Starting phenix.real_space_refine on Tue Aug 26 14:01:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9f_29864/08_2025/8g9f_29864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9f_29864/08_2025/8g9f_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g9f_29864/08_2025/8g9f_29864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9f_29864/08_2025/8g9f_29864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g9f_29864/08_2025/8g9f_29864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9f_29864/08_2025/8g9f_29864.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.38, per 1000 atoms: 0.20 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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... Secondary structure from input PDB file: 102 helices and 21 sheets defined 49.3% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 658 through 663 Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.657A pdb=" N ASN A 683 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 701 Processing helix chain 'A' and resid 707 through 716 Processing helix chain 'A' and resid 724 through 729 removed outlier: 3.935A pdb=" N ARG A 729 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 733 Processing helix chain 'A' and resid 734 through 760 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 775 through 782 removed outlier: 3.546A pdb=" N GLY A 782 " --> pdb=" O ARG A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 799 removed outlier: 4.054A pdb=" N LEU A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 872 Processing helix chain 'A' and resid 905 through 927 removed outlier: 3.527A pdb=" N GLN A 927 " --> pdb=" O GLN A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 952 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 965 through 990 Processing helix chain 'A' and resid 1010 through 1029 removed outlier: 3.764A pdb=" N SER A1028 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1096 Processing helix chain 'A' and resid 1100 through 1121 Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1144 through 1147 Processing helix chain 'A' and resid 1148 through 1161 removed outlier: 3.693A pdb=" N GLY A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1198 removed outlier: 4.298A pdb=" N GLU A1198 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1210 Processing helix chain 'A' and resid 1211 through 1221 removed outlier: 3.883A pdb=" N VAL A1215 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A1219 " --> pdb=" O VAL A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1238 through 1242 Processing helix chain 'A' and resid 1252 through 1258 Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 4.195A pdb=" N LEU A1264 " --> pdb=" O PRO A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1270 Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1304 through 1306 No H-bonds generated for 'chain 'A' and resid 1304 through 1306' Processing helix chain 'A' and resid 1315 through 1318 Processing helix chain 'A' and resid 1319 through 1340 Processing helix chain 'A' and resid 1381 through 1395 Processing helix chain 'A' and resid 1397 through 1404 Processing helix chain 'A' and resid 1407 through 1415 Processing helix chain 'A' and resid 1419 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 1451 Processing helix chain 'B' and resid 212 through 236 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.862A pdb=" N PHE B 334 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 371 Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 397 through 413 Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'C' and resid 41 through 65 Processing helix chain 'C' and resid 69 through 84 Processing helix chain 'C' and resid 95 through 116 removed outlier: 3.617A pdb=" N PHE C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 140 Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 161 through 168 Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 180 through 186 Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 219 through 242 removed outlier: 3.572A pdb=" N ILE C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 4.007A pdb=" N SER C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 278 through 289 removed outlier: 3.774A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 304 removed outlier: 3.692A pdb=" N LEU C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 323 Processing helix chain 'C' and resid 325 through 339 Processing helix chain 'C' and resid 343 through 350 Processing helix chain 'C' and resid 351 through 359 Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 396 through 407 Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 425 through 438 Processing helix chain 'C' and resid 449 through 461 Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 10 through 22 Proline residue: D 16 - end of helix Processing helix chain 'D' and resid 24 through 34 Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 64 through 76 Processing helix chain 'D' and resid 89 through 96 removed outlier: 5.050A pdb=" N ASN D 94 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 121 removed outlier: 5.236A pdb=" N ASP D 119 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 121 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 151 removed outlier: 4.359A pdb=" N MET D 137 " --> pdb=" O CYS D 133 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 178 Processing helix chain 'D' and resid 180 through 192 Processing helix chain 'D' and resid 211 through 230 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 238 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 250 through 263 removed outlier: 3.802A pdb=" N ARG D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU D 255 " --> pdb=" O GLU D 251 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 260 " --> pdb=" O SER D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 281 Processing helix chain 'D' and resid 286 through 289 Processing helix chain 'D' and resid 290 through 301 Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.673A pdb=" N SER D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY D 311 " --> pdb=" O