Starting phenix.real_space_refine on Sat Aug 8 00:00:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukb_64233/08_2026/9ukb_64233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukb_64233/08_2026/9ukb_64233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ukb_64233/08_2026/9ukb_64233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukb_64233/08_2026/9ukb_64233.map" model { file = "/net/cci-nas-00/data/ceres_data/9ukb_64233/08_2026/9ukb_64233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukb_64233/08_2026/9ukb_64233.cif" } resolution = 4.51 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= 0.003 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 93 5.16 5 C 15077 2.51 5 N 4241 2.21 5 O 4485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23905 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2350 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "B" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2350 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2361 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 1 Chain: "D" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2466 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain: "E" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2481 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "F" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2507 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain: "G" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2454 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 10, 'TRANS': 297} Chain: "N" Number of atoms: 6843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6843 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 58, 'TRANS': 831} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.20 Number of scatterers: 23905 At special positions: 0 Unit cell: (120.056, 131.922, 166.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 9 15.00 O 4485 8.00 N 4241 7.00 C 15077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 969.3 milliseconds 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5654 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 30 sheets defined 49.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 151 through 159 removed outlier: 4.005A pdb=" N GLN A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 221 through 231 Processing helix chain 'A' and resid 232 through 237 removed outlier: 6.029A pdb=" N HIS A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.449A pdb=" N ALA A 258 " --> pdb=" O MET A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.622A pdb=" N ALA A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.631A pdb=" N PHE A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 298 removed outlier: 3.841A pdb=" N CYS A 298 " --> pdb=" O LEU A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.633A pdb=" N THR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.528A pdb=" N LEU B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 221 through 233 Processing helix chain 'B' and resid 238 through 262 Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.731A pdb=" N VAL B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.767A pdb=" N ARG B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 298 removed outlier: 3.809A pdb=" N CYS B 298 " --> pdb=" O LEU B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 298' Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.503A pdb=" N PHE B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.881A pdb=" N GLY C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 88 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.766A pdb=" N GLN C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 149 through 158 removed outlier: 4.084A pdb=" N VAL C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.858A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 241 through 262 removed outlier: 3.667A pdb=" N LYS C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.550A pdb=" N VAL C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 299 through 315 removed outlier: 4.173A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.884A pdb=" N LEU D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 removed outlier: 4.229A pdb=" N ILE D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 127 through 133 Processing helix chain 'D' and resid 153 through 160 removed outlier: 4.236A pdb=" N VAL D 157 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU D 159 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 removed outlier: 3.668A pdb=" N MET D 208 " --> pdb=" O ASN D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 238 through 262 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.672A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 314 removed outlier: 3.964A pdb=" N ALA D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 76 