Starting phenix.real_space_refine on Sat Mar 16 05:11:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/03_2024/8p50_17435_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/03_2024/8p50_17435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/03_2024/8p50_17435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/03_2024/8p50_17435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/03_2024/8p50_17435_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/03_2024/8p50_17435_updated.pdb" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 8611 2.51 5 N 2426 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13714 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1574, 12389 Classifications: {'peptide': 1574} Link IDs: {'PTRANS': 59, 'TRANS': 1514} Chain breaks: 1 Chain: "B" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1292 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 3, 'TRANS': 157} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 865 residue: pdb=" N SER A 5 " occ=0.82 ... (4 atoms not shown) pdb=" OG SER A 5 " occ=0.00 residue: pdb=" N ASP A 7 " occ=0.16 ... (6 atoms not shown) pdb=" OD2 ASP A 7 " occ=0.00 residue: pdb=" N PHE A 8 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 8 " occ=0.00 residue: pdb=" N THR A 9 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 9 " occ=0.00 residue: pdb=" N LEU A 11 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 11 " occ=0.61 residue: pdb=" N ASN A 13 " occ=0.05 ... (6 atoms not shown) pdb=" ND2 ASN A 13 " occ=0.19 residue: pdb=" N THR A 14 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 14 " occ=0.00 residue: pdb=" N ILE A 16 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE A 16 " occ=0.90 residue: pdb=" N ASP A 17 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 17 " occ=0.00 residue: pdb=" N GLY A 18 " occ=0.31 ... (2 atoms not shown) pdb=" O GLY A 18 " occ=0.39 residue: pdb=" N GLN A 19 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN A 19 " occ=0.00 residue: pdb=" N ILE A 20 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE A 20 " occ=0.00 ... (remaining 853 not shown) Time building chain proxies: 7.75, per 1000 atoms: 0.57 Number of scatterers: 13714 At special positions: 0 Unit cell: (99.9, 111.6, 150.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 3 15.00 Mg 1 11.99 O 2632 8.00 N 2426 7.00 C 8611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3242 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 11 sheets defined 47.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 6 through 21 Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.526A pdb=" N GLN A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 94 through 131 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 148 through 171 removed outlier: 4.436A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 201 Processing helix chain 'A' and resid 204 through 215 removed outlier: 4.581A pdb=" N ALA A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 314 through 323 removed outlier: 4.114A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 466 through 488 Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 501 through 516 removed outlier: 3.900A pdb=" N ARG A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 542 through 557 Processing helix chain 'A' and resid 562 through 574 removed outlier: 4.641A pdb=" N LYS A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 583 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 591 through 597 Processing helix chain 'A' and resid 599 through 622 removed outlier: 4.351A pdb=" N GLU A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'A' and resid 660 through 673 Proline residue: A 667 - end of helix removed outlier: 3.638A pdb=" N LEU A 673 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 697 removed outlier: 4.074A pdb=" N LEU A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 691 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Proline residue: A 692 - end of helix Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 736 through 739 Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 782 through 794 removed outlier: 4.209A pdb=" N VAL A 790 " --> pdb=" O THR A 786 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU A 793 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 817 Processing helix chain 'A' and resid 824 through 833 removed outlier: 5.029A pdb=" N VAL A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 856 removed outlier: 3.714A pdb=" N GLU A 855 " --> pdb=" O LYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 880 removed outlier: 3.812A pdb=" N ARG A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Proline residue: A 875 - end of helix removed outlier: 3.686A pdb=" N GLN A 879 " --> pdb=" O PRO A 875 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLY A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 929 through 936 Processing helix chain 'A' and resid 938 through 944 Processing helix chain 'A' and resid 950 through 952 No H-bonds generated for 'chain 'A' and resid 950 through 952' Processing helix chain 'A' and resid 986 through 988 No H-bonds generated for 'chain 'A' and resid 986 through 988' Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1066 through 1069 No H-bonds generated for 'chain 'A' and resid 1066 through 1069' Processing helix chain 'A' and resid 1126 through 1151 removed outlier: 3.811A pdb=" N GLN A1133 " --> pdb=" O ARG A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1208 removed outlier: 5.220A pdb=" N ALA A1178 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1192 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A1194 " --> pdb=" O ASN A1191 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A1195 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A1199 " --> pdb=" O GLN A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1258 removed outlier: 3.529A pdb=" N ILE A1226 " --> pdb=" O GLN A1223 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP A1236 " --> pdb=" O ALA A1233 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR A1237 " --> pdb=" O GLN A1234 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A1257 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1262 No H-bonds generated for 'chain 'A' and resid 1260 through 1262' Processing helix chain 'A' and resid 1282 through 1290 Processing helix chain 'A' and resid 1299 through 1307 Processing helix chain 'A' and resid 1322 through 1331 Processing helix chain 'A' and resid 1336 through 1357 Processing helix chain 'A' and resid 1359 through 1373 removed outlier: 3.583A pdb=" N THR A1362 " --> pdb=" O LEU A1359 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ALA A1363 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A1364 " --> pdb=" O GLN A1361 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A1365 " --> pdb=" O THR A1362 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A1369 " --> pdb=" O SER A1366 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A1371 " --> pdb=" O ASP A1368 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A1372 " --> pdb=" O PHE A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1428 removed outlier: 3.737A pdb=" N ARG A1402 " --> pdb=" O TYR A1398 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A1406 " --> pdb=" O ARG A1402 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N GLU A1413 " --> pdb=" O ALA A1409 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ALA A1414 " --> pdb=" O SER A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1442 Processing helix chain 'A' and resid 1449 through 1453 Processing helix chain 'A' and resid 1463 through 1472 Processing helix chain 'A' and resid 1516 through 1527 Processing helix chain 'A' and resid 1532 through 1535 No H-bonds generated for 'chain 'A' and resid 1532 through 1535' Processing helix chain 'A' and resid 1554 through 1559 removed outlier: 3.857A pdb=" N ALA A1558 " --> pdb=" O THR A1554 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLU A1559 " --> pdb=" O GLY A1555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1554 through 1559' Processing helix chain 'A' and resid 1577 through 1588 Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 72 through 81 Proline residue: B 76 - end of helix removed outlier: 4.980A pdb=" N ARG B 79 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N HIS B 80 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 81' Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 136 through 142 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 166 through 177 Processing sheet with id= A, first strand: chain 'A' and resid 275 through 277 removed outlier: 3.694A pdb=" N ILE A 240 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 258 through 261 Processing sheet with id= C, first strand: chain 'A' and resid 335 through 339 removed outlier: 3.584A pdb=" N GLY A 360 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 450 through 454 Processing sheet with id= E, first strand: chain 'A' and resid 720 through 722 Processing sheet with id= F, first strand: chain 'A' and resid 946 through 948 removed outlier: 5.824A pdb=" N GLU A 975 " --> pdb=" O LYS A 968 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS A 968 " --> pdb=" O GLU A 975 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU A 977 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU A 966 " --> pdb=" O GLU A 977 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 979 " --> pdb=" O ALA A 964 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA A 964 " --> pdb=" O THR A 979 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 962 " --> pdb=" O ALA A 993 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 993 " --> pdb=" O GLY A 962 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A1022 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU A 996 " --> pdb=" O PHE A1022 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE A1024 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1009 through 1014 removed outlier: 3.834A pdb=" N ALA A1009 " --> pdb=" O HIS A1047 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A1033 " --> pdb=" O VAL A1064 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER A1037 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A1060 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1079 through 1086 Processing sheet with id= I, first strand: chain 'A' and resid 1097 through 1101 Processing sheet with id= J, first strand: chain 'A' and resid 1377 through 1379 removed outlier: 3.509A pdb=" N SER A1477 " --> pdb=" O SER A1492 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 153 through 157 removed outlier: 6.525A pdb=" N LEU B 121 " --> pdb=" O TYR B 154 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLN B 156 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 123 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 92 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 20 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR B 64 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET B 22 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TRP B 66 " --> pdb=" O MET B 22 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLY B 24 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 68 " --> pdb=" O GLY B 24 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1506 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: 5.68 Time building geometry restraints manager: 6.24 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: 4656 1.34 - 1.46: 2462 1.46 - 1.57: 6764 1.57 - 1.69: 5 1.69 - 1.81: 80 Bond restraints: 13967 Sorted by residual: bond pdb=" CD ARG A1530 " pdb=" NE ARG A1530 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.37e+00 bond pdb=" CA ARG A1530 " pdb=" CB ARG A1530 " ideal model delta sigma weight residual 1.529 1.508 0.021 1.40e-02 5.10e+03 2.19e+00 bond pdb=" CA GLY A 678 " pdb=" C GLY A 678 " ideal model delta sigma weight residual 1.517 1.502 0.015 1.08e-02 8.57e+03 1.89e+00 bond pdb=" C THR A 305 " pdb=" N PRO A 306 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" CB GLU A 207 " pdb=" CG GLU A 207 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.65e+00 ... (remaining 13962 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.40: 345 106.40 - 113.34: 7582 113.34 - 120.28: 5234 120.28 - 127.22: 5638 127.22 - 134.16: 116 Bond angle restraints: 18915 Sorted by residual: angle pdb=" C PRO A 91 " pdb=" N GLY A 92 " pdb=" CA GLY A 92 " ideal model delta sigma weight residual 119.92 123.41 -3.49 9.60e-01 1.09e+00 1.32e+01 angle pdb=" N SER A 301 " pdb=" CA SER A 301 " pdb=" C SER A 301 " ideal model delta sigma weight residual 109.81 117.73 -7.92 2.21e+00 2.05e-01 1.28e+01 angle pdb=" C LYS A1357 " pdb=" N VAL A1358 " pdb=" CA VAL A1358 " ideal model delta sigma weight residual 121.97 115.63 6.34 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C THR B 48 " pdb=" N ILE B 49 " pdb=" CA ILE B 49 " ideal model delta sigma weight residual 120.77 125.71 -4.94 1.46e+00 4.69e-01 1.15e+01 angle pdb=" CA ARG A 344 " pdb=" CB ARG A 344 " pdb=" CG ARG A 344 " ideal model delta sigma weight residual 114.10 107.49 6.61 2.00e+00 2.50e-01 1.09e+01 ... (remaining 18910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.87: 8291 32.87 - 65.74: 122 65.74 - 98.61: 31 98.61 - 131.47: 2 131.47 - 164.34: 3 Dihedral angle restraints: 8449 sinusoidal: 3411 harmonic: 5038 Sorted by residual: dihedral pdb=" O3B GTP B1001 " pdb=" O3A GTP B1001 " pdb=" PB GTP B1001 " pdb=" PA GTP B1001 " ideal model delta sinusoidal sigma weight residual -68.92 95.42 -164.34 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C8 GTP B1001 " pdb=" C1' GTP B1001 " pdb=" N9 GTP B1001 " pdb=" O4' GTP B1001 " ideal model delta sinusoidal sigma weight residual 104.59 -55.97 160.57 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' GTP B1001 " pdb=" O5' GTP B1001 " pdb=" PA GTP B1001 " pdb=" O3A GTP B1001 " ideal model delta sinusoidal sigma weight residual 69.27 -63.95 133.22 1 2.00e+01 2.50e-03 4.04e+01 ... (remaining 8446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1360 0.040 - 0.080: 520 0.080 - 0.120: 181 0.120 - 0.161: 33 0.161 - 0.201: 6 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA PHE A 687 " pdb=" N PHE A 687 " pdb=" C PHE A 687 " pdb=" CB PHE A 687 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE A 359 " pdb=" CA ILE A 359 " pdb=" CG1 ILE A 359 " pdb=" CG2 ILE A 359 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA VAL A 217 " pdb=" N VAL A 217 " pdb=" C VAL A 217 " pdb=" CB VAL A 217 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 2097 not shown) Planarity restraints: 2487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A1405 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C THR A1405 " -0.067 2.00e-02 2.50e+03 pdb=" O THR A1405 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL A1406 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1408 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C LEU A1408 " 0.063 2.00e-02 2.50e+03 pdb=" O LEU A1408 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA A1409 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 677 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLU A 677 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 677 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 678 " -0.019 2.00e-02 2.50e+03 ... (remaining 2484 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 103 2.50 - 3.10: 11015 3.10 - 3.70: 20854 3.70 - 4.30: 29710 4.30 - 4.90: 47318 Nonbonded interactions: 109000 Sorted by model distance: nonbonded pdb=" O2B GTP B1001 " pdb="MG MG B1002 " model vdw 1.901 2.170 nonbonded pdb=" O3G GTP B1001 " pdb="MG MG B1002 " model vdw 2.002 2.170 nonbonded pdb=" OG1 THR B 31 " pdb=" OG1 THR B 48 " model vdw 2.092 2.440 nonbonded pdb=" O1A GTP B1001 " pdb="MG MG B1002 " model vdw 2.103 2.170 nonbonded pdb=" OD1 ASP A1318 " pdb=" NH1 ARG A1345 " model vdw 2.148 2.520 ... (remaining 108995 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.40 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.900 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: 6.390 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 40.530 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0320 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 : 0.004 0.039 13967 Z= 0.283 Angle : 0.875 7.940 18915 Z= 0.499 Chirality : 0.048 0.201 2100 Planarity : 0.009 0.097 2487 Dihedral : 14.212 164.342 5207 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.18), residues: 1729 helix: -1.36 (0.15), residues: 817 sheet: -0.48 (0.33), residues: 196 loop : -1.31 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 556 HIS 0.015 0.002 HIS A 63 PHE 0.033 0.003 PHE A 823 TYR 0.029 0.005 TYR A 820 ARG 0.024 0.003 ARG A1208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.5491 (mt) cc_final: -0.6056 (mt) REVERT: A 56 LEU cc_start: 0.6403 (tp) cc_final: 0.6096 (tp) REVERT: A 233 MET cc_start: 0.3090 (mtt) cc_final: 0.2830 (mmm) REVERT: A 421 GLU cc_start: 0.3242 (tp30) cc_final: 0.1670 (mt-10) REVERT: A 437 MET cc_start: 0.7694 (ttt) cc_final: 0.7283 (tmm) REVERT: A 519 ILE cc_start: 0.0065 (mt) cc_final: -0.2672 (mm) REVERT: A 541 ASN cc_start: 0.4731 (t0) cc_final: 0.4304 (t0) REVERT: A 544 LYS cc_start: 0.4106 (mttt) cc_final: 0.3823 (mttt) REVERT: A 555 VAL cc_start: 0.1530 (t) cc_final: 0.1303 (p) REVERT: A 780 ILE cc_start: 0.1706 (mt) cc_final: -0.0004 (mm) REVERT: A 954 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7467 (ttt180) REVERT: A 1210 ASN cc_start: 0.7834 (m-40) cc_final: 0.6916 (t0) REVERT: A 1245 VAL cc_start: 0.7177 (m) cc_final: 0.5161 (m) REVERT: A 1404 MET cc_start: -0.2311 (tpp) cc_final: -0.3653 (tpp) REVERT: A 1513 PHE cc_start: -0.3203 (m-80) cc_final: -0.3444 (m-80) REVERT: B 113 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9123 (tp30) REVERT: B 146 HIS cc_start: 0.7079 (m-70) cc_final: 0.6575 (p90) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.3133 time to fit residues: 134.1284 Evaluate side-chains 178 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 135 optimal weight: 0.1980 chunk 52 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 432 GLN A 509 GLN A 549 GLN A 756 GLN A1070 GLN A1142 HIS A1526 HIS B 52 ASN B 128 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0468 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13967 Z= 0.243 Angle : 0.678 9.127 18915 Z= 0.363 Chirality : 0.043 0.243 2100 Planarity : 0.005 0.075 2487 Dihedral : 9.291 157.668 1926 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.14 % Allowed : 1.84 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1729 helix: 0.19 (0.18), residues: 817 sheet: -0.52 (0.34), residues: 192 loop : -0.45 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 556 HIS 0.010 0.001 HIS A 63 PHE 0.017 0.002 PHE A 827 TYR 0.016 0.002 TYR A1046 ARG 0.010 0.001 ARG A1278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.5843 (mt) cc_final: -0.6517 (mt) REVERT: A 432 GLN cc_start: 0.1036 (OUTLIER) cc_final: -0.0282 (pm20) REVERT: A 541 ASN cc_start: 0.4758 (t0) cc_final: 0.4349 (t0) REVERT: A 602 TYR cc_start: -0.5882 (t80) cc_final: -0.6234 (t80) REVERT: A 780 ILE cc_start: 0.1548 (mt) cc_final: 0.1102 (mm) REVERT: A 867 ASP cc_start: -0.2781 (m-30) cc_final: -0.2986 (m-30) REVERT: A 954 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7345 (tpt-90) REVERT: A 1210 ASN cc_start: 0.7659 (m-40) cc_final: 0.6726 (t0) REVERT: A 1288 ILE cc_start: 0.7230 (mt) cc_final: 0.6907 (mm) REVERT: A 1420 VAL cc_start: 0.3742 (p) cc_final: 0.3536 (p) REVERT: B 146 HIS cc_start: 0.7074 (m-70) cc_final: 0.6596 (p90) outliers start: 2 outliers final: 0 residues processed: 218 average time/residue: 0.2955 time to fit residues: 90.8601 Evaluate side-chains 143 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 43 optimal weight: 0.0470 chunk 157 optimal weight: 0.7980 chunk 170 optimal weight: 30.0000 chunk 140 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 509 GLN A1100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0446 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13967 Z= 0.156 Angle : 0.613 8.181 18915 Z= 0.319 Chirality : 0.041 0.183 2100 Planarity : 0.005 0.052 2487 Dihedral : 8.738 168.512 1926 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.14 % Allowed : 1.36 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1729 helix: 0.60 (0.18), residues: 814 sheet: -0.56 (0.35), residues: 186 loop : -0.32 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 556 HIS 0.007 0.001 HIS A 119 PHE 0.020 0.002 PHE A1244 TYR 0.031 0.001 TYR A 433 ARG 0.008 0.000 ARG A1294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLN cc_start: 0.0661 (OUTLIER) cc_final: -0.0330 (pm20) REVERT: A 725 ASP cc_start: -0.3068 (t0) cc_final: -0.3539 (t0) REVERT: A 780 ILE cc_start: 0.1298 (mt) cc_final: 0.0843 (mm) REVERT: A 867 ASP cc_start: -0.3308 (m-30) cc_final: -0.3522 (m-30) REVERT: A 954 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7495 (ttt90) REVERT: A 1288 ILE cc_start: 0.7002 (mt) cc_final: 0.6648 (mm) REVERT: A 1420 VAL cc_start: 0.3617 (p) cc_final: 0.3399 (p) REVERT: A 1527 LEU cc_start: 0.2275 (mt) cc_final: 0.1840 (mm) REVERT: B 146 HIS cc_start: 0.7165 (m-70) cc_final: 0.6681 (p90) REVERT: B 150 HIS cc_start: 0.6936 (m170) cc_final: 0.6560 (m-70) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.3184 time to fit residues: 87.3942 Evaluate side-chains 143 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0501 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13967 Z= 0.203 Angle : 0.595 8.109 18915 Z= 0.311 Chirality : 0.041 0.356 2100 Planarity : 0.005 0.100 2487 Dihedral : 8.379 173.066 1926 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1729 helix: 0.63 (0.18), residues: 813 sheet: -0.54 (0.34), residues: 190 loop : -0.34 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 556 HIS 0.008 0.001 HIS A 821 PHE 0.016 0.002 PHE A 8 TYR 0.026 0.002 TYR A1398 ARG 0.008 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLN cc_start: 0.0559 (OUTLIER) cc_final: -0.0263 (pm20) REVERT: A 486 LEU cc_start: 0.8134 (tt) cc_final: 0.7680 (mt) REVERT: A 598 LEU cc_start: 0.2641 (mm) cc_final: 0.2186 (mm) REVERT: A 725 ASP cc_start: -0.2181 (t0) cc_final: -0.2436 (t0) REVERT: A 780 ILE cc_start: 0.1065 (mt) cc_final: 0.0606 (mm) REVERT: A 867 ASP cc_start: -0.3166 (m-30) cc_final: -0.3372 (m-30) REVERT: A 1288 ILE cc_start: 0.7015 (mt) cc_final: 0.6685 (mm) REVERT: A 1420 VAL cc_start: 0.3798 (p) cc_final: 0.3580 (p) REVERT: B 146 HIS cc_start: 0.7184 (m-70) cc_final: 0.6613 (p90) REVERT: B 150 HIS cc_start: 0.6984 (m170) cc_final: 0.6588 (m-70) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.2918 time to fit residues: 71.9157 Evaluate side-chains 128 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 0.9990 chunk 94 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 42 optimal weight: 0.0470 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 509 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1583 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0466 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13967 Z= 0.145 Angle : 0.574 8.236 18915 Z= 0.297 Chirality : 0.040 0.169 2100 Planarity : 0.004 0.047 2487 Dihedral : 7.957 160.774 1926 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1729 helix: 0.74 (0.18), residues: 803 sheet: -0.53 (0.35), residues: 182 loop : -0.36 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 66 HIS 0.006 0.001 HIS A 119 PHE 0.021 0.001 PHE A1244 TYR 0.023 0.001 TYR B 35 ARG 0.015 0.001 ARG A1351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.5120 (mt) cc_final: -0.6066 (mt) REVERT: A 432 GLN cc_start: 0.0791 (OUTLIER) cc_final: 0.0186 (pm20) REVERT: A 514 LEU cc_start: 0.4632 (mt) cc_final: 0.4289 (mt) REVERT: A 954 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7691 (ttt90) REVERT: A 1224 LEU cc_start: 0.0958 (tt) cc_final: 0.0692 (tt) REVERT: A 1288 ILE cc_start: 0.7000 (mt) cc_final: 0.6665 (mm) REVERT: A 1420 VAL cc_start: 0.3774 (p) cc_final: 0.3422 (p) REVERT: A 1527 LEU cc_start: 0.1527 (mt) cc_final: 0.1275 (mm) REVERT: B 146 HIS cc_start: 0.7170 (m-70) cc_final: 0.6590 (p90) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.2829 time to fit residues: 70.2216 Evaluate side-chains 135 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 167 optimal weight: 40.0000 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 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 13 ASN A 43 GLN A 432 GLN A 509 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0518 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13967 Z= 0.189 Angle : 0.582 7.674 18915 Z= 0.302 Chirality : 0.040 0.156 2100 Planarity : 0.004 0.048 2487 Dihedral : 7.729 151.522 1926 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 0.14 % Allowed : 1.23 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1729 helix: 0.73 (0.18), residues: 806 sheet: -0.47 (0.35), residues: 192 loop : -0.31 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 556 HIS 0.009 0.001 HIS A 119 PHE 0.015 0.002 PHE A 30 TYR 0.017 0.001 TYR B 35 ARG 0.018 0.001 ARG A1240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLN cc_start: 0.1167 (OUTLIER) cc_final: 0.0615 (pm20) REVERT: A 946 THR cc_start: -0.5790 (m) cc_final: -0.6456 (p) REVERT: A 954 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7535 (ttt180) REVERT: A 1288 ILE cc_start: 0.7037 (mt) cc_final: 0.6684 (mm) REVERT: A 1420 VAL cc_start: 0.3976 (p) cc_final: 0.3738 (p) REVERT: B 146 HIS cc_start: 0.7281 (m-70) cc_final: 0.6620 (p90) REVERT: B 171 ASP cc_start: 0.8376 (t70) cc_final: 0.8160 (t0) outliers start: 2 outliers final: 0 residues processed: 160 average time/residue: 0.2713 time to fit residues: 63.7810 Evaluate side-chains 123 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 166 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0496 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13967 Z= 0.138 Angle : 0.554 7.397 18915 Z= 0.285 Chirality : 0.039 0.172 2100 Planarity : 0.004 0.047 2487 Dihedral : 7.538 148.081 1926 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 0.07 % Allowed : 1.16 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1729 helix: 0.78 (0.19), residues: 804 sheet: -0.40 (0.35), residues: 195 loop : -0.23 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 556 HIS 0.008 0.001 HIS A 119 PHE 0.010 0.001 PHE A 30 TYR 0.016 0.001 TYR B 35 ARG 0.010 0.000 ARG A1240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.5292 (mt) cc_final: -0.5506 (mt) REVERT: A 432 GLN cc_start: 0.0871 (OUTLIER) cc_final: 0.0484 (pm20) REVERT: A 848 MET cc_start: 0.0095 (tmm) cc_final: -0.0123 (tmm) REVERT: A 954 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7548 (ttt180) REVERT: A 1346 ILE cc_start: -0.2815 (mt) cc_final: -0.3300 (mt) REVERT: A 1420 VAL cc_start: 0.3837 (p) cc_final: 0.3458 (p) REVERT: B 146 HIS cc_start: 0.7299 (m-70) cc_final: 0.6619 (p90) REVERT: B 171 ASP cc_start: 0.8328 (t70) cc_final: 0.8119 (t0) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2945 time to fit residues: 70.3048 Evaluate side-chains 122 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 0.0010 chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 131 optimal weight: 9.9990 chunk 151 optimal weight: 0.0170 overall best weight: 1.3028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 ASN ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0507 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13967 Z= 0.145 Angle : 0.553 8.693 18915 Z= 0.286 Chirality : 0.039 0.161 2100 Planarity : 0.004 0.047 2487 Dihedral : 7.444 148.285 1926 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 0.07 % Allowed : 0.75 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1729 helix: 0.75 (0.18), residues: 804 sheet: -0.28 (0.36), residues: 195 loop : -0.23 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 556 HIS 0.008 0.001 HIS A 119 PHE 0.035 0.001 PHE A1424 TYR 0.016 0.001 TYR B 35 ARG 0.006 0.000 ARG A1208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 954 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7570 (ttt180) REVERT: B 146 HIS cc_start: 0.7347 (m-70) cc_final: 0.6619 (p90) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.2731 time to fit residues: 63.7541 Evaluate side-chains 120 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 67 optimal weight: 0.0970 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0515 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13967 Z= 0.152 Angle : 0.566 8.134 18915 Z= 0.290 Chirality : 0.039 0.169 2100 Planarity : 0.004 0.047 2487 Dihedral : 7.414 149.112 1926 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1729 helix: 0.77 (0.18), residues: 806 sheet: -0.23 (0.36), residues: 200 loop : -0.27 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 556 HIS 0.007 0.001 HIS A 119 PHE 0.016 0.001 PHE A1384 TYR 0.028 0.001 TYR A 433 ARG 0.005 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.4812 (mt) cc_final: -0.5173 (mt) REVERT: A 432 GLN cc_start: 0.0638 (OUTLIER) cc_final: -0.0218 (pm20) REVERT: A 954 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7559 (ttt180) REVERT: A 1404 MET cc_start: -0.2125 (ttm) cc_final: -0.2371 (ttm) REVERT: B 146 HIS cc_start: 0.7365 (m-70) cc_final: 0.6652 (p90) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.2739 time to fit residues: 62.8002 Evaluate side-chains 127 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN A 432 GLN A 517 ASN A 575 ASN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 GLN A1095 GLN ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0605 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13967 Z= 0.327 Angle : 0.715 10.762 18915 Z= 0.379 Chirality : 0.043 0.163 2100 Planarity : 0.005 0.048 2487 Dihedral : 7.888 153.326 1926 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1729 helix: 0.31 (0.18), residues: 796 sheet: -0.29 (0.38), residues: 189 loop : -0.49 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 556 HIS 0.008 0.002 HIS A 821 PHE 0.028 0.003 PHE A 30 TYR 0.026 0.002 TYR A 433 ARG 0.010 0.001 ARG A1531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLN cc_start: 0.0570 (OUTLIER) cc_final: 0.0155 (pm20) REVERT: A 954 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7351 (ttt180) REVERT: A 1083 MET cc_start: 0.3228 (tpt) cc_final: 0.2729 (tpp) REVERT: B 81 TYR cc_start: 0.7076 (m-10) cc_final: 0.6502 (m-80) REVERT: B 146 HIS cc_start: 0.7443 (m-70) cc_final: 0.6626 (p-80) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.2673 time to fit residues: 57.2624 Evaluate side-chains 103 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 57 optimal weight: 0.0570 chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN A 432 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 HIS ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.270985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.227364 restraints weight = 100858.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.228925 restraints weight = 87633.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.228947 restraints weight = 76198.798| |-----------------------------------------------------------------------------| r_work (final): 0.4838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4838 r_free = 0.4838 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5831 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4434 r_free = 0.4434 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7351 | |-----------------------------------------------------------------------------| r_final: 0.4434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0355 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13967 Z= 0.203 Angle : 0.607 7.478 18915 Z= 0.317 Chirality : 0.041 0.172 2100 Planarity : 0.004 0.048 2487 Dihedral : 7.769 155.592 1926 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1729 helix: 0.52 (0.18), residues: 798 sheet: -0.20 (0.39), residues: 189 loop : -0.44 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 556 HIS 0.007 0.001 HIS A 119 PHE 0.016 0.002 PHE A 30 TYR 0.023 0.002 TYR A 433 ARG 0.007 0.001 ARG A1351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2997.46 seconds wall clock time: 53 minutes 42.93 seconds (3222.93 seconds total)