Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 04:10:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9f_29864/08_2023/8g9f_29864_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9f_29864/08_2023/8g9f_29864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9f_29864/08_2023/8g9f_29864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9f_29864/08_2023/8g9f_29864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9f_29864/08_2023/8g9f_29864_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9f_29864/08_2023/8g9f_29864_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 3 6.06 5 S 101 5.16 5 C 11995 2.51 5 N 3198 2.21 5 O 3481 1.98 5 H 18758 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 37540 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 17195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 17195 Classifications: {'peptide': 1063} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1009} Chain breaks: 3 Chain: "B" Number of atoms: 6745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6745 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 23, 'TRANS': 402} Chain breaks: 2 Chain: "C" Number of atoms: 7326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 7326 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain: "D" Number of atoms: 6263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6263 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 18, 'TRANS': 362} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14369 SG CYS A1280 61.486 53.391 120.866 1.00115.64 S ATOM 14415 SG CYS A1283 58.046 52.733 122.141 1.00 79.59 S ATOM 14770 SG CYS A1307 58.950 56.125 121.081 1.00111.08 S ATOM 14842 SG CYS A1312 60.321 54.682 124.271 1.00108.25 S ATOM 15411 SG CYS A1345 42.742 50.419 79.606 1.00 78.37 S ATOM 15487 SG CYS A1350 40.689 47.506 80.314 1.00 63.44 S ATOM 15786 SG CYS A1368 43.655 47.132 78.214 1.00 72.21 S ATOM 15823 SG CYS A1371 40.822 48.796 76.806 1.00 77.96 S ATOM 29868 SG CYS C 373 46.863 89.409 87.870 1.00 60.41 S ATOM 30116 SG CYS C 390 42.263 91.241 83.358 1.00 64.67 S ATOM 30768 SG CYS C 430 44.519 95.150 87.978 1.00 57.98 S ATOM 28526 SG CYS C 293 40.504 90.189 89.184 1.00 72.78 S ATOM 33233 SG CYS D 123 76.416 123.433 28.507 1.00149.94 S ATOM 33243 SG CYS D 124 75.990 121.294 25.324 1.00124.51 S ATOM 33316 SG CYS D 130 79.004 123.041 26.092 1.00110.13 S ATOM 33362 SG CYS D 133 78.316 120.312 28.289 1.00122.86 S Time building chain proxies: 15.47, per 1000 atoms: 0.41 Number of scatterers: 37540 At special positions: 0 Unit cell: (114.8, 157.44, 136.94, 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) Zn 3 29.99 Fe 4 26.01 S 101 16.00 O 3481 8.00 N 3198 7.00 C 11995 6.00 H 18758 1.00 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: 30.84 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 373 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 390 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 430 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 293 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1500 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1283 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1307 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1280 " pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1368 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1350 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1371 " pdb=" ZN D 500 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 130 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 133 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 123 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 124 " Number of angles added : 18 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4414 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 14 sheets defined 41.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain 'A' and resid 410 through 419 Processing helix chain 'A' and resid 421 through 424 No H-bonds generated for 'chain 'A' and resid 421 through 424' Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 659 through 662 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 725 through 732 removed outlier: 3.935A pdb=" N ARG A 729 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 759 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'A' and resid 906 through 926 Processing helix chain 'A' and resid 932 through 957 removed outlier: 4.823A pdb=" N TYR A 953 " --> pdb=" O ALA A 949 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY A 954 " --> pdb=" O ASN A 950 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 989 Processing helix chain 'A' and resid 1011 through 1028 removed outlier: 3.764A pdb=" N SER A1028 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1095 Processing helix chain 'A' and resid 1101 through 1120 Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1145 through 1147 No H-bonds generated for 'chain 'A' and resid 1145 through 1147' Processing helix chain 'A' and resid 1149 through 1160 Processing helix chain 'A' and resid 1191 through 1197 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1212 through 1220 removed outlier: 4.336A pdb=" N ILE A1219 " --> pdb=" O VAL A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1235 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1252 through 1257 Processing helix chain 'A' and resid 1266 through 1269 No H-bonds generated for 'chain 'A' and resid 1266 through 1269' Processing helix chain 'A' and resid 1297 through 1299 No H-bonds generated for 'chain 'A' and resid 1297 through 1299' Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1316 through 1339 removed outlier: 3.835A pdb=" N VAL A1320 " --> pdb=" O LEU A1317 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE A1321 " --> pdb=" O ASP A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1396 removed outlier: 3.734A pdb=" N PHE A1396 " --> pdb=" O TYR A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1403 Processing helix chain 'A' and resid 1408 through 1414 Processing helix chain 'A' and resid 1420 through 1439 removed outlier: 3.570A pdb=" N THR A1432 " --> pdb=" O LYS A1428 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A1433 " --> pdb=" O LEU A1429 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A1439 " --> pdb=" O GLN A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1450 No H-bonds generated for 'chain 'A' and resid 1447 through 1450' Processing helix chain 'B' and resid 213 through 235 Processing helix chain 'B' and resid 276 through 279 No H-bonds generated for 'chain 'B' and resid 276 through 279' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 358 through 370 Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 476 through 481 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'C' and resid 41 through 64 Processing helix chain 'C' and resid 70 through 83 Processing helix chain 'C' and resid 96 through 115 removed outlier: 3.617A pdb=" N PHE C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 140 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 169 through 175 Processing helix chain 'C' and resid 181 through 185 Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 220 through 242 Processing helix chain 'C' and resid 244 through 247 No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'C' and resid 250 through 256 Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 279 through 288 removed outlier: 4.076A pdb=" N ASP C 283 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 303 removed outlier: 3.692A pdb=" N LEU C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 326 through 338 Processing helix chain 'C' and resid 344 through 349 Processing helix chain 'C' and resid 352 through 358 Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 391 through 394 No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 397 through 406 Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 450 through 460 Processing helix chain 'D' and resid 8 through 21 Proline residue: D 12 - end of helix removed outlier: 4.326A pdb=" N LEU D 15 " --> pdb=" O PRO D 12 " (cutoff:3.500A) Proline residue: D 16 - end of helix Processing helix chain 'D' and resid 25 through 36 removed outlier: 5.606A pdb=" N GLY D 35 " --> pdb=" O TRP D 31 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 90 through 95 removed outlier: 5.050A pdb=" N ASN D 94 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 120 removed outlier: 5.236A pdb=" N ASP D 119 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 150 removed outlier: 3.639A pdb=" N ARG D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 No H-bonds generated for 'chain 'D' and resid 174 through 177' Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 212 through 229 removed outlier: 3.579A pdb=" N ARG D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR D 224 " --> pdb=" O MET D 220 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS D 227 " --> pdb=" O ARG D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 248 removed outlier: 4.556A pdb=" N LYS D 244 " --> pdb=" O GLN D 240 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 245 " --> pdb=" O CYS D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 removed outlier: 4.736A pdb=" N GLU D 255 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG D 259 " --> pdb=" O SER D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 280 Processing helix chain 'D' and resid 291 through 300 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 349 through 358 removed outlier: 3.734A pdb=" N ASN D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 385 Processing helix chain 'D' and resid 389 through 408 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.589A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 516 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N SER A 379 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA A 518 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 390 Processing sheet with id= C, first strand: chain 'A' and resid 689 through 692 removed outlier: 6.603A pdb=" N VAL A 547 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE A 557 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL A 558 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 849 through 851 removed outlier: 6.578A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1035 through 1040 removed outlier: 3.918A pdb=" N ASP A1035 " --> pdb=" O ASP A 859 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 857 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE A1039 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE A 855 " --> pdb=" O ILE A1039 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN A1005 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL A 994 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1131 through 1134 Processing sheet with id= G, first strand: chain 'A' and resid 1276 through 1279 Processing sheet with id= H, first strand: chain 'A' and resid 1343 through 1345 Processing sheet with id= I, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.221A pdb=" N VAL B 537 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 472 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 539 " --> pdb=" O THR B 472 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE B 555 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL B 540 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 557 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 283 through 285 removed outlier: 6.320A pdb=" N THR B 307 " --> pdb=" O PRO B 316 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 453 through 456 removed outlier: 6.550A pdb=" N LEU B 420 " --> pdb=" O HIS B 454 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 456 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE B 422 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N CYS B 346 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR B 570 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER B 592 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG B 597 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 170 " --> pdb=" O ARG B 597 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 190 through 193 Processing sheet with id= M, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.591A pdb=" N VAL D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 108 through 113 733 hydrogen bonds defined for protein. 2001 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: 14.91 Time building geometry restraints manager: 31.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 18719 1.13 - 1.42: 7964 1.42 - 1.71: 11127 1.71 - 1.99: 139 1.99 - 2.28: 12 Bond restraints: 37961 Sorted by residual: bond pdb=" CA TYR D 19 " pdb=" C TYR D 19 " ideal model delta sigma weight residual 1.522 1.507 0.015 1.38e-02 5.25e+03 1.14e+00 bond pdb=" CB VAL A 558 " pdb=" CG2 VAL A 558 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.59e-01 bond pdb=" C PHE C 136 " pdb=" O PHE C 136 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.55e-01 bond pdb=" N ARG D 20 " pdb=" CA ARG D 20 " ideal model delta sigma weight residual 1.458 1.446 0.011 1.28e-02 6.10e+03 7.94e-01 bond pdb=" CG PRO B 513 " pdb=" CD PRO B 513 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 7.88e-01 ... (remaining 37956 not shown) Histogram of bond angle deviations from ideal: 73.59 - 85.67: 12 85.67 - 97.75: 0 97.75 - 109.83: 29014 109.83 - 121.91: 33254 121.91 - 133.99: 6435 Bond angle restraints: 68715 Sorted by residual: angle pdb=" CA TRP D 242 " pdb=" CB TRP D 242 " pdb=" CG TRP D 242 " ideal model delta sigma weight residual 113.60 118.91 -5.31 1.90e+00 2.77e-01 7.82e+00 angle pdb=" N GLU C 93 " pdb=" CA GLU C 93 " pdb=" C GLU C 93 " ideal model delta sigma weight residual 110.80 105.20 5.60 2.13e+00 2.20e-01 6.91e+00 angle pdb=" C PRO C 86 " pdb=" N TYR C 87 " pdb=" CA TYR C 87 " ideal model delta sigma weight residual 122.08 118.37 3.71 1.53e+00 4.27e-01 5.89e+00 angle pdb=" N THR B 529 " pdb=" CA THR B 529 " pdb=" C THR B 529 " ideal model delta sigma weight residual 109.81 114.61 -4.80 2.21e+00 2.05e-01 4.71e+00 angle pdb=" N LYS C 104 " pdb=" CA LYS C 104 " pdb=" C LYS C 104 " ideal model delta sigma weight residual 111.02 108.57 2.45 1.22e+00 6.72e-01 4.02e+00 ... (remaining 68710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 13848 17.84 - 35.68: 1079 35.68 - 53.52: 279 53.52 - 71.36: 78 71.36 - 89.20: 30 Dihedral angle restraints: 15314 sinusoidal: 7219 harmonic: 8095 Sorted by residual: dihedral pdb=" CA VAL D 171 " pdb=" C VAL D 171 " pdb=" N CYS D 172 " pdb=" CA CYS D 172 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP A 632 " pdb=" CB ASP A 632 " pdb=" CG ASP A 632 " pdb=" OD1 ASP A 632 " ideal model delta sinusoidal sigma weight residual -30.00 -86.02 56.02 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU B 273 " pdb=" CG GLU B 273 " pdb=" CD GLU B 273 " pdb=" OE1 GLU B 273 " ideal model delta sinusoidal sigma weight residual 0.00 -89.20 89.20 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 15311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1828 0.030 - 0.060: 680 0.060 - 0.090: 195 0.090 - 0.120: 129 0.120 - 0.151: 19 Chirality restraints: 2851 Sorted by residual: chirality pdb=" CA ILE D 80 " pdb=" N ILE D 80 " pdb=" C ILE D 80 " pdb=" CB ILE D 80 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A1004 " pdb=" N ILE A1004 " pdb=" C ILE A1004 " pdb=" CB ILE A1004 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE D 333 " pdb=" N ILE D 333 " pdb=" C ILE D 333 " pdb=" CB ILE D 333 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 2848 not shown) Planarity restraints: 5527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 18 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C TYR D 18 " 0.070 2.00e-02 2.50e+03 pdb=" O TYR D 18 " -0.026 2.00e-02 2.50e+03 pdb=" N TYR D 19 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 88 " -0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO C 89 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 89 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 89 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 145 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C ASP D 145 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP D 145 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG D 146 " -0.014 2.00e-02 2.50e+03 ... (remaining 5524 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1446 2.17 - 2.77: 74222 2.77 - 3.38: 104590 3.38 - 3.99: 137797 3.99 - 4.60: 214400 Nonbonded interactions: 532455 Sorted by model distance: nonbonded pdb="HH21 ARG D 30 " pdb=" OD2 ASP D 403 " model vdw 1.558 1.850 nonbonded pdb=" O LEU A1135 " pdb=" H GLY A1168 " model vdw 1.565 1.850 nonbonded pdb=" O GLN A 397 " pdb=" H GLY A 401 " model vdw 1.571 1.850 nonbonded pdb=" HH TYR D 28 " pdb=" OG SER D 318 " model vdw 1.572 1.850 nonbonded pdb=" OE1 GLU A 416 " pdb=" HG1 THR A 472 " model vdw 1.573 1.850 ... (remaining 532450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 0.560 Extract box with map and model: 17.470 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 134.760 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 19203 Z= 0.211 Angle : 0.496 5.598 25963 Z= 0.276 Chirality : 0.040 0.151 2851 Planarity : 0.004 0.083 3335 Dihedral : 16.164 89.203 7276 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.18), residues: 2299 helix: 0.59 (0.17), residues: 986 sheet: 0.58 (0.30), residues: 280 loop : -0.09 (0.20), residues: 1033 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 3.283 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 1.0447 time to fit residues: 332.9366 Evaluate side-chains 101 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 209 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 GLN A1026 ASN A1107 ASN C 405 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 19203 Z= 0.305 Angle : 0.522 5.048 25963 Z= 0.273 Chirality : 0.040 0.139 2851 Planarity : 0.004 0.049 3335 Dihedral : 4.000 19.525 2539 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.83 (0.18), residues: 2299 helix: 1.20 (0.17), residues: 981 sheet: 0.64 (0.29), residues: 291 loop : 0.01 (0.20), residues: 1027 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 3.167 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 outliers start: 24 outliers final: 10 residues processed: 114 average time/residue: 0.8685 time to fit residues: 144.0958 Evaluate side-chains 94 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4180 time to fit residues: 11.7334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 0.2980 chunk 142 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19203 Z= 0.193 Angle : 0.468 6.339 25963 Z= 0.242 Chirality : 0.039 0.141 2851 Planarity : 0.003 0.041 3335 Dihedral : 3.834 20.050 2539 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.20 (0.18), residues: 2299 helix: 1.59 (0.17), residues: 980 sheet: 0.65 (0.30), residues: 289 loop : 0.16 (0.20), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 3.295 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 outliers start: 7 outliers final: 3 residues processed: 94 average time/residue: 0.8579 time to fit residues: 120.4591 Evaluate side-chains 81 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 2.934 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3968 time to fit residues: 6.2174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 19203 Z= 0.293 Angle : 0.496 6.312 25963 Z= 0.256 Chirality : 0.039 0.132 2851 Planarity : 0.003 0.038 3335 Dihedral : 3.836 19.161 2539 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.13 (0.18), residues: 2299 helix: 1.57 (0.17), residues: 976 sheet: 0.55 (0.29), residues: 299 loop : 0.12 (0.20), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 3.393 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 outliers start: 10 outliers final: 4 residues processed: 87 average time/residue: 0.9115 time to fit residues: 120.5863 Evaluate side-chains 80 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 3.775 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5715 time to fit residues: 9.3365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 3 optimal weight: 0.0040 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19203 Z= 0.221 Angle : 0.462 6.643 25963 Z= 0.238 Chirality : 0.039 0.134 2851 Planarity : 0.003 0.036 3335 Dihedral : 3.771 18.982 2539 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.22 (0.18), residues: 2299 helix: 1.69 (0.17), residues: 976 sheet: 0.50 (0.29), residues: 299 loop : 0.15 (0.20), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 3.411 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 outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.8346 time to fit residues: 105.0629 Evaluate side-chains 76 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3900 time to fit residues: 5.8855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 185 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 19203 Z= 0.255 Angle : 0.471 5.033 25963 Z= 0.242 Chirality : 0.039 0.133 2851 Planarity : 0.003 0.040 3335 Dihedral : 3.752 18.391 2539 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.24 (0.18), residues: 2299 helix: 1.71 (0.17), residues: 976 sheet: 0.57 (0.30), residues: 291 loop : 0.12 (0.20), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 3.215 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 outliers start: 6 outliers final: 3 residues processed: 79 average time/residue: 0.8271 time to fit residues: 98.3976 Evaluate side-chains 74 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4008 time to fit residues: 6.1936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19203 Z= 0.209 Angle : 0.453 5.007 25963 Z= 0.233 Chirality : 0.039 0.134 2851 Planarity : 0.003 0.036 3335 Dihedral : 3.701 18.316 2539 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.18), residues: 2299 helix: 1.80 (0.17), residues: 975 sheet: 0.60 (0.30), residues: 290 loop : 0.21 (0.20), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 2.986 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 outliers start: 4 outliers final: 1 residues processed: 78 average time/residue: 0.8537 time to fit residues: 98.8556 Evaluate side-chains 71 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3904 time to fit residues: 4.7289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 202 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 19203 Z= 0.136 Angle : 0.439 4.933 25963 Z= 0.223 Chirality : 0.039 0.138 2851 Planarity : 0.003 0.035 3335 Dihedral : 3.606 17.924 2539 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.54 (0.18), residues: 2299 helix: 2.00 (0.17), residues: 974 sheet: 0.64 (0.30), residues: 286 loop : 0.29 (0.20), residues: 1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.8747 time to fit residues: 98.6194 Evaluate side-chains 70 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 3.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.0010 chunk 194 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 206 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19203 Z= 0.164 Angle : 0.444 5.749 25963 Z= 0.225 Chirality : 0.038 0.135 2851 Planarity : 0.003 0.035 3335 Dihedral : 3.560 17.761 2539 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.18), residues: 2299 helix: 2.03 (0.17), residues: 975 sheet: 0.66 (0.31), residues: 278 loop : 0.30 (0.20), residues: 1046 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 3.212 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 outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.8633 time to fit residues: 89.4494 Evaluate side-chains 69 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 3.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 9.9990 chunk 133 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 141 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19203 Z= 0.175 Angle : 0.446 5.607 25963 Z= 0.226 Chirality : 0.038 0.134 2851 Planarity : 0.003 0.035 3335 Dihedral : 3.544 17.468 2539 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.59 (0.18), residues: 2299 helix: 2.06 (0.17), residues: 975 sheet: 0.66 (0.31), residues: 278 loop : 0.30 (0.20), residues: 1046 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 3.203 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 outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.8389 time to fit residues: 91.7703 Evaluate side-chains 69 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 3.370 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 188 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.038627 restraints weight = 199005.893| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.12 r_work: 0.2614 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 19203 Z= 0.132 Angle : 0.443 9.860 25963 Z= 0.222 Chirality : 0.038 0.142 2851 Planarity : 0.003 0.035 3335 Dihedral : 3.484 17.281 2539 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.73 (0.18), residues: 2299 helix: 2.17 (0.17), residues: 970 sheet: 0.73 (0.31), residues: 282 loop : 0.37 (0.20), residues: 1047 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6119.26 seconds wall clock time: 110 minutes 24.36 seconds (6624.36 seconds total)