through 88 removed outlier: 3.584A pdb=" N ILE E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.644A pdb=" N GLY E 146 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 154 through 159 removed outlier: 4.069A pdb=" N GLU E 159 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 210 Processing helix chain 'E' and resid 221 through 233 Processing helix chain 'E' and resid 241 through 261 Processing helix chain 'E' and resid 271 through 284 Processing helix chain 'E' and resid 285 through 292 Processing helix chain 'E' and resid 294 through 298 removed outlier: 3.931A pdb=" N CYS E 298 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.893A pdb=" N ALA E 304 " --> pdb=" O GLU E 300 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 23 Processing helix chain 'F' and resid 50 through 63 removed outlier: 4.371A pdb=" N ALA F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 88 removed outlier: 4.581A pdb=" N ILE F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.745A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 removed outlier: 4.378A pdb=" N VAL F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 211 removed outlier: 3.687A pdb=" N ASP F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.969A pdb=" N ASN F 227 " --> pdb=" O ASP F 223 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS F 232 " --> pdb=" O ILE F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 261 removed outlier: 3.612A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 302 through 314 Processing helix chain 'G' and resid 331 through 335 Processing helix chain 'G' and resid 336 through 355 removed outlier: 4.149A pdb=" N ASN G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G 354 " --> pdb=" O GLN G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 370 Processing helix chain 'G' and resid 371 through 373 No H-bonds generated for 'chain 'G' and resid 371 through 373' Processing helix chain 'G' and resid 387 through 389 No H-bonds generated for 'chain 'G' and resid 387 through 389' Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.600A pdb=" N ILE G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 428 Processing helix chain 'G' and resid 429 through 450 removed outlier: 3.944A pdb=" N THR G 433 " --> pdb=" O GLY G 429 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL G 434 " --> pdb=" O ARG G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 475 Processing helix chain 'G' and resid 498 through 507 removed outlier: 4.940A pdb=" N ARG G 504 " --> pdb=" O ARG G 500 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASN G 505 " --> pdb=" O ARG G 501 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU G 506 " --> pdb=" O ALA G 502 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY G 507 " --> pdb=" O ARG G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 511 Processing helix chain 'G' and resid 519 through 533 Processing helix chain 'G' and resid 551 through 558 removed outlier: 3.775A pdb=" N VAL G 557 " --> pdb=" O SER G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 578 removed outlier: 3.988A pdb=" N GLU G 564 " --> pdb=" O GLY G 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 609 through 620 removed outlier: 3.954A pdb=" N LEU G 615 " --> pdb=" O MET G 611 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 374 Processing helix chain 'N' and resid 391 through 395 removed outlier: 3.924A pdb=" N LEU N 395 " --> pdb=" O ASP N 392 " (cutoff:3.500A) Processing helix chain 'N' and resid 402 through 418 removed outlier: 3.981A pdb=" N ALA N 415 " --> pdb=" O LEU N 411 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA N 416 " --> pdb=" O ARG N 412 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU N 417 " --> pdb=" O ALA N 413 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 438 removed outlier: 3.583A pdb=" N ALA N 434 " --> pdb=" O ALA N 430 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA N 437 " --> pdb=" O ARG N 433 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY N 438 " --> pdb=" O ALA N 434 " (cutoff:3.500A) Processing helix chain 'N' and resid 455 through 464 removed outlier: 4.281A pdb=" N ALA N 460 " --> pdb=" O ASN N 456 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU N 461 " --> pdb=" O GLN N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 466 through 478 removed outlier: 3.736A pdb=" N GLU N 474 " --> pdb=" O GLN N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 479 through 483 Processing helix chain 'N' and resid 516 through 521 removed outlier: 4.414A pdb=" N TYR N 521 " --> pdb=" O PRO N 517 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 541 removed outlier: 3.709A pdb=" N ILE N 533 " --> pdb=" O PRO N 529 " (cutoff:3.500A) Processing helix chain 'N' and resid 571 through 578 removed outlier: 3.543A pdb=" N ALA N 575 " --> pdb=" O CYS N 571 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL N 576 " --> pdb=" O TYR N 572 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE N 577 " --> pdb=" O PRO N 573 " (cutoff:3.500A) Processing helix chain 'N' and resid 594 through 602 removed outlier: 4.194A pdb=" N ARG N 599 " --> pdb=" O THR N 595 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG N 600 " --> pdb=" O GLN N 596 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 635 removed outlier: 3.727A pdb=" N LEU N 628 " --> pdb=" O ASP N 624 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL N 629 " --> pdb=" O LEU N 625 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA N 635 " --> pdb=" O GLU N 631 " (cutoff:3.500A) Processing helix chain 'N' and resid 639 through 658 removed outlier: 3.654A pdb=" N LEU N 651 " --> pdb=" O LYS N 647 " (cutoff:3.500A) Processing helix chain 'N' and resid 670 through 688 Processing helix chain 'N' and resid 704 through 709 removed outlier: 3.555A pdb=" N LEU N 709 " --> pdb=" O LEU N 705 " (cutoff:3.500A) Processing helix chain 'N' and resid 710 through 715 removed outlier: 3.622A pdb=" N ALA N 714 " --> pdb=" O LEU N 710 " (cutoff:3.500A) Processing helix chain 'N' and resid 721 through 725 Processing helix chain 'N' and resid 727 through 731 Processing helix chain 'N' and resid 732 through 741 Processing helix chain 'N' and resid 763 through 770 removed outlier: 3.722A pdb=" N SER N 770 " --> pdb=" O LEU N 766 " (cutoff:3.500A) Processing helix chain 'N' and resid 776 through 793 removed outlier: 3.684A pdb=" N THR N 780 " --> pdb=" O ILE N 776 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA N 788 " --> pdb=" O ILE N 784 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 793 " --> pdb=" O ALA N 789 " (cutoff:3.500A) Processing helix chain 'N' and resid 802 through 815 removed outlier: 4.229A pdb=" N SER N 811 " --> pdb=" O ALA N 807 " (cutoff:3.500A) Processing helix chain 'N' and resid 815 through 837 removed outlier: 3.639A pdb=" N MET N 819 " --> pdb=" O GLN N 815 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY N 824 " --> pdb=" O VAL N 820 " (cutoff:3.500A) Proline residue: N 825 - end of helix Processing helix chain 'N' and resid 847 through 851 Processing helix chain 'N' and resid 872 through 881 removed outlier: 3.883A pdb=" N GLU N 877 " --> pdb=" O PRO N 873 " (cutoff:3.500A) Processing helix chain 'N' and resid 881 through 894 removed outlier: 4.120A pdb=" N ASP N 893 " --> pdb=" O ARG N 889 " (cutoff:3.500A) Processing helix chain 'N' and resid 915 through 924 Processing helix chain 'N' and resid 945 through 950 Processing helix chain 'N' and resid 961 through 968 Processing helix chain 'N' and resid 969 through 985 removed outlier: 3.774A pdb=" N ALA N 973 " --> pdb=" O PRO N 969 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU N 985 " --> pdb=" O ALA N 981 " (cutoff:3.500A) Processing helix chain 'N' and resid 992 through 1007 Processing helix chain 'N' and resid 1011 through 1019 removed outlier: 3.820A pdb=" N ARG N1017 " --> pdb=" O GLN N1013 " (cutoff:3.500A) Processing helix chain 'N' and resid 1034 through 1041 removed outlier: 3.658A pdb=" N LEU N1038 " --> pdb=" O GLY N1034 " (cutoff:3.500A) Processing helix chain 'N' and resid 1046 through 1058 removed outlier: 4.235A pdb=" N LEU N1050 " --> pdb=" O GLY N1046 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA N1051 " --> pdb=" O ARG N1047 " (cutoff:3.500A) Processing helix chain 'N' and resid 1072 through 1082 removed outlier: 4.021A pdb=" N GLU N1077 " --> pdb=" O GLY N1073 " (cutoff:3.500A) Processing helix chain 'N' and resid 1099 through 1117 removed outlier: 4.178A pdb=" N TYR N1103 " --> pdb=" O SER N1099 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY N1108 " --> pdb=" O GLN N1104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER N1115 " --> pdb=" O ALA N1111 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR N1117 " --> pdb=" O VAL N1113 " (cutoff:3.500A) Processing helix chain 'N' and resid 1138 through 1149 removed outlier: 3.780A pdb=" N GLU N1142 " --> pdb=" O ALA N1138 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER N1144 " --> pdb=" O GLU N1140 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL N1147 " --> pdb=" O LEU N1143 " (cutoff:3.500A) Processing helix chain 'N' and resid 1153 through 1162 Processing helix chain 'N' and resid 1166 through 1186 removed outlier: 3.706A pdb=" N GLU N1170 " --> pdb=" O LYS N1166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR N1174 " --> pdb=" O GLU N1170 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL N1175 " --> pdb=" O ILE N1171 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP N1176 " --> pdb=" O ALA N1172 " (cutoff:3.500A) Processing helix chain 'N' and resid 1191 through 1200 removed outlier: 3.873A pdb=" N GLN N1198 " --> pdb=" O GLU N1194 " (cutoff:3.500A) Processing helix chain 'N' and resid 1203 