Starting phenix.real_space_refine (version: dev) on Mon Dec 12 07:58:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eio_28160/12_2022/8eio_28160_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eio_28160/12_2022/8eio_28160.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eio_28160/12_2022/8eio_28160_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eio_28160/12_2022/8eio_28160_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eio_28160/12_2022/8eio_28160_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eio_28160/12_2022/8eio_28160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eio_28160/12_2022/8eio_28160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eio_28160/12_2022/8eio_28160_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eio_28160/12_2022/8eio_28160_updated.pdb" } resolution = 2.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9550 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 9287 Classifications: {'peptide': 1162} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1130} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 178 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'D12': 1, 'VX8': 1, 'WJX': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 6.09, per 1000 atoms: 0.64 Number of scatterers: 9550 At special positions: 0 Unit cell: (76.388, 83.824, 143.988, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 F 5 9.00 O 1680 8.00 N 1581 7.00 C 6228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 4 sheets defined 65.4% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 removed outlier: 3.516A pdb=" N LYS A 8 " --> pdb=" O PRO A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 8' Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 18 through 29 Proline residue: A 22 - end of helix removed outlier: 3.701A pdb=" N ARG A 25 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 26 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 27 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 28 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 29 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 63 removed outlier: 3.996A pdb=" N ARG A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 96 removed outlier: 3.558A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 4.023A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 166 removed outlier: 3.830A pdb=" N ILE A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.908A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 4.147A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYS A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 174' Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.877A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 218 removed outlier: 3.953A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TRP A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 3.520A pdb=" N GLY A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 267 removed outlier: 3.755A pdb=" N GLY A 228 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 237 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 245 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 253 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 256 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 260 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET A 265 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 278 through 328 removed outlier: 3.517A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.503A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.800A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.672A pdb=" N LEU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.904A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 580 through 589 Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.634A pdb=" N LYS A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 612' Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 847 through 853 Processing helix chain 'A' and resid 857 through 884 Processing helix chain 'A' and resid 909 through 926 removed outlier: 3.780A pdb=" N SER A 912 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR A 913 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP A 924 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 958 removed outlier: 3.609A pdb=" N LEU A 935 " --> pdb=" O PHE A 931 " (cutoff:3.500A) Proline residue: A 936 - end of helix removed outlier: 3.536A pdb=" N THR A 943 " --> pdb=" O HIS A 939 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.950A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1011 removed outlier: 3.558A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Proline residue: A 988 - end of helix removed outlier: 3.546A pdb=" N VAL A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1018 No H-bonds generated for 'chain 'A' and resid 1015 through 1018' Processing helix chain 'A' and resid 1020 through 1060 removed outlier: 3.682A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.505A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1068 Processing helix chain 'A' and resid 1071 through 1121 removed outlier: 3.788A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1167 removed outlier: 4.204A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1143 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1257 Processing helix chain 'A' and resid 1279 through 1285 removed outlier: 3.719A pdb=" N LYS A1284 " --> pdb=" O GLN A1280 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A1285 " --> pdb=" O GLN A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1322 Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1348 through 1362 removed outlier: 3.739A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1390 removed outlier: 3.709A pdb=" N GLN A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1407 Processing helix chain 'A' and resid 1427 through 1432 Processing helix chain 'A' and resid 1435 through 1439 Processing helix chain 'A' and resid 1443 through 1449 removed outlier: 3.817A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 16 Processing sheet with id= A, first strand: chain 'A' and resid 446 through 448 Processing sheet with id= B, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.505A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG A 600 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL A 456 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 602 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N GLY A 458 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1232 through 1234 Processing sheet with id= D, first strand: chain 'A' and resid 1420 through 1424 removed outlier: 6.522A pdb=" N VAL A1397 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU A1242 " --> pdb=" O VAL A1397 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A1399 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N GLY A1244 " --> pdb=" O LEU A1399 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1468 1.31 - 1.44: 2646 1.44 - 1.56: 5550 1.56 - 1.69: 13 1.69 - 1.81: 79 Bond restraints: 9756 Sorted by residual: bond pdb=" C19 WJX A1508 " pdb=" S WJX A1508 " ideal model delta sigma weight residual 1.822 1.622 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C2 WJX A1508 " pdb=" C3 WJX A1508 " ideal model delta sigma weight residual 1.345 1.536 -0.191 2.00e-02 2.50e+03 9.13e+01 bond pdb=" N WJX A1508 " pdb=" C5 WJX A1508 " ideal model delta sigma weight residual 1.537 1.363 0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" C1 WJX A1508 " pdb=" C4 WJX A1508 " ideal model delta sigma weight residual 1.362 1.520 -0.158 2.00e-02 2.50e+03 6.26e+01 bond pdb=" C18 WJX A1508 " pdb=" N4 WJX A1508 " ideal model delta sigma weight residual 1.507 1.387 0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 9751 not shown) Histogram of bond angle deviations from ideal: 59.69 - 75.91: 7 75.91 - 92.12: 1 92.12 - 108.34: 349 108.34 - 124.55: 12684 124.55 - 140.77: 185 Bond angle restraints: 13226 Sorted by residual: angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O5' ATP A1503 " ideal model delta sigma weight residual 110.65 69.23 41.42 3.49e+00 8.21e-02 1.41e+02 angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O5' ATP A1504 " ideal model delta sigma weight residual 110.65 69.39 41.26 3.49e+00 8.21e-02 1.40e+02 angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O2A ATP A1503 " ideal model delta sigma weight residual 114.42 74.15 40.27 3.53e+00 8.04e-02 1.30e+02 angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O2A ATP A1504 " ideal model delta sigma weight residual 114.42 75.27 39.15 3.53e+00 8.04e-02 1.23e+02 angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 131.50 8.37 1.00e+00 1.00e+00 7.01e+01 ... (remaining 13221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 5631 28.79 - 57.58: 118 57.58 - 86.38: 9 86.38 - 115.17: 1 115.17 - 143.96: 1 Dihedral angle restraints: 5760 sinusoidal: 2332 harmonic: 3428 Sorted by residual: dihedral pdb=" C13 WJX A1508 " pdb=" O WJX A1508 " pdb=" C12 WJX A1508 " pdb=" N3 WJX A1508 " ideal model delta sinusoidal sigma weight residual 170.93 -45.11 -143.96 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C18 WJX A1508 " pdb=" N4 WJX A1508 " pdb=" S WJX A1508 " pdb=" C19 WJX A1508 " ideal model delta sinusoidal sigma weight residual 147.30 42.83 104.47 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" N LEU A 878 " pdb=" CA LEU A 878 " pdb=" CB LEU A 878 " pdb=" CG LEU A 878 " ideal model delta sinusoidal sigma weight residual -60.00 -116.18 56.18 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 5757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 1518 0.178 - 0.357: 0 0.357 - 0.535: 0 0.535 - 0.713: 0 0.713 - 0.892: 1 Chirality restraints: 1519 Sorted by residual: chirality pdb=" C13 VX8 A1507 " pdb=" C12 VX8 A1507 " pdb=" C14 VX8 A1507 " pdb=" C22 VX8 A1507 " both_signs ideal model delta sigma weight residual True 1.48 -0.58 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA HIS A 139 " pdb=" N HIS A 139 " pdb=" C HIS A 139 " pdb=" CB HIS A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE A1295 " pdb=" N ILE A1295 " pdb=" C ILE A1295 " pdb=" CB ILE A1295 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1516 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 WJX A1508 " -0.162 2.00e-02 2.50e+03 1.67e-01 3.50e+02 pdb=" C6 WJX A1508 " 0.185 2.00e-02 2.50e+03 pdb=" N4 WJX A1508 " -0.216 2.00e-02 2.50e+03 pdb=" O1 WJX A1508 " 0.011 2.00e-02 2.50e+03 pdb=" S WJX A1508 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WJX A1508 " -0.019 2.00e-02 2.50e+03 2.60e-02 1.53e+01 pdb=" C18 WJX A1508 " 0.051 2.00e-02 2.50e+03 pdb=" C5 WJX A1508 " -0.009 2.00e-02 2.50e+03 pdb=" C6 WJX A1508 " -0.009 2.00e-02 2.50e+03 pdb=" C7 WJX A1508 " -0.024 2.00e-02 2.50e+03 pdb=" C8 WJX A1508 " -0.023 2.00e-02 2.50e+03 pdb=" C9 WJX A1508 " -0.005 2.00e-02 2.50e+03 pdb=" N1 WJX A1508 " -0.005 2.00e-02 2.50e+03 pdb=" N2 WJX A1508 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1377 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A1378 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A1378 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1378 " -0.017 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 18 2.57 - 3.15: 7596 3.15 - 3.74: 14070 3.74 - 4.32: 20715 4.32 - 4.90: 33717 Nonbonded interactions: 76116 Sorted by model distance: nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 1.991 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.001 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1502 " model vdw 2.051 2.170 nonbonded pdb=" OE1 GLN A 493 " pdb="MG MG A1501 " model vdw 2.105 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 2.131 2.170 ... (remaining 76111 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6228 2.51 5 N 1581 2.21 5 O 1680 1.98 5 F 5 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.130 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: 18.420 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 29.220 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.200 9756 Z= 0.351 Angle : 1.040 41.418 13226 Z= 0.401 Chirality : 0.045 0.892 1519 Planarity : 0.005 0.167 1604 Dihedral : 11.610 143.960 3542 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.95 % Favored : 98.96 % Rotamer Outliers : 1.09 % 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: -0.27 (0.23), residues: 1152 helix: -0.09 (0.17), residues: 741 sheet: -0.43 (0.58), residues: 84 loop : 0.14 (0.34), residues: 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.185 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 183 average time/residue: 1.3606 time to fit residues: 265.9743 Evaluate side-chains 88 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 0.1580 time to fit residues: 1.9916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 98 GLN A 452 GLN A 609 HIS A 634 GLN A1100 GLN A1238 GLN A1280 GLN A1313 GLN A1375 HIS A1412 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9756 Z= 0.269 Angle : 0.566 7.136 13226 Z= 0.303 Chirality : 0.042 0.160 1519 Planarity : 0.004 0.032 1604 Dihedral : 7.942 130.472 1332 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.44 % Rotamer Outliers : 4.64 % 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: 0.66 (0.24), residues: 1152 helix: 0.83 (0.19), residues: 743 sheet: -0.20 (0.56), residues: 88 loop : -0.02 (0.35), residues: 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 96 time to evaluate : 1.383 Fit side-chains outliers start: 47 outliers final: 7 residues processed: 127 average time/residue: 1.1518 time to fit residues: 158.2402 Evaluate side-chains 85 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.6491 time to fit residues: 3.0612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1035 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9756 Z= 0.196 Angle : 0.491 7.554 13226 Z= 0.262 Chirality : 0.040 0.141 1519 Planarity : 0.004 0.030 1604 Dihedral : 7.807 130.282 1332 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.44 % Rotamer Outliers : 3.66 % 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: 1.00 (0.25), residues: 1152 helix: 1.19 (0.19), residues: 744 sheet: -0.01 (0.56), residues: 88 loop : -0.20 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 1.242 Fit side-chains outliers start: 37 outliers final: 14 residues processed: 123 average time/residue: 1.1542 time to fit residues: 153.6031 Evaluate side-chains 92 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.7901 time to fit residues: 5.8198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 9756 Z= 0.289 Angle : 0.560 6.956 13226 Z= 0.294 Chirality : 0.043 0.164 1519 Planarity : 0.004 0.034 1604 Dihedral : 8.103 130.309 1332 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.26 % Favored : 97.66 % Rotamer Outliers : 4.55 % 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: 0.80 (0.25), residues: 1152 helix: 1.06 (0.19), residues: 742 sheet: -0.10 (0.54), residues: 90 loop : -0.33 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 87 time to evaluate : 1.186 Fit side-chains outliers start: 46 outliers final: 16 residues processed: 123 average time/residue: 1.1039 time to fit residues: 147.4336 Evaluate side-chains 95 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.4518 time to fit residues: 3.1615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 0.0970 chunk 101 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 9756 Z= 0.139 Angle : 0.461 8.424 13226 Z= 0.243 Chirality : 0.038 0.133 1519 Planarity : 0.003 0.030 1604 Dihedral : 7.721 131.027 1332 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.82 % Favored : 98.09 % Rotamer Outliers : 3.56 % 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: 1.28 (0.25), residues: 1152 helix: 1.45 (0.20), residues: 740 sheet: 0.32 (0.57), residues: 88 loop : -0.28 (0.34), residues: 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 89 time to evaluate : 1.221 Fit side-chains outliers start: 36 outliers final: 16 residues processed: 117 average time/residue: 1.1953 time to fit residues: 151.0375 Evaluate side-chains 94 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.6905 time to fit residues: 3.0324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.0670 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 9756 Z= 0.140 Angle : 0.456 8.194 13226 Z= 0.237 Chirality : 0.038 0.132 1519 Planarity : 0.003 0.029 1604 Dihedral : 7.611 130.472 1332 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.08 % Favored : 97.83 % Rotamer Outliers : 3.16 % 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: 1.43 (0.25), residues: 1152 helix: 1.58 (0.20), residues: 739 sheet: 0.40 (0.58), residues: 86 loop : -0.25 (0.34), residues: 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 1.162 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 111 average time/residue: 1.0960 time to fit residues: 132.2928 Evaluate side-chains 94 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 1.1551 time to fit residues: 2.8547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9756 Z= 0.279 Angle : 0.546 7.116 13226 Z= 0.286 Chirality : 0.042 0.150 1519 Planarity : 0.004 0.032 1604 Dihedral : 7.986 130.083 1332 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1152 helix: 1.25 (0.19), residues: 741 sheet: 0.15 (0.56), residues: 90 loop : -0.33 (0.34), residues: 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 85 time to evaluate : 1.207 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 112 average time/residue: 1.1665 time to fit residues: 142.0233 Evaluate side-chains 94 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.7186 time to fit residues: 3.1981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9756 Z= 0.156 Angle : 0.480 8.377 13226 Z= 0.251 Chirality : 0.038 0.131 1519 Planarity : 0.003 0.030 1604 Dihedral : 7.784 131.399 1332 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 3.06 % 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: 1.28 (0.25), residues: 1152 helix: 1.46 (0.20), residues: 745 sheet: 0.30 (0.56), residues: 92 loop : -0.32 (0.34), residues: 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 1.176 Fit side-chains outliers start: 31 outliers final: 17 residues processed: 107 average time/residue: 1.1659 time to fit residues: 135.6144 Evaluate side-chains 96 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.7765 time to fit residues: 3.3323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 9756 Z= 0.128 Angle : 0.458 10.497 13226 Z= 0.236 Chirality : 0.037 0.145 1519 Planarity : 0.003 0.030 1604 Dihedral : 7.517 130.482 1332 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.17 % 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: 1.51 (0.26), residues: 1152 helix: 1.65 (0.20), residues: 746 sheet: 0.56 (0.59), residues: 86 loop : -0.32 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 1.226 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 104 average time/residue: 1.1959 time to fit residues: 134.9143 Evaluate side-chains 94 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 1.5479 time to fit residues: 3.2935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9756 Z= 0.188 Angle : 0.498 9.851 13226 Z= 0.257 Chirality : 0.039 0.138 1519 Planarity : 0.004 0.030 1604 Dihedral : 7.694 129.340 1332 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.98 % 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: 1.36 (0.25), residues: 1152 helix: 1.52 (0.20), residues: 745 sheet: 0.44 (0.57), residues: 91 loop : -0.32 (0.34), residues: 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.120 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 94 average time/residue: 1.1712 time to fit residues: 119.5519 Evaluate side-chains 93 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1902 time to fit residues: 2.1601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 0.0170 chunk 95 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 81 optimal weight: 0.3980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105074 restraints weight = 14009.982| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.70 r_work: 0.3228 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9756 Z= 0.120 Angle : 0.454 9.094 13226 Z= 0.233 Chirality : 0.037 0.140 1519 Planarity : 0.003 0.031 1604 Dihedral : 7.422 129.765 1332 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 1.68 % 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: 1.57 (0.26), residues: 1152 helix: 1.69 (0.20), residues: 746 sheet: 0.66 (0.60), residues: 85 loop : -0.29 (0.33), residues: 321 =============================================================================== Job complete usr+sys time: 3370.70 seconds wall clock time: 60 minutes 55.16 seconds (3655.16 seconds total)