ASN D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 removed outlier: 4.529A pdb=" N ASP D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 357 Processing helix chain 'D' and resid 381 through 386 Processing helix chain 'D' and resid 388 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 516 through 520 removed outlier: 9.419A pdb=" N VAL A 516 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER A 375 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ALA A 518 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS A 377 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL A 520 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER A 379 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 430 through 438 removed outlier: 7.695A pdb=" N GLU A 451 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS A 475 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 394 through 397 removed outlier: 6.181A pdb=" N ARG A 395 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS A 402 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 609 through 612 removed outlier: 8.588A pdb=" N GLU A 610 " --> pdb=" O HIS A 582 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS A 584 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA A 612 " --> pdb=" O CYS A 584 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A 586 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL A 558 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS A 545 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE A 560 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER A 543 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA A 562 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER A 541 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A 564 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 539 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N HIS A 566 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL A 537 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 634 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 851 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: 6.701A pdb=" N SER A1001 " --> pdb=" O GLY A 997 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY A 997 " --> pdb=" O SER A1001 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET A1003 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 851 removed outlier: 18.066A pdb=" N ASP A1037 " --> pdb=" O GLY A1060 " (cutoff:3.500A) removed outlier: 14.703A pdb=" N GLY A1060 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N ILE A1039 " --> pdb=" O PRO A1058 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LYS A1041 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N VAL A1056 " --> pdb=" O LYS A1041 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A1043 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU A1054 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU A1045 " --> pdb=" O ALA A1052 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA A1052 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1131 through 1134 Processing sheet with id=AA8, first strand: chain 'A' and resid 1131 through 1134 Processing sheet with id=AA9, first strand: chain 'A' and resid 1276 through 1279 Processing sheet with id=AB1, first strand: chain 'A' and resid 1293 through 1294 Processing sheet with id=AB2, first strand: chain 'A' and resid 1353 through 1354 Processing sheet with id=AB3, first strand: chain 'A' and resid 1444 through 1446 Processing sheet with id=AB4, first strand: chain 'B' and resid 170 through 175 removed outlier: 6.633A pdb=" N VAL B 170 " --> pdb=" O ARG B 597 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG B 597 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER B 592 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR B 570 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N CYS B 346 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS B 375 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL B 423 " --> pdb=" O CYS B 375 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 377 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 420 " --> pdb=" O HIS B 454 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.600A pdb=" N VAL B 468 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE B 539 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 470 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 283 through 285 removed outlier: 6.434A pdb=" N GLU B 249 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY B 306 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 251 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET B 304 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 253 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 302 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE B 303 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU B 319 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU B 305 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AB8, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 159 Processing sheet with id=AC1, first strand: chain 'D' and resid 55 through 60 removed outlier: 3.591A pdb=" N VAL D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR D 59 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE D 47 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA D 84 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER D 48 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE D 82 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR D 50 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE D 80 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 55 through 60 removed outlier: 3.591A pdb=" N VAL D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR D 59 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE D 47 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA D 84 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER D 48 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE D 82 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR D 50 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE D 80 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 108 through 113 899 hydrogen bonds defined for protein. 2508 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: 10.86 Time building geometry restraints manager: 5.07 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: 0.00 - 1.12: 65252 1.12 - 2.24: 3270 2.24 - 3.36: 136 3.36 - 4.48: 53 4.48 - 5.60: 4 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: 16038 17.84 - 35.68: 1237 35.68 - 53.52: 449 53.52 - 71.36: 104 71.36 - 89.20: 30 Dihedral angle restraints: 17858 sinusoidal: 9763 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 17855 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: 1385 2.17 - 2.77: 74091 2.77 - 3.38: 104475 3.38 - 3.99: 137572 3.99 - 4.60: 214165 Nonbonded interactions: 531688 Sorted by model distance: nonbonded pdb="HH21 ARG D 30 " pdb=" OD2 ASP D 403 " model vdw 1.558 2.450 nonbonded pdb=" O LEU A1135 " pdb=" H GLY A1168 " model vdw 1.565 2.450 nonbonded pdb=" O GLN A 397 " pdb=" H GLY A 401 " model vdw 1.571 2.450 nonbonded pdb=" HH TYR D 28 " pdb=" OG SER D 318 " model vdw 1.572 2.450 nonbonded pdb=" OE1 GLU A 416 " pdb=" HG1 THR A 472 " model vdw 1.573 2.450 ... (remaining 531683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.100 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: 0.260 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 57.590 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.530 ------------------------------------------------------------------------------- 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 : 0.004 0.190 19219 Z= 0.169 Angle : 0.528 14.667 25993 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 % Allowed : 14.58 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 88 TYR 0.014 0.001 TYR D 117 PHE 0.012 0.001 PHE A 341 TRP 0.017 0.001 TRP D 170 HIS 0.005 0.001 HIS B 386 Details of bonding type rmsd covalent geometry : bond 0.00324 (19203) covalent geometry : angle 0.49591 (25963) hydrogen bonds : bond 0.13139 ( 887) hydrogen bonds : angle 6.24641 ( 2508) metal coordination : bond 0.07057 ( 16) metal coordination : angle 5.34693 ( 30) *********************** 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 to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.149 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 revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.5550 time to fit residues: 174.5046 Evaluate side-chains 103 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 869 GLN A1026 ASN A1107 ASN C 168 HIS C 405 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.039813 restraints weight = 201480.641| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.32 r_work: 0.2643 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 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 : 0.004 0.040 19219 Z= 0.160 Angle : 0.537 7.704 25993 Z= 0.279 Chirality : 0.040 0.148 2851 Planarity : 0.004 0.048 3335 Dihedral : 4.083 19.411 2539 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.04 % Allowed : 15.43 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.18), residues: 2299 helix: 1.49 (0.17), residues: 981 sheet: 0.64 (0.30), residues: 281 loop : -0.01 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 19 TYR 0.014 0.001 TYR A 732 PHE 0.011 0.001 PHE D 29 TRP 0.012 0.001 TRP D 242 HIS 0.012 0.001 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.00352 (19203) covalent geometry : angle 0.52475 (25963) hydrogen bonds : bond 0.04425 ( 887) hydrogen bonds : angle 5.07177 ( 2508) metal coordination : bond 0.00687 ( 16) metal coordination : angle 3.44469 ( 30) *********************** 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 124 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: B 484 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: D 75 MET cc_start: 0.8406 (mpp) cc_final: 0.8102 (mpp) outliers start: 22 outliers final: 5 residues processed: 122 average time/residue: 0.4304 time to fit residues: 75.5118 Evaluate side-chains 98 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 220 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 227 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.051839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.038453 restraints weight = 203380.306| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.15 r_work: 0.2587 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19219 Z= 0.219 Angle : 0.525 7.448 25993 Z= 0.270 Chirality : 0.040 0.147 2851 Planarity : 0.004 0.063 3335 Dihedral : 4.034 20.129 2539 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.76 % Allowed : 15.10 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.18), residues: 2299 helix: 1.68 (0.17), residues: 989 sheet: 0.52 (0.29), residues: 287 loop : -0.01 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 19 TYR 0.014 0.001 TYR A 732 PHE 0.011 0.001 PHE D 29 TRP 0.013 0.001 TRP D 242 HIS 0.005 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00475 (19203) covalent geometry : angle 0.51397 (25963) hydrogen bonds : bond 0.04004 ( 887) hydrogen bonds : angle 4.82091 ( 2508) metal coordination : bond 0.01180 ( 16) metal coordination : angle 3.14659 ( 30) *********************** 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 106 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1418 LEU cc_start: 0.9288 (mp) cc_final: 0.9027 (tp) REVERT: B 484 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8489 (tm-30) REVERT: D 114 MET cc_start: 0.8236 (tpp) cc_final: 0.7986 (tpp) outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 0.3882 time to fit residues: 57.7485 Evaluate side-chains 88 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 158 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 153 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 162 optimal weight: 0.4980 chunk 192 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 212 optimal weight: 0.0030 chunk 8 optimal weight: 2.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.052667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.039213 restraints weight = 197693.489| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.13 r_work: 0.2645 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19219 Z= 0.102 Angle : 0.478 7.514 25993 Z= 0.243 Chirality : 0.039 0.147 2851 Planarity : 0.004 0.043 3335 Dihedral : 3.913 19.499 2539 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.47 % Allowed : 14.67 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.18), residues: 2299 helix: 1.94 (0.17), residues: 989 sheet: 0.55 (0.30), residues: 287 loop : 0.12 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.012 0.001 TYR A 732 PHE 0.011 0.001 PHE C 44 TRP 0.014 0.001 TRP D 242 HIS 0.004 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00232 (19203) covalent geometry : angle 0.46757 (25963) hydrogen bonds : bond 0.03529 ( 887) hydrogen bonds : angle 4.55247 ( 2508) metal coordination : bond 0.00452 ( 16) metal coordination : angle 3.00258 ( 30) *********************** 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 95 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.977 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: A 1418 LEU cc_start: 0.9207 (mp) cc_final: 0.8996 (tp) REVERT: D 114 MET cc_start: 0.8050 (tpp) cc_final: 0.7814 (tpp) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 0.3763 time to fit residues: 52.9759 Evaluate side-chains 85 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 186 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.051293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.037752 restraints weight = 201121.693| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.13 r_work: 0.2600 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19219 Z= 0.209 Angle : 0.505 8.641 25993 Z= 0.258 Chirality : 0.039 0.138 2851 Planarity : 0.004 0.041 3335 Dihedral : 3.932 18.621 2539 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.66 % Allowed : 14.48 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.18), residues: 2299 helix: 1.89 (0.17), residues: 992 sheet: 0.38 (0.29), residues: 292 loop : 0.00 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.012 0.001 TYR A 732 PHE 0.009 0.001 PHE C 44 TRP 0.012 0.001 TRP D 242 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00456 (19203) covalent geometry : angle 0.49273 (25963) hydrogen bonds : bond 0.03591 ( 887) hydrogen bonds : angle 4.59360 ( 2508) metal coordination : bond 0.00977 ( 16) metal coordination : angle 3.25714 ( 30) *********************** 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 94 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1418 LEU cc_start: 0.9236 (mp) cc_final: 0.9013 (tp) outliers start: 14 outliers final: 10 residues processed: 92 average time/residue: 0.4407 time to fit residues: 59.7127 Evaluate side-chains 86 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1416 LYS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 419 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 103 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 212 optimal weight: 0.0570 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.038206 restraints weight = 199448.364| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.18 r_work: 0.2614 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19219 Z= 0.111 Angle : 0.466 8.489 25993 Z= 0.236 Chirality : 0.039 0.140 2851 Planarity : 0.003 0.039 3335 Dihedral : 3.835 17.990 2539 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.47 % Allowed : 14.72 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.18), residues: 2299 helix: 2.09 (0.17), residues: 991 sheet: 0.45 (0.29), residues: 293 loop : 0.08 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 312 TYR 0.011 0.001 TYR A 732 PHE 0.010 0.001 PHE C 44 TRP 0.013 0.001 TRP D 242 HIS 0.004 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00247 (19203) covalent geometry : angle 0.45313 (25963) hydrogen bonds : bond 0.03348 ( 887) hydrogen bonds : angle 4.40297 ( 2508) metal coordination : bond 0.00551 ( 16) metal coordination : angle 3.18681 ( 30) *********************** 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 90 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1418 LEU cc_start: 0.9213 (mp) cc_final: 0.8991 (tp) REVERT: D 114 MET cc_start: 0.8182 (tpp) cc_final: 0.7959 (tpp) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.3897 time to fit residues: 51.6388 Evaluate side-chains 85 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1416 LYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 419 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.051146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.037754 restraints weight = 201482.785| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.10 r_work: 0.2593 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19219 Z= 0.182 Angle : 0.486 9.506 25993 Z= 0.247 Chirality : 0.039 0.136 2851 Planarity : 0.004 0.038 3335 Dihedral : 3.854 17.619 2539 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.66 % Allowed : 14.48 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.18), residues: 2299 helix: 2.03 (0.17), residues: 992 sheet: 0.40 (0.30), residues: 282 loop : 0.05 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 312 TYR 0.012 0.001 TYR A 732 PHE 0.010 0.001 PHE C 44 TRP 0.012 0.001 TRP D 242 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00399 (19203) covalent geometry : angle 0.47254 (25963) hydrogen bonds : bond 0.03420 ( 887) hydrogen bonds : angle 4.45016 ( 2508) metal coordination : bond 0.00889 ( 16) metal coordination : angle 3.40317 ( 30) *********************** 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 91 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.155 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: D 114 MET cc_start: 0.8268 (tpp) cc_final: 0.8041 (tpp) outliers start: 14 outliers final: 10 residues processed: 90 average time/residue: 0.3930 time to fit residues: 53.0954 Evaluate side-chains 83 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1416 LYS Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 419 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 216 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 169 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.051345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.037979 restraints weight = 199052.768| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.10 r_work: 0.2599 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19219 Z= 0.139 Angle : 0.471 8.501 25993 Z= 0.238 Chirality : 0.039 0.135 2851 Planarity : 0.003 0.039 3335 Dihedral : 3.805 17.140 2539 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.52 % Allowed : 14.48 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.18), residues: 2299 helix: 2.15 (0.17), residues: 992 sheet: 0.32 (0.29), residues: 289 loop : 0.05 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1163 TYR 0.011 0.001 TYR A 732 PHE 0.010 0.001 PHE C 44 TRP 0.012 0.001 TRP D 242 HIS 0.003 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00311 (19203) covalent geometry : angle 0.45803 (25963) hydrogen bonds : bond 0.03288 ( 887) hydrogen bonds : angle 4.34783 ( 2508) metal coordination : bond 0.00639 ( 16) metal coordination : angle 3.24292 ( 30) *********************** 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 88 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.960 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: D 114 MET cc_start: 0.8293 (tpp) cc_final: 0.8066 (tpp) REVERT: D 220 MET cc_start: 0.8721 (ttm) cc_final: 0.8249 (ppp) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.3516 time to fit residues: 45.5537 Evaluate side-chains 84 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1233 MET Chi-restraints excluded: chain A residue 1416 LYS Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 419 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 147 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 204 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.038159 restraints weight = 200614.079| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.11 r_work: 0.2606 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19219 Z= 0.113 Angle : 0.468 8.533 25993 Z= 0.236 Chirality : 0.039 0.149 2851 Planarity : 0.003 0.038 3335 Dihedral : 3.765 16.702 2539 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.57 % Allowed : 14.62 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.18), residues: 2299 helix: 2.21 (0.17), residues: 992 sheet: 0.33 (0.29), residues: 289 loop : 0.09 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1163 TYR 0.010 0.001 TYR A 732 PHE 0.009 0.001 PHE C 44 TRP 0.013 0.001 TRP D 242 HIS 0.004 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00255 (19203) covalent geometry : angle 0.45608 (25963) hydrogen bonds : bond 0.03221 ( 887) hydrogen bonds : angle 4.28135 ( 2508) metal coordination : bond 0.00503 ( 16) metal coordination : angle 3.17308 ( 30) *********************** 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 88 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.802 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: D 114 MET cc_start: 0.8225 (tpp) cc_final: 0.7991 (tpp) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.3760 time to fit residues: 48.6931 Evaluate side-chains 84 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1416 LYS Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 419 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 183 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.038057 restraints weight = 199951.533| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.11 r_work: 0.2602 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19219 Z= 0.126 Angle : 0.470 8.481 25993 Z= 0.237 Chirality : 0.039 0.146 2851 Planarity : 0.003 0.038 3335 Dihedral : 3.735 16.334 2539 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.43 % Allowed : 14.77 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.18), residues: 2299 helix: 2.23 (0.17), residues: 992 sheet: 0.35 (0.29), residues: 288 loop : 0.08 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1163 TYR 0.010 0.001 TYR C 426 PHE 0.020 0.001 PHE D 101 TRP 0.013 0.001 TRP D 242 HIS 0.003 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00283 (19203) covalent geometry : angle 0.45818 (25963) hydrogen bonds : bond 0.03179 ( 887) hydrogen bonds : angle 4.26712 ( 2508) metal coordination : bond 0.00573 ( 16) metal coordination : angle 3.12451 ( 30) ********************** 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 83 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.064 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: D 114 MET cc_start: 0.8250 (tpp) cc_final: 0.8027 (tpp) outliers start: 9 outliers final: 9 residues processed: 82 average time/residue: 0.3784 time to fit residues: 46.9844 Evaluate side-chains 81 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1416 LYS Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 419 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 163 optimal weight: 0.0070 chunk 4 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 204 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 overall best weight: 2.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.050705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.037413 restraints weight = 200459.587| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.08 r_work: 0.2577 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19219 Z= 0.195 Angle : 0.501 8.990 25993 Z= 0.254 Chirality : 0.039 0.137 2851 Planarity : 0.004 0.038 3335 Dihedral : 3.804 16.284 2539 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.52 % Allowed : 14.58 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.18), residues: 2299 helix: 2.11 (0.17), residues: 993 sheet: 0.34 (0.29), residues: 282 loop : 0.02 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1163 TYR 0.011 0.001 TYR B 522 PHE 0.009 0.001 PHE D 29 TRP 0.010 0.001 TRP D 242 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00428 (19203) covalent geometry : angle 0.48751 (25963) hydrogen bonds : bond 0.03371 ( 887) hydrogen bonds : angle 4.38022 ( 2508) metal coordination : bond 0.00905 ( 16) metal coordination : angle 3.38968 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7375.69 seconds wall clock time: 126 minutes 16.78 seconds (7576.78 seconds total)