through 1214 Processing helix chain 'N' and resid 1214 through 1231 removed outlier: 3.512A pdb=" N LEU N1218 " --> pdb=" O ASN N1214 " (cutoff:3.500A) Processing helix chain 'N' and resid 1240 through 1255 removed outlier: 4.167A pdb=" N GLU N1246 " --> pdb=" O ARG N1242 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER N1249 " --> pdb=" O LEU N1245 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU N1252 " --> pdb=" O LEU N1248 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN N1253 " --> pdb=" O SER N1249 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS N1254 " --> pdb=" O VAL N1250 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU N1255 " --> pdb=" O HIS N1251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 70 removed outlier: 6.205A pdb=" N LEU A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR A 184 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 140 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 93 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP A 141 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 95 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 113 Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.184A pdb=" N VAL B 67 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA B 185 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL B 69 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 114 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 16 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.351A pdb=" N VAL C 67 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA C 185 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 69 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AB1, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.845A pdb=" N LEU C 166 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG C 171 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.476A pdb=" N LEU D 138 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR D 184 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE D 140 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 67 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ALA D 185 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL D 69 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 111 through 115 Processing sheet with id=AB5, first strand: chain 'D' and resid 164 through 165 Processing sheet with id=AB6, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AB7, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.189A pdb=" N LEU E 138 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR E 184 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE E 140 " --> pdb=" O THR E 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 108 through 113 Processing sheet with id=AB9, first strand: chain 'E' and resid 164 through 165 Processing sheet with id=AC1, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AC2, first strand: chain 'F' and resid 92 through 95 removed outlier: 6.396A pdb=" N VAL F 93 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL F 67 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 71 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 108 through 115 Processing sheet with id=AC4, first strand: chain 'G' and resid 327 through 330 removed outlier: 3.643A pdb=" N GLU G 327 " --> pdb=" O LEU G 487 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR G 415 " --> pdb=" O LYS G 452 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLU G 454 " --> pdb=" O THR G 415 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL G 417 " --> pdb=" O GLU G 454 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU G 456 " --> pdb=" O VAL G 417 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU G 419 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N PHE G 458 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU G 421 " --> pdb=" O PHE G 458 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N THR G 460 " --> pdb=" O LEU G 421 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL G 416 " --> pdb=" O ILE G 540 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET G 542 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR G 418 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE G 544 " --> pdb=" O THR G 418 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL G 420 " --> pdb=" O ILE G 544 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ILE G 585 " --> pdb=" O LEU G 541 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET G 543 " --> pdb=" O ILE G 585 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 382 through 385 Processing sheet with id=AC6, first strand: chain 'N' and resid 451 through 454 removed outlier: 4.475A pdb=" N GLU N 451 " --> pdb=" O LEU N 495 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 548 through 549 removed outlier: 6.835A pdb=" N VAL N 548 " --> pdb=" O