outlier: 3.519A pdb=" N ILE A1266 " --> pdb=" O TYR A1262 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A1276 " --> pdb=" O PHE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1295 Processing helix chain 'A' and resid 1296 through 1301 removed outlier: 3.653A pdb=" N MET A1300 " --> pdb=" O SER A1296 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A1301 " --> pdb=" O VAL A1297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1296 through 1301' Processing helix chain 'A' and resid 1304 through 1320 removed outlier: 3.607A pdb=" N VAL A1308 " --> pdb=" O PRO A1304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A1314 " --> pdb=" O ARG A1310 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A1320 " --> pdb=" O LEU A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1335 Processing helix chain 'A' and resid 1338 through 1350 removed outlier: 3.549A pdb=" N LYS A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP A1350 " --> pdb=" O LYS A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1357 removed outlier: 3.878A pdb=" N LEU A1354 " --> pdb=" O ASP A1350 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A1355 " --> pdb=" O SER A1351 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1364 removed outlier: 3.644A pdb=" N ASP A1361 " --> pdb=" O CYS A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1367 No H-bonds generated for 'chain 'A' and resid 1365 through 1367' Processing helix chain 'A' and resid 1371 through 1381 Processing helix chain 'A' and resid 1381 through 1386 Processing helix chain 'A' and resid 1386 through 1397 removed outlier: 4.440A pdb=" N VAL A1390 " --> pdb=" O ASN A1386 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE A1392 " --> pdb=" O GLY A1388 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A1396 " --> pdb=" O ILE A1392 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A1397 " --> pdb=" O GLU A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1403 removed outlier: 3.774A pdb=" N HIS A1402 " --> pdb=" O ASP A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1418 removed outlier: 4.065A pdb=" N SER A1418 " --> pdb=" O ALA A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1465 removed outlier: 3.655A pdb=" N LEU A1457 " --> pdb=" O GLN A1453 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A1458 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A1462 " --> pdb=" O LYS A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1485 Processing helix chain 'A' and resid 1499 through 1509 Processing helix chain 'A' and resid 1512 through 1518 removed outlier: 3.642A pdb=" N SER A1516 " --> pdb=" O GLY A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1526 Processing helix chain 'A' and resid 1596 through 1617 removed outlier: 3.886A pdb=" N MET A1605 " --> pdb=" O ARG A1601 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP A1606 " --> pdb=" O LEU A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1638 removed outlier: 3.811A pdb=" N LEU A1632 " --> pdb=" O GLU A1628 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A1635 " --> pdb=" O GLU A1631 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 152 removed outlier: 3.531A pdb=" N LEU D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET D 152 " --> pdb=" O MET D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 169 removed outlier: 4.129A pdb=" N GLU D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 130 through 166 removed outlier: 3.672A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 126 removed outlier: 4.067A pdb=" N ASP C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 143 removed outlier: 3.606A pdb=" N GLU C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 166 removed outlier: 3.506A pdb=" N MET C 149 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'E' and resid 130 through 168 removed outlier: 3.608A pdb=" N GLU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.327A pdb=" N LEU A 173 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE A 158 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLY A 147 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 493 Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 655 Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 604 Processing sheet with id=AA6, first strand: chain 'A' and resid 704 through 706 Processing sheet with id=AA7, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 3.771A pdb=" N ILE A1040 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A1161 " --> pdb=" O ILE A1040 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1433 through 1434 Processing sheet with id=AA9, first strand: chain 'A' and resid 1468 through 1471 removed outlier: 6.301A pdb=" N LEU A1469 " --> pdb=" O ILE A1492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1545 through 1547 747 hydrogen bonds defined for protein. 2115 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: 2.16 Time building geometry restraints manager: 1.57 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: 4583 1.34 - 1.46: 2630 1.46 - 1.58: 7145 1.58 - 1.70: 0 1.70 - 1.81: 164 Bond restraints: 14522 Sorted by residual: bond pdb=" N MET A 918 " pdb=" CA MET A 918 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.19e+01 bond pdb=" N VAL A1151 " pdb=" CA VAL A1151 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.18e+01 bond pdb=" N VAL A1404 " pdb=" CA VAL A1404 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.12e+01 bond pdb=" N ILE A1283 " pdb=" CA ILE A1283 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.01e+01 bond pdb=" N VAL A1011 " pdb=" CA VAL A1011 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.86e+00 ... (remaining 14517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 18178 1.33 - 2.67: 1159 2.67 - 4.00: 275 4.00 - 5.33: 64 5.33 - 6.66: 12 Bond angle restraints: 19688 Sorted by residual: angle pdb=" CA GLY A 816 " pdb=" C GLY A 816 " pdb=" O GLY A 816 " ideal model delta sigma weight residual 122.13 118.09 4.04 8.90e-01 1.26e+00 2.07e+01 angle pdb=" CA PHE A1254 " pdb=" CB PHE A1254 " pdb=" CG PHE A1254 " ideal model delta sigma weight residual 113.80 118.26 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" C ARG A 873 " pdb=" N PRO A 874 " pdb=" CA PRO A 874 " ideal model delta sigma weight residual 118.97 123.45 -4.48 1.04e+00 9.25e-01 1.86e+01 angle pdb=" N MET A1284 " pdb=" CA MET A1284 " pdb=" C MET A1284 " ideal model delta sigma weight residual 112.59 107.37 5.22 1.22e+00 6.72e-01 1.83e+01 angle pdb=" N TYR E 163 " pdb=" CA TYR E 163 " pdb=" C TYR E 163 " ideal model delta sigma weight residual 111.28 106.94 4.34 1.09e+00 8.42e-01 1.59e+01 ... (remaining 19683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 8107 15.18 - 30.36: 534 30.36 - 45.54: 118 45.54 - 60.72: 50 60.72 - 75.90: 19 Dihedral angle restraints: 8828 sinusoidal: 3550 harmonic: 5278 Sorted by residual: dihedral pdb=" CB CYS A1557 " pdb=" SG CYS A1557 " pdb=" SG CYS A1579 " pdb=" CB CYS A1579 " ideal model delta sinusoidal sigma weight residual -86.00 -150.23 64.23 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CA MET D 152 " pdb=" C MET D 152 " pdb=" N LYS D 153 " pdb=" CA LYS D 153 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA MET D 145 " pdb=" C MET D 145 " pdb=" N LYS D 146 " pdb=" CA LYS D 146 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1660 0.049 - 0.097: 462 0.097 - 0.146: 115 0.146 - 0.194: 30 0.194 - 0.243: 7 Chirality restraints: 2274 Sorted by residual: chirality pdb=" CA ILE A1177 " pdb=" N ILE A1177 " pdb=" C ILE A1177 " pdb=" CB ILE A1177 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE E 140 " pdb=" N ILE E 140 " pdb=" C ILE E 140 " pdb=" CB ILE E 140 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE E 119 " pdb=" N ILE E 119 " pdb=" C ILE E 119 " pdb=" CB ILE E 119 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2271 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 464 " -0.255 9.50e-02 1.11e+02 1.14e-01 8.00e+00 pdb=" NE ARG A 464 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 464 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 464 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 464 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1140 " 0.227 9.50e-02 1.11e+02 1.02e-01 6.36e+00 pdb=" NE ARG A1140 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A1140 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1140 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A1140 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1584 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO A1585 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A1585 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1585 " 0.033 5.00e-02 4.00e+02 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 115 2.61 - 3.18: 12652 3.18 - 3.76: 21915 3.76 - 4.33: 30650 4.33 - 4.90: 49705 Nonbonded interactions: 115037 Sorted by model distance: nonbonded pdb=" OE2 GLU A1020 " pdb="ZN ZN A1801 " model vdw 2.038 2.230 nonbonded pdb=" O THR D 147 " pdb=" OG1 THR D 151 " model vdw 2.254 3.040 nonbonded pdb=" O ASP A1613 " pdb=" OG1 THR A1616 " model vdw 2.256 3.040 nonbonded pdb=" NH1 ARG A1116 " pdb=" OE2 GLU A1234 " model vdw 2.294 3.120 nonbonded pdb=" O TYR A1566 " pdb=" N GLU A1570 " model vdw 2.305 3.120 ... (remaining 115032 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 116 through 167) selection = (chain 'E' and resid 116 through 167) } 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: 1.970 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.260 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.005 0.043 14526 Z= 0.371 Angle : 0.771 6.664 19690 Z= 0.517 Chirality : 0.050 0.243 2274 Planarity : 0.007 0.114 2483 Dihedral : 12.139 75.898 5401 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1782 helix: 0.99 (0.17), residues: 934 sheet: -1.11 (0.57), residues: 73 loop : -1.49 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 143 TYR 0.015 0.001 TYR A 109 PHE 0.020 0.002 PHE A1426 TRP 0.020 0.001 TRP A 638 HIS 0.004 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00524 (14522) covalent geometry : angle 0.77054 (19688) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.50617 ( 2) hydrogen bonds : bond 0.25062 ( 747) hydrogen bonds : angle 7.24467 ( 2115) metal coordination : bond 0.00383 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 971 GLU cc_start: 0.7981 (tp30) cc_final: 0.7656 (tp30) REVERT: A 1095 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8695 (tp40) REVERT: A 1453 GLN cc_start: 0.8673 (pm20) cc_final: 0.8464 (pm20) REVERT: A 1459 MET cc_start: 0.8213 (mmp) cc_final: 0.7826 (mmp) REVERT: A 1464 LEU cc_start: 0.9282 (mt) cc_final: 0.9042 (mp) REVERT: A 1577 MET cc_start: 0.6897 (tpt) cc_final: 0.6601 (mmm) REVERT: D 156 MET cc_start: 0.7615 (mmp) cc_final: 0.7355 (mmt) REVERT: B 133 ILE cc_start: 0.9160 (pt) cc_final: 0.8919 (mp) REVERT: B 142 ASP cc_start: 0.8589 (t0) cc_final: 0.8227 (t0) REVERT: C 133 ILE cc_start: 0.8898 (mm) cc_final: 0.8099 (mm) REVERT: C 140 ILE cc_start: 0.8483 (pt) cc_final: 0.8143 (pp) REVERT: C 143 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7477 (mtm-85) REVERT: C 160 ASP cc_start: 0.8870 (m-30) cc_final: 0.8524 (m-30) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.6095 time to fit residues: 153.4014 Evaluate side-chains 192 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A1050 HIS A1178 HIS ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** 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 = 0.3725 r_free = 0.3725 target = 0.116345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.069236 restraints weight = 25299.517| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.62 r_work: 0.2760 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14526 Z= 0.160 Angle : 0.604 10.777 19690 Z= 0.313 Chirality : 0.041 0.149 2274 Planarity : 0.005 0.049 2483 Dihedral : 4.007 22.595 1960 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.45 % Allowed : 8.75 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1782 helix: 1.36 (0.17), residues: 980 sheet: -1.33 (0.56), residues: 74 loop : -1.26 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 143 TYR 0.027 0.002 TYR A 109 PHE 0.020 0.002 PHE A 604 TRP 0.025 0.001 TRP A 638 HIS 0.010 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00354 (14522) covalent geometry : angle 0.60431 (19688) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.42385 ( 2) hydrogen bonds : bond 0.06250 ( 747) hydrogen bonds : angle 4.95863 ( 2115) metal coordination : bond 0.00485 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 965 GLU cc_start: 0.8477 (tp30) cc_final: 0.8158 (mm-30) REVERT: A 971 GLU cc_start: 0.8767 (tp30) cc_final: 0.8291 (tp30) REVERT: A 1095 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8723 (tp40) REVERT: A 1148 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7277 (p) REVERT: A 1459 MET cc_start: 0.8902 (mmp) cc_final: 0.8567 (mmp) REVERT: A 1577 MET cc_start: 0.7165 (tpt) cc_final: 0.6814 (mmm) REVERT: D 152 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8466 (ptm) REVERT: D 163 TYR cc_start: 0.8522 (t80) cc_final: 0.8222 (t80) REVERT: B 133 ILE cc_start: 0.9168 (pt) cc_final: 0.8525 (mp) REVERT: B 142 ASP cc_start: 0.9036 (t0) cc_final: 0.8806 (t0) REVERT: B 149 MET cc_start: 0.9080 (tpp) cc_final: 0.8762 (tpt) REVERT: E 132 ARG cc_start: 0.8489 (ptm-80) cc_final: 0.7408 (ptm-80) REVERT: E 134 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8121 (tm) REVERT: E 149 MET cc_start: 0.8876 (mmm) cc_final: 0.8523 (mtm) REVERT: E 150 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8807 (mm-30) outliers start: 23 outliers final: 6 residues processed: 212 average time/residue: 0.6261 time to fit residues: 144.8644 Evaluate side-chains 197 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 160 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN E 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.116409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.069365 restraints weight = 25540.582| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.64 r_work: 0.2757 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14526 Z= 0.135 Angle : 0.558 9.876 19690 Z= 0.286 Chirality : 0.040 0.138 2274 Planarity : 0.004 0.047 2483 Dihedral : 3.972 20.483 1960 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.76 % Allowed : 10.45 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1782 helix: 1.50 (0.17), residues: 973 sheet: -1.07 (0.56), residues: 76 loop : -1.09 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 132 TYR 0.028 0.001 TYR A 109 PHE 0.018 0.001 PHE A 604 TRP 0.024 0.001 TRP A 638 HIS 0.012 0.001 HIS A1439 Details of bonding type rmsd covalent geometry : bond 0.00304 (14522) covalent geometry : angle 0.55819 (19688) SS BOND : bond 0.00208 ( 1) SS BOND : angle 0.23912 ( 2) hydrogen bonds : bond 0.04963 ( 747) hydrogen bonds : angle 4.51037 ( 2115) metal coordination : bond 0.00566 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 918 MET cc_start: 0.7936 (tpp) cc_final: 0.7717 (mmm) REVERT: A 961 ASP cc_start: 0.7359 (t0) cc_final: 0.7060 (m-30) REVERT: A 965 GLU cc_start: 0.8463 (tp30) cc_final: 0.8192 (mm-30) REVERT: A 971 GLU cc_start: 0.8798 (tp30) cc_final: 0.8319 (tp30) REVERT: A 1148 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7258 (p) REVERT: A 1355 MET cc_start: 0.8437 (pp-130) cc_final: 0.8073 (ppp) REVERT: A 1459 MET cc_start: 0.8958 (mmp) cc_final: 0.8599 (mmp) REVERT: A 1577 MET cc_start: 0.7230 (tpt) cc_final: 0.6859 (mmm) REVERT: A 1604 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8968 (mm) REVERT: B 133 ILE cc_start: 0.9011 (pt) cc_final: 0.8644 (mp) REVERT: B 143 ARG cc_start: 0.8559 (mtm110) cc_final: 0.8349 (mtm-85) REVERT: C 133 ILE cc_start: 0.8577 (mm) cc_final: 0.8189 (mm) REVERT: E 132 ARG cc_start: 0.8265 (ptm-80) cc_final: 0.7772 (ptm-80) REVERT: E 136 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7941 (mm-30) REVERT: E 149 MET cc_start: 0.8964 (mmm) cc_final: 0.8666 (mtp) outliers start: 28 outliers final: 9 residues processed: 207 average time/residue: 0.5650 time to fit residues: 128.1642 Evaluate side-chains 201 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 160 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A1023 HIS ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.113729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.065825 restraints weight = 25451.622| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.64 r_work: 0.2685 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14526 Z= 0.215 Angle : 0.602 8.670 19690 Z= 0.308 Chirality : 0.043 0.151 2274 Planarity : 0.004 0.045 2483 Dihedral : 4.206 23.556 1960 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.39 % Allowed : 11.08 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1782 helix: 1.53 (0.17), residues: 977 sheet: -1.19 (0.54), residues: 89 loop : -1.03 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 132 TYR 0.027 0.002 TYR A 109 PHE 0.022 0.002 PHE A 230 TRP 0.023 0.002 TRP A 638 HIS 0.009 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00522 (14522) covalent geometry : angle 0.60209 (19688) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.20219 ( 2) hydrogen bonds : bond 0.05128 ( 747) hydrogen bonds : angle 4.41391 ( 2115) metal coordination : bond 0.01090 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8559 (tm) REVERT: A 971 GLU cc_start: 0.8769 (tp30) cc_final: 0.8305 (tp30) REVERT: A 1148 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7447 (p) REVERT: A 1459 MET cc_start: 0.9065 (mmp) cc_final: 0.8758 (mmp) REVERT: A 1577 MET cc_start: 0.7277 (tpt) cc_final: 0.6864 (mmm) REVERT: A 1604 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8972 (mm) REVERT: D 146 LYS cc_start: 0.8267 (mmtp) cc_final: 0.7959 (mmtp) REVERT: D 149 MET cc_start: 0.8587 (tpp) cc_final: 0.8253 (tpp) REVERT: D 150 GLU cc_start: 0.8808 (pm20) cc_final: 0.8272 (pm20) REVERT: D 160 ASP cc_start: 0.8696 (m-30) cc_final: 0.8451 (m-30) REVERT: C 154 LEU cc_start: 0.8965 (tt) cc_final: 0.8674 (tm) REVERT: E 132 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.7690 (ptm-80) REVERT: E 136 GLU cc_start: 0.8656 (mm-30) cc_final: 0.7966 (mm-30) REVERT: E 149 MET cc_start: 0.9070 (mmm) cc_final: 0.8556 (mtt) REVERT: E 150 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8846 (mm-30) outliers start: 38 outliers final: 9 residues processed: 210 average time/residue: 0.6580 time to fit residues: 150.9077 Evaluate side-chains 192 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain C residue 127 HIS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 160 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 167 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 145 optimal weight: 0.0980 chunk 148 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 71 optimal weight: 0.4980 chunk 130 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 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 399 ASN A1323 GLN ** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 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 = 0.3699 r_free = 0.3699 target = 0.114658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.067400 restraints weight = 25559.706| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.63 r_work: 0.2709 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14526 Z= 0.146 Angle : 0.568 13.785 19690 Z= 0.287 Chirality : 0.041 0.158 2274 Planarity : 0.004 0.045 2483 Dihedral : 4.132 23.936 1960 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.76 % Allowed : 12.66 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.20), residues: 1782 helix: 1.58 (0.17), residues: 977 sheet: -0.95 (0.59), residues: 78 loop : -0.96 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 132 TYR 0.025 0.001 TYR A 109 PHE 0.019 0.001 PHE A 230 TRP 0.022 0.002 TRP A 638 HIS 0.008 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00345 (14522) covalent geometry : angle 0.56847 (19688) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.21425 ( 2) hydrogen bonds : bond 0.04468 ( 747) hydrogen bonds : angle 4.28894 ( 2115) metal coordination : bond 0.00651 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8532 (tm) REVERT: A 971 GLU cc_start: 0.8780 (tp30) cc_final: 0.8306 (tp30) REVERT: A 1148 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7378 (p) REVERT: A 1355 MET cc_start: 0.8449 (pp-130) cc_final: 0.8124 (ppp) REVERT: A 1459 MET cc_start: 0.9069 (mmp) cc_final: 0.8868 (mmp) REVERT: A 1591 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7678 (mmt-90) REVERT: A 1604 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8985 (mm) REVERT: D 139 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8691 (mmmm) REVERT: D 146 LYS cc_start: 0.8305 (mmtp) cc_final: 0.7937 (mmtp) REVERT: D 149 MET cc_start: 0.8581 (tpp) cc_final: 0.8330 (tpp) REVERT: D 150 GLU cc_start: 0.8762 (pm20) cc_final: 0.8282 (pm20) REVERT: D 160 ASP cc_start: 0.8683 (m-30) cc_final: 0.8426 (m-30) REVERT: B 139 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8746 (mmmm) REVERT: E 149 MET cc_start: 0.9067 (mmm) cc_final: 0.8611 (mtt) outliers start: 28 outliers final: 9 residues processed: 209 average time/residue: 0.6047 time to fit residues: 138.1783 Evaluate side-chains 199 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1325 GLU Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 127 HIS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 160 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.114015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.066431 restraints weight = 25296.126| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.62 r_work: 0.2685 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14526 Z= 0.187 Angle : 0.590 11.658 19690 Z= 0.299 Chirality : 0.041 0.143 2274 Planarity : 0.004 0.057 2483 Dihedral : 4.179 24.078 1960 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.70 % Allowed : 14.04 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.20), residues: 1782 helix: 1.57 (0.17), residues: 976 sheet: -0.88 (0.56), residues: 88 loop : -0.94 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 132 TYR 0.025 0.002 TYR A 109 PHE 0.021 0.001 PHE A 230 TRP 0.022 0.002 TRP A 881 HIS 0.007 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00452 (14522) covalent geometry : angle 0.58966 (19688) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.20886 ( 2) hydrogen bonds : bond 0.04601 ( 747) hydrogen bonds : angle 4.28022 ( 2115) metal coordination : bond 0.00854 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 THR cc_start: 0.9069 (m) cc_final: 0.8684 (p) REVERT: A 528 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8579 (tm) REVERT: A 971 GLU cc_start: 0.8754 (tp30) cc_final: 0.8282 (tp30) REVERT: A 1148 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7414 (p) REVERT: A 1176 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8819 (p) REVERT: A 1355 MET cc_start: 0.8428 (pp-130) cc_final: 0.8060 (ppp) REVERT: A 1459 MET cc_start: 0.9092 (mmp) cc_final: 0.8854 (mmp) REVERT: A 1530 ARG cc_start: 0.8449 (tpp-160) cc_final: 0.7613 (tmm160) REVERT: A 1577 MET cc_start: 0.7169 (mmm) cc_final: 0.6492 (mmm) REVERT: A 1604 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8980 (mm) REVERT: D 139 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8693 (mmmm) REVERT: D 146 LYS cc_start: 0.8412 (mmtp) cc_final: 0.7930 (mmtp) REVERT: D 149 MET cc_start: 0.8673 (tpp) cc_final: 0.8336 (tpt) REVERT: D 150 GLU cc_start: 0.8799 (pm20) cc_final: 0.8278 (pm20) REVERT: D 160 ASP cc_start: 0.8664 (m-30) cc_final: 0.8432 (m-30) REVERT: B 133 ILE cc_start: 0.9018 (pt) cc_final: 0.8633 (mp) REVERT: B 139 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8729 (mmmm) REVERT: E 140 ILE cc_start: 0.9275 (mm) cc_final: 0.9028 (pp) REVERT: E 149 MET cc_start: 0.9070 (mmm) cc_final: 0.8595 (mtt) outliers start: 27 outliers final: 12 residues processed: 207 average time/residue: 0.6289 time to fit residues: 142.4743 Evaluate side-chains 200 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1325 GLU Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 127 HIS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 160 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 147 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.114334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.066690 restraints weight = 25235.688| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.63 r_work: 0.2697 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14526 Z= 0.162 Angle : 0.587 10.872 19690 Z= 0.297 Chirality : 0.041 0.136 2274 Planarity : 0.004 0.054 2483 Dihedral : 4.182 23.606 1960 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.76 % Allowed : 14.11 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1782 helix: 1.57 (0.17), residues: 982 sheet: -0.77 (0.56), residues: 88 loop : -0.92 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 132 TYR 0.029 0.001 TYR D 163 PHE 0.020 0.001 PHE A 230 TRP 0.023 0.002 TRP A 881 HIS 0.007 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00387 (14522) covalent geometry : angle 0.58719 (19688) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.17022 ( 2) hydrogen bonds : bond 0.04358 ( 747) hydrogen bonds : angle 4.21892 ( 2115) metal coordination : bond 0.00712 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 THR cc_start: 0.9078 (m) cc_final: 0.8642 (p) REVERT: A 528 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8609 (tm) REVERT: A 971 GLU cc_start: 0.8740 (tp30) cc_final: 0.8268 (tp30) REVERT: A 1148 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7388 (p) REVERT: A 1355 MET cc_start: 0.8412 (pp-130) cc_final: 0.8008 (ppp) REVERT: A 1459 MET cc_start: 0.9121 (mmp) cc_final: 0.8820 (mmp) REVERT: A 1530 ARG cc_start: 0.8430 (tpp-160) cc_final: 0.7590 (tmm160) REVERT: A 1577 MET cc_start: 0.7129 (mmm) cc_final: 0.6467 (tpt) REVERT: A 1604 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9010 (mm) REVERT: D 139 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8669 (mmmm) REVERT: D 146 LYS cc_start: 0.8452 (mmtp) cc_final: 0.7974 (mmtp) REVERT: D 149 MET cc_start: 0.8675 (tpp) cc_final: 0.8411 (tpt) REVERT: D 150 GLU cc_start: 0.8751 (pm20) cc_final: 0.8234 (pm20) REVERT: D 160 ASP cc_start: 0.8651 (m-30) cc_final: 0.8443 (m-30) REVERT: B 139 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8728 (mmmm) REVERT: E 132 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8404 (mtm-85) REVERT: E 140 ILE cc_start: 0.9278 (mm) cc_final: 0.9072 (pp) outliers start: 28 outliers final: 10 residues processed: 208 average time/residue: 0.6043 time to fit residues: 137.9740 Evaluate side-chains 196 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1325 GLU Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 127 HIS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 160 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 143 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 58 optimal weight: 0.0070 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.069348 restraints weight = 25236.272| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.60 r_work: 0.2741 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14526 Z= 0.113 Angle : 0.571 10.420 19690 Z= 0.286 Chirality : 0.039 0.141 2274 Planarity : 0.004 0.055 2483 Dihedral : 4.038 20.559 1960 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.51 % Allowed : 14.99 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1782 helix: 1.69 (0.17), residues: 966 sheet: -0.79 (0.63), residues: 73 loop : -0.83 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 132 TYR 0.024 0.001 TYR A 109 PHE 0.017 0.001 PHE A 230 TRP 0.027 0.001 TRP A 881 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00252 (14522) covalent geometry : angle 0.57071 (19688) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.17031 ( 2) hydrogen bonds : bond 0.03727 ( 747) hydrogen bonds : angle 4.12046 ( 2115) metal coordination : bond 0.00333 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8547 (tm) REVERT: A 815 ARG cc_start: 0.8750 (ttm110) cc_final: 0.8338 (ttp-170) REVERT: A 971 GLU cc_start: 0.8762 (tp30) cc_final: 0.8342 (tp30) REVERT: A 1229 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8776 (mm-40) REVERT: A 1355 MET cc_start: 0.8387 (pp-130) cc_final: 0.8046 (ppp) REVERT: A 1459 MET cc_start: 0.9108 (mmp) cc_final: 0.8859 (mmp) REVERT: A 1530 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.7519 (tmm160) REVERT: A 1577 MET cc_start: 0.7052 (mmm) cc_final: 0.6429 (tpt) REVERT: A 1604 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9021 (mm) REVERT: D 139 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8599 (mmmm) REVERT: D 143 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8400 (mtp180) REVERT: D 146 LYS cc_start: 0.8396 (mmtp) cc_final: 0.7905 (mmtp) REVERT: D 149 MET cc_start: 0.8627 (tpp) cc_final: 0.8256 (tpt) REVERT: D 150 GLU cc_start: 0.8715 (pm20) cc_final: 0.8178 (pm20) REVERT: B 133 ILE cc_start: 0.8874 (pt) cc_final: 0.8592 (pp) REVERT: B 136 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8318 (pp20) REVERT: B 139 LYS cc_start: 0.8911 (tppp) cc_final: 0.8695 (mmmm) REVERT: B 154 LEU cc_start: 0.9105 (mt) cc_final: 0.8865 (mm) REVERT: C 154 LEU cc_start: 0.8903 (tt) cc_final: 0.8667 (tm) outliers start: 24 outliers final: 9 residues processed: 207 average time/residue: 0.5741 time to fit residues: 130.2987 Evaluate side-chains 194 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1325 GLU Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 127 HIS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain E residue 134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 64 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 27 optimal weight: 0.0670 chunk 165 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.069085 restraints weight = 25154.415| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.62 r_work: 0.2745 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14526 Z= 0.120 Angle : 0.589 10.214 19690 Z= 0.297 Chirality : 0.040 0.189 2274 Planarity : 0.004 0.063 2483 Dihedral : 4.007 20.128 1960 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.94 % Allowed : 15.74 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1782 helix: 1.72 (0.17), residues: 965 sheet: -0.76 (0.62), residues: 73 loop : -0.79 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 132 TYR 0.027 0.001 TYR D 163 PHE 0.017 0.001 PHE A 230 TRP 0.028 0.001 TRP A 881 HIS 0.007 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00269 (14522) covalent geometry : angle 0.58919 (19688) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.18464 ( 2) hydrogen bonds : bond 0.03744 ( 747) hydrogen bonds : angle 4.11745 ( 2115) metal coordination : bond 0.00380 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8517 (tm) REVERT: A 815 ARG cc_start: 0.8772 (ttm110) cc_final: 0.8367 (ttp-170) REVERT: A 971 GLU cc_start: 0.8769 (tp30) cc_final: 0.8345 (tp30) REVERT: A 1229 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8747 (mm-40) REVERT: A 1355 MET cc_start: 0.8400 (pp-130) cc_final: 0.8042 (ppp) REVERT: A 1459 MET cc_start: 0.9147 (mmp) cc_final: 0.8939 (mmp) REVERT: A 1486 LEU cc_start: 0.9038 (tp) cc_final: 0.8773 (tp) REVERT: A 1530 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.7519 (tmm160) REVERT: A 1577 MET cc_start: 0.7011 (mmm) cc_final: 0.6110 (mmm) REVERT: A 1604 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9038 (mm) REVERT: D 139 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8607 (mmmm) REVERT: D 143 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8381 (mtp180) REVERT: D 146 LYS cc_start: 0.8432 (mmtp) cc_final: 0.7962 (mmtp) REVERT: D 149 MET cc_start: 0.8573 (tpp) cc_final: 0.8356 (tpp) REVERT: D 150 GLU cc_start: 0.8715 (pm20) cc_final: 0.8212 (pm20) REVERT: B 133 ILE cc_start: 0.8876 (pt) cc_final: 0.8599 (pp) REVERT: B 143 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8164 (mtm-85) REVERT: B 154 LEU cc_start: 0.9119 (mt) cc_final: 0.8892 (mm) REVERT: C 143 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7697 (ptp90) REVERT: E 132 ARG cc_start: 0.8654 (mtm-85) cc_final: 0.8309 (mtm-85) outliers start: 15 outliers final: 6 residues processed: 195 average time/residue: 0.5853 time to fit residues: 125.4640 Evaluate side-chains 193 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 1325 GLU Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain C residue 127 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 0.4980 chunk 174 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A1180 GLN ** B 127 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 = 0.3715 r_free = 0.3715 target = 0.115710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.068510 restraints weight = 25311.664| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.60 r_work: 0.2729 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14526 Z= 0.140 Angle : 0.613 11.614 19690 Z= 0.308 Chirality : 0.041 0.202 2274 Planarity : 0.004 0.064 2483 Dihedral : 4.052 20.933 1960 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.82 % Allowed : 15.93 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1782 helix: 1.65 (0.17), residues: 972 sheet: -0.51 (0.57), residues: 88 loop : -0.78 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 132 TYR 0.028 0.001 TYR D 163 PHE 0.018 0.001 PHE A 230 TRP 0.030 0.001 TRP A 881 HIS 0.006 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00329 (14522) covalent geometry : angle 0.61283 (19688) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.21528 ( 2) hydrogen bonds : bond 0.03963 ( 747) hydrogen bonds : angle 4.15075 ( 2115) metal coordination : bond 0.00563 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8563 (tm) REVERT: A 697 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: A 971 GLU cc_start: 0.8775 (tp30) cc_final: 0.8354 (tp30) REVERT: A 1229 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8768 (mm-40) REVERT: A 1355 MET cc_start: 0.8343 (pp-130) cc_final: 0.7973 (ppp) REVERT: A 1459 MET cc_start: 0.9151 (mmp) cc_final: 0.8942 (mmp) REVERT: A 1530 ARG cc_start: 0.8390 (tpp-160) cc_final: 0.7506 (tmm160) REVERT: A 1577 MET cc_start: 0.7021 (mmm) cc_final: 0.6108 (mmm) REVERT: A 1604 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9051 (mm) REVERT: D 139 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8601 (mmmm) REVERT: D 143 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8290 (mtp180) REVERT: D 146 LYS cc_start: 0.8471 (mmtp) cc_final: 0.7986 (mmtp) REVERT: D 149 MET cc_start: 0.8614 (tpp) cc_final: 0.8387 (tpp) REVERT: D 150 GLU cc_start: 0.8704 (pm20) cc_final: 0.8203 (pm20) REVERT: B 143 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8180 (mtm-85) REVERT: B 154 LEU cc_start: 0.9140 (mt) cc_final: 0.8913 (mm) REVERT: C 143 ARG cc_start: 0.8339 (mtm-85) cc_final: 0.7821 (ptp90) REVERT: E 132 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8116 (mtm-85) outliers start: 13 outliers final: 7 residues processed: 188 average time/residue: 0.6115 time to fit residues: 125.6104 Evaluate side-chains 189 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 1325 GLU Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain C residue 127 HIS Chi-restraints excluded: chain E residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 67 optimal weight: 0.0010 chunk 107 optimal weight: 0.0980 chunk 27 optimal weight: 0.0030 chunk 136 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 0.0040 overall best weight: 0.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 399 ASN ** B 127 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 = 0.3755 r_free = 0.3755 target = 0.118552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071902 restraints weight = 25244.870| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.63 r_work: 0.2799 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14526 Z= 0.110 Angle : 0.599 11.253 19690 Z= 0.298 Chirality : 0.040 0.229 2274 Planarity : 0.004 0.064 2483 Dihedral : 3.936 18.995 1960 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.82 % Allowed : 16.25 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1782 helix: 1.63 (0.17), residues: 972 sheet: -0.63 (0.62), residues: 73 loop : -0.73 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 132 TYR 0.025 0.001 TYR A 109 PHE 0.016 0.001 PHE A1341 TRP 0.031 0.001 TRP A 881 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00237 (14522) covalent geometry : angle 0.59909 (19688) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.23802 ( 2) hydrogen bonds : bond 0.03283 ( 747) hydrogen bonds : angle 4.03977 ( 2115) metal coordination : bond 0.00161 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6028.77 seconds wall clock time: 103 minutes 14.41 seconds (6194.41 seconds total)