ILE N 583 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS N 582 " --> pdb=" O VAL N 604 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'N' and resid 614 through 615 Processing sheet with id=AC9, first strand: chain 'N' and resid 900 through 905 removed outlier: 6.717A pdb=" N PHE N 901 " --> pdb=" O THR N 957 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ARG N 959 " --> pdb=" O PHE N 901 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU N 903 " --> pdb=" O ARG N 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'N' and resid 927 through 928 Processing sheet with id=AD2, first strand: chain 'N' and resid 1024 through 1025 removed outlier: 4.315A pdb=" N TYR N1060 " --> pdb=" O GLY N1025 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 1084 through 1089 1003 hydrogen bonds defined for protein. 2877 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: 4.29 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8138 1.34 - 1.46: 4171 1.46 - 1.58: 11926 1.58 - 1.69: 15 1.69 - 1.81: 166 Bond restraints: 24416 Sorted by residual: bond pdb=" O3A ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.685 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.94e+01 ... (remaining 24411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 33090 4.03 - 8.06: 115 8.06 - 12.09: 10 12.09 - 16.12: 0 16.12 - 20.15: 3 Bond angle restraints: 33218 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 106.80 20.15 3.00e+00 1.11e-01 4.51e+01 angle pdb=" PB ANP E 401 " pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 126.95 107.10 19.85 3.00e+00 1.11e-01 4.38e+01 angle pdb=" N VAL F 157 " pdb=" CA VAL F 157 " pdb=" C VAL F 157 " ideal model delta sigma weight residual 111.44 103.25 8.19 1.34e+00 5.57e-01 3.73e+01 angle pdb=" N GLU F 159 " pdb=" CA GLU F 159 " pdb=" C GLU F 159 " ideal model delta sigma weight residual 113.19 103.71 9.48 1.58e+00 4.01e-01 3.60e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 109.87 17.08 3.00e+00 1.11e-01 3.24e+01 ... (remaining 33213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13217 17.93 - 35.86: 1099 35.86 - 53.78: 227 53.78 - 71.71: 69 71.71 - 89.64: 21 Dihedral angle restraints: 14633 sinusoidal: 5859 harmonic: 8774 Sorted by residual: dihedral pdb=" CA MET C 28 " pdb=" C MET C 28 " pdb=" N MET C 29 " pdb=" CA MET C 29 " ideal model delta harmonic sigma weight residual 180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ARG C 87 " pdb=" C ARG C 87 " pdb=" N LEU C 88 " pdb=" CA LEU C 88 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LEU F 196 " pdb=" C LEU F 196 " pdb=" N TYR F 197 " pdb=" CA TYR F 197 " ideal model delta harmonic sigma weight residual 180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 14630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2911 0.053 - 0.106: 688 0.106 - 0.159: 99 0.159 - 0.212: 5 0.212 - 0.265: 6 Chirality restraints: 3709 Sorted by residual: chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ILE A 282 " pdb=" N ILE A 282 " pdb=" C ILE A 282 " pdb=" CB ILE A 282 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 3706 not shown) Planarity restraints: 4359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 156 " 0.015 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" C ARG F 156 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG F 156 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL F 157 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 63 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" C TYR F 63 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR F 63 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN F 64 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 55 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.15e+00 pdb=" C LEU C 55 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU C 55 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA C 56 " 0.017 2.00e-02 2.50e+03 ... (remaining 4356 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2368 2.74 - 3.28: 26270 3.28 - 3.82: 41717 3.82 - 4.36: 48440 4.36 - 4.90: 77876 Nonbonded interactions: 196671 Sorted by model distance: nonbonded pdb=" OD1 ASN N 441 " pdb=" OH TYR N 485 " model vdw 2.201 3.040 nonbonded pdb=" O SER B 269 " pdb=" OG1 THR B 272 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU G 564 " pdb=" NE ARG G 568 " model vdw 2.217 3.120 nonbonded pdb=" O ASP A 50 " pdb=" OG1 THR A 54 " model vdw 2.220 3.040 nonbonded pdb=" O PHE C 179 " pdb=" NH1 ARG C 180 " model vdw 2.220 3.120 ... (remaining 196666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 317) selection = (chain 'B' and resid 9 through 317) selection = (chain 'C' and (resid 9 through 188 or resid 203 through 317)) selection = (chain 'D' and (resid 9 through 188 or resid 203 through 317)) selection = (chain 'E' and (resid 9 through 188 or resid 203 through 317)) selection = (chain 'F' and (resid 9 through 188 or resid 203 through 317)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.620 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 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 0.145 24416 Z= 0.208 Angle : 0.710 20.151 33218 Z= 0.370 Chirality : 0.045 0.265 3709 Planarity : 0.005 0.061 4359 Dihedral : 14.574 89.641 8979 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.71 % Favored : 93.19 % Rotamer: Outliers : 0.44 % Allowed : 0.52 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.16), residues: 3010 helix: -0.23 (0.14), residues: 1257 sheet: -0.78 (0.28), residues: 349 loop : -1.00 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 250 TYR 0.025 0.001 TYR N 532 PHE 0.042 0.002 PHE C 61 TRP 0.035 0.002 TRP N1156 HIS 0.005 0.001 HIS F 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 (24416) covalent geometry : angle 0.71027 / 0.37 (33218) hydrogen bonds : bond 0.16513 / 11.37 ( 1003) hydrogen bonds : angle 7.30233 / 5.15 ( 2877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 771 time to evaluate : 0.803 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 revert: symmetry clash revert: 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 68 MET cc_start: 0.7101 (ptp) cc_final: 0.6871 (ptp) REVERT: A 151 MET cc_start: 0.8210 (mmp) cc_final: 0.7636 (mmp) REVERT: A 159 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7188 (mt-10) REVERT: A 174 ARG cc_start: 0.8076 (mmp80) cc_final: 0.7409 (mmp80) REVERT: A 242 ARG cc_start: 0.8348 (tpt90) cc_final: 0.7545 (tpt90) REVERT: A 248 MET cc_start: 0.8601 (ptp) cc_final: 0.8372 (ptp) REVERT: A 288 PHE cc_start: 0.8445 (t80) cc_final: 0.7936 (t80) REVERT: B 46 ASP cc_start: 0.8192 (m-30) cc_final: 0.7920 (m-30) REVERT: B 48 LEU cc_start: 0.8072 (tt) cc_final: 0.7857 (tt) REVERT: B 57 ILE cc_start: 0.8747 (mt) cc_final: 0.8232 (mt) REVERT: B 61 PHE cc_start: 0.8819 (m-80) cc_final: 0.8404 (m-80) REVERT: B 80 HIS cc_start: 0.8410 (t70) cc_final: 0.7995 (t70) REVERT: B 89 ASN cc_start: 0.6997 (t0) cc_final: 0.6791 (t0) REVERT: B 109 LYS cc_start: 0.8357 (mptt) cc_final: 0.7695 (mptt) REVERT: B 135 ASN cc_start: 0.7762 (p0) cc_final: 0.7292 (p0) REVERT: B 138 LEU cc_start: 0.7909 (tp) cc_final: 0.7593 (tp) REVERT: B 227 ASN cc_start: 0.9018 (m110) cc_final: 0.8610 (m110) REVERT: B 254 MET cc_start: 0.7746 (mpp) cc_final: 0.7244 (mpp) REVERT: B 256 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8715 (ttp80) REVERT: B 257 GLN cc_start: 0.8892 (tt0) cc_final: 0.8605 (tt0) REVERT: B 271 ARG cc_start: 0.8309 (ttt-90) cc_final: 0.7989 (ttt180) REVERT: B 285 ASP cc_start: 0.8154 (p0) cc_final: 0.7773 (p0) REVERT: B 294 PHE cc_start: 0.8421 (t80) cc_final: 0.8159 (t80) REVERT: B 310 TYR cc_start: 0.7232 (t80) cc_final: 0.6834 (t80) REVERT: C 29 MET cc_start: 0.6823 (tpt) cc_final: 0.6492 (tpt) REVERT: C 51 ARG cc_start: 0.7619 (tmt-80) cc_final: 0.7412 (tmt-80) REVERT: C 119 GLN cc_start: 0.8498 (pm20) cc_final: 0.8051 (pm20) REVERT: C 141 ASP cc_start: 0.7287 (t0) cc_final: 0.6835 (t0) REVERT: C 143 TYR cc_start: 0.8552 (t80) cc_final: 0.8236 (t80) REVERT: C 152 PHE cc_start: 0.7562 (m-80) cc_final: 0.7216 (m-80) REVERT: C 154 ILE cc_start: 0.8809 (mt) cc_final: 0.8544 (mt) REVERT: C 230 LEU cc_start: 0.8710 (mt) cc_final: 0.8472 (mt) REVERT: C 248 MET cc_start: 0.9037 (mtp) cc_final: 0.8340 (mtp) REVERT: C 257 GLN cc_start: 0.8663 (tp40) cc_final: 0.8143 (tp40) REVERT: C 288 PHE cc_start: 0.8211 (t80) cc_final: 0.6966 (t80) REVERT: C 292 LEU cc_start: 0.7971 (mt) cc_final: 0.7546 (mt) REVERT: C 310 TYR cc_start: 0.7399 (t80) cc_final: 0.6998 (t80) REVERT: D 37 ASP cc_start: 0.7164 (m-30) cc_final: 0.6849 (m-30) REVERT: D 44 ASP cc_start: 0.7374 (m-30) cc_final: 0.6734 (m-30) REVERT: D 50 ASP cc_start: 0.7688 (t70) cc_final: 0.7478 (t70) REVERT: D 53 THR cc_start: 0.8473 (p) cc_final: 0.8236 (p) REVERT: D 92 CYS cc_start: 0.7787 (t) cc_final: 0.7475 (t) REVERT: D 123 PHE cc_start: 0.7637 (t80) cc_final: 0.7246 (t80) REVERT: D 124 LYS cc_start: 0.7510 (mmpt) cc_final: 0.7143 (mmpt) REVERT: D 144 ASP cc_start: 0.7153 (p0) cc_final: 0.6829 (p0) REVERT: D 155 GLN cc_start: 0.7443 (tm-30) cc_final: 0.7192 (tm-30) REVERT: D 179 PHE cc_start: 0.8423 (t80) cc_final: 0.7819 (t80) REVERT: D 201 GLN cc_start: 0.6647 (mp-120) cc_final: 0.6238 (mp-120) REVERT: D 205 GLN cc_start: 0.7801 (mp10) cc_final: 0.7168 (mp10) REVERT: D 208 MET cc_start: 0.7827 (ptp) cc_final: 0.7018 (ptp) REVERT: D 217 LEU cc_start: 0.8099 (tt) cc_final: 0.7834 (tt) REVERT: D 227 ASN cc_start: 0.8726 (m110) cc_final: 0.8380 (m110) REVERT: D 248 MET cc_start: 0.8387 (ttm) cc_final: 0.8001 (ttm) REVERT: D 251 VAL cc_start: 0.8934 (t) cc_final: 0.8347 (t) REVERT: D 254 MET cc_start: 0.8710 (mtm) cc_final: 0.8296 (mtm) REVERT: D 257 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7357 (tp-100) REVERT: D 297 LYS cc_start: 0.8555 (ptmt) cc_final: 0.8351 (ptmt) REVERT: E 29 MET cc_start: 0.6940 (mmp) cc_final: 0.6730 (mmp) REVERT: E 88 LEU cc_start: 0.8834 (mt) cc_final: 0.8626 (mm) REVERT: E 143 TYR cc_start: 0.8554 (t80) cc_final: 0.8179 (t80) REVERT: E 166 LEU cc_start: 0.7857 (mt) cc_final: 0.7644 (mt) REVERT: E 208 MET cc_start: 0.8129 (tpt) cc_final: 0.7814 (tpt) REVERT: E 243 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7507 (mm-30) REVERT: E 250 ARG cc_start: 0.8264 (mmt180) cc_final: 0.7701 (mmt180) REVERT: E 253 ASP cc_start: 0.7418 (m-30) cc_final: 0.7100 (m-30) REVERT: E 257 GLN cc_start: 0.8112 (mp10) cc_final: 0.7443 (mp10) REVERT: E 261 ASN cc_start: 0.8615 (m-40) cc_final: 0.8295 (m-40) REVERT: E 279 ASN cc_start: 0.8544 (m-40) cc_final: 0.8280 (m-40) REVERT: E 285 ASP cc_start: 0.8521 (t70) cc_final: 0.8278 (t0) REVERT: E 288 PHE cc_start: 0.7043 (t80) cc_final: 0.6751 (t80) REVERT: E 309 PHE cc_start: 0.8186 (m-80) cc_final: 0.7723 (m-80) REVERT: E 317 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7538 (mm-30) REVERT: F 58 LEU cc_start: 0.8894 (mt) cc_final: 0.8666 (mt) REVERT: F 63 TYR cc_start: 0.7173 (m-10) cc_final: 0.6871 (m-10) REVERT: F 68 MET cc_start: 0.7326 (tmm) cc_final: 0.6948 (tmm) REVERT: F 152 PHE cc_start: 0.7566 (m-10) cc_final: 0.7238 (m-10) REVERT: F 278 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8350 (mt-10) REVERT: F 297 LYS cc_start: 0.8630 (mppt) cc_final: 0.8409 (mppt) REVERT: F 301 LEU cc_start: 0.8222 (mp) cc_final: 0.7860 (mp) REVERT: G 369 LEU cc_start: 0.7785 (tp) cc_final: 0.7575 (tp) REVERT: G 370 MET cc_start: 0.6607 (tpt) cc_final: 0.5878 (tpt) REVERT: G 391 LEU cc_start: 0.8320 (mt) cc_final: 0.8102 (mt) REVERT: G 432 ILE cc_start: 0.9210 (tt) cc_final: 0.8774 (tt) REVERT: G 480 ASN cc_start: 0.8873 (t0) cc_final: 0.8605 (t0) REVERT: G 489 HIS cc_start: 0.8240 (m170) cc_final: 0.7631 (m170) REVERT: G 509 MET cc_start: 0.8651 (ppp) cc_final: 0.8093 (ppp) REVERT: G 524 LEU cc_start: 0.9152 (mt) cc_final: 0.8807 (mt) REVERT: G 531 LEU cc_start: 0.8422 (tp) cc_final: 0.8113 (tp) REVERT: G 543 MET cc_start: 0.7081 (tpt) cc_final: 0.6718 (tpt) REVERT: N 411 LEU cc_start: 0.8475 (mt) cc_final: 0.8274 (mt) REVERT: N 436 MET cc_start: 0.7889 (tpt) cc_final: 0.7170 (tpt) REVERT: N 677 LYS cc_start: 0.7728 (ptpp) cc_final: 0.7481 (ptpp) REVERT: N 681 TYR cc_start: 0.8182 (t80) cc_final: 0.7452 (t80) REVERT: N 695 HIS cc_start: 0.5817 (t-90) cc_final: 0.5352 (t-90) REVERT: N 890 TYR cc_start: 0.6897 (t80) cc_final: 0.6373 (t80) REVERT: N 1085 VAL cc_start: 0.8171 (m) cc_final: 0.7849 (p) REVERT: N 1145 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7033 (mtm180) REVERT: N 1155 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8315 (mtmm) REVERT: N 1235 THR cc_start: 0.8013 (p) cc_final: 0.7566 (p) REVERT: N 1243 PHE cc_start: 0.8105 (t80) cc_final: 0.7248 (t80) outliers start: 11 outliers final: 2 residues processed: 779 average time/residue: 0.1561 time to fit residues: 183.7715 Evaluate side-chains 753 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 751 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN C 73 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN E 73 HIS ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS ** N 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 470 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.170145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.135666 restraints weight = 49664.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140962 restraints weight = 31527.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.144845 restraints weight = 22038.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.147597 restraints weight = 16477.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.149734 restraints weight = 12991.159| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24416 Z= 0.184 Angle : 0.612 8.621 33218 Z= 0.324 Chirality : 0.044 0.196 3709 Planarity : 0.005 0.058 4359 Dihedral : 8.067 80.894 3443 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.54 % Favored : 92.43 % Rotamer: Outliers : 0.24 % Allowed : 3.99 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.15), residues: 3010 helix: -0.27 (0.14), residues: 1316 sheet: -0.81 (0.28), residues: 347 loop : -1.07 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 66 TYR 0.019 0.002 TYR A 143 PHE 0.028 0.002 PHE E 288 TRP 0.018 0.002 TRP N1156 HIS 0.008 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (24416) covalent geometry : angle 0.61209 / 0.32 (33218) hydrogen bonds : bond 0.04660 / 3.15 ( 1003) hydrogen bonds : angle 6.11756 / 4.34 ( 2877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 780 time to evaluate : 0.541 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7440 (m-80) cc_final: 0.7210 (m-80) REVERT: A 94 ARG cc_start: 0.7331 (ptm-80) cc_final: 0.6979 (ptm-80) REVERT: A 151 MET cc_start: 0.8354 (mmp) cc_final: 0.7761 (mmp) REVERT: A 159 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 174 ARG cc_start: 0.8087 (mmp80) cc_final: 0.7484 (mmp80) REVERT: A 182 PHE cc_start: 0.7979 (m-10) cc_final: 0.7676 (m-10) REVERT: A 207 GLN cc_start: 0.6709 (pm20) cc_final: 0.6463 (pm20) REVERT: A 242 ARG cc_start: 0.8673 (tpt90) cc_final: 0.7906 (tpt90) REVERT: A 248 MET cc_start: 0.8452 (ptp) cc_final: 0.8245 (ptp) REVERT: A 256 ARG cc_start: 0.8801 (ttm170) cc_final: 0.8540 (ttm170) REVERT: A 288 PHE cc_start: 0.8340 (t80) cc_final: 0.7836 (t80) REVERT: B 11 LEU cc_start: 0.8961 (mm) cc_final: 0.8759 (mm) REVERT: B 46 ASP cc_start: 0.8209 (m-30) cc_final: 0.7886 (m-30) REVERT: B 48 LEU cc_start: 0.8112 (tt) cc_final: 0.7897 (tt) REVERT: B 80 HIS cc_start: 0.8516 (t70) cc_final: 0.8049 (t70) REVERT: B 109 LYS cc_start: 0.8399 (mptt) cc_final: 0.7695 (mptt) REVERT: B 135 ASN cc_start: 0.7735 (p0) cc_final: 0.7301 (p0) REVERT: B 138 LEU cc_start: 0.7858 (tp) cc_final: 0.7455 (tp) REVERT: B 169 GLN cc_start: 0.8492 (mm110) cc_final: 0.8246 (mm-40) REVERT: B 210 ARG cc_start: 0.8508 (mmp80) cc_final: 0.8279 (mmp80) REVERT: B 254 MET cc_start: 0.7938 (mpp) cc_final: 0.7562 (mpp) REVERT: B 268 MET cc_start: 0.7699 (mmp) cc_final: 0.7470 (mmp) REVERT: B 271 ARG cc_start: 0.8573 (ttt-90) cc_final: 0.8268 (ttt-90) REVERT: B 282 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7969 (mp) REVERT: B 285 ASP cc_start: 0.7961 (p0) cc_final: 0.7592 (p0) REVERT: B 310 TYR cc_start: 0.7597 (t80) cc_final: 0.7076 (t80) REVERT: C 51 ARG cc_start: 0.7569 (tmt-80) cc_final: 0.7322 (tmt-80) REVERT: C 119 GLN cc_start: 0.8569 (pm20) cc_final: 0.8136 (pm20) REVERT: C 141 ASP cc_start: 0.7253 (t0) cc_final: 0.6894 (t0) REVERT: C 152 PHE cc_start: 0.7537 (m-80) cc_final: 0.7189 (m-80) REVERT: C 230 LEU cc_start: 0.8808 (mt) cc_final: 0.8591 (mt) REVERT: C 238 ASN cc_start: 0.8980 (p0) cc_final: 0.8727 (p0) REVERT: C 244 ILE cc_start: 0.8872 (mp) cc_final: 0.8659 (mp) REVERT: C 248 MET cc_start: 0.8982 (mtp) cc_final: 0.8476 (mtp) REVERT: C 257 GLN cc_start: 0.8727 (tp40) cc_final: 0.8211 (tp40) REVERT: C 288 PHE cc_start: 0.8284 (t80) cc_final: 0.7086 (t80) REVERT: C 292 LEU cc_start: 0.8030 (mt) cc_final: 0.7502 (mt) REVERT: D 37 ASP cc_start: 0.7294 (m-30) cc_final: 0.6943 (m-30) REVERT: D 44 ASP cc_start: 0.7507 (m-30) cc_final: 0.6932 (m-30) REVERT: D 50 ASP cc_start: 0.7759 (t70) cc_final: 0.7465 (t70) REVERT: D 53 THR cc_start: 0.8452 (p) cc_final: 0.8185 (p) REVERT: D 123 PHE cc_start: 0.7645 (t80) cc_final: 0.7205 (t80) REVERT: D 124 LYS cc_start: 0.7737 (mmpt) cc_final: 0.7360 (mmpt) REVERT: D 130 TRP cc_start: 0.8585 (t60) cc_final: 0.7898 (t60) REVERT: D 144 ASP cc_start: 0.7419 (p0) cc_final: 0.7052 (p0) REVERT: D 179 PHE cc_start: 0.8494 (t80) cc_final: 0.7822 (t80) REVERT: D 182 PHE cc_start: 0.7475 (m-80) cc_final: 0.7218 (m-80) REVERT: D 201 GLN cc_start: 0.6569 (mp-120) cc_final: 0.6169 (mp-120) REVERT: D 205 GLN cc_start: 0.7729 (mp10) cc_final: 0.7240 (mp10) REVERT: D 208 MET cc_start: 0.7971 (ptp) cc_final: 0.7193 (ptp) REVERT: D 209 ASP cc_start: 0.8062 (t0) cc_final: 0.7524 (t0) REVERT: D 224 ASN cc_start: 0.8142 (m110) cc_final: 0.7915 (m110) REVERT: D 227 ASN cc_start: 0.8773 (m110) cc_final: 0.8424 (m110) REVERT: D 248 MET cc_start: 0.8451 (ttm) cc_final: 0.8070 (ttm) REVERT: D 251 VAL cc_start: 0.8906 (t) cc_final: 0.8374 (t) REVERT: D 254 MET cc_start: 0.8719 (mtm) cc_final: 0.8249 (mtm) REVERT: D 257 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7153 (tp-100) REVERT: D 261 ASN cc_start: 0.8589 (m-40) cc_final: 0.7876 (m110) REVERT: D 268 MET cc_start: 0.7785 (mmp) cc_final: 0.7548 (mmp) REVERT: E 46 ASP cc_start: 0.7763 (t0) cc_final: 0.7332 (t0) REVERT: E 49 PHE cc_start: 0.7478 (m-10) cc_final: 0.7155 (m-10) REVERT: E 143 TYR cc_start: 0.8650 (t80) cc_final: 0.7609 (t80) REVERT: E 152 PHE cc_start: 0.8876 (m-80) cc_final: 0.8358 (m-80) REVERT: E 166 LEU cc_start: 0.7896 (mt) cc_final: 0.7642 (mt) REVERT: E 248 MET cc_start: 0.7645 (mmm) cc_final: 0.7404 (mmm) REVERT: E 250 ARG cc_start: 0.8352 (mmt180) cc_final: 0.7938 (mmt180) REVERT: E 261 ASN cc_start: 0.8645 (m-40) cc_final: 0.8324 (m-40) REVERT: E 285 ASP cc_start: 0.8437 (t70) cc_final: 0.8161 (t0) REVERT: E 300 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7252 (mm-30) REVERT: E 309 PHE cc_start: 0.8165 (m-80) cc_final: 0.7741 (m-80) REVERT: E 317 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7546 (mm-30) REVERT: F 42 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7585 (tm-30) REVERT: F 68 MET cc_start: 0.7498 (tmm) cc_final: 0.7115 (tmm) REVERT: F 100 HIS cc_start: 0.8203 (m-70) cc_final: 0.7786 (m-70) REVERT: F 147 ARG cc_start: 0.7822 (ptp-170) cc_final: 0.7358 (ptp-170) REVERT: F 152 PHE cc_start: 0.7636 (m-10) cc_final: 0.7424 (m-10) REVERT: F 157 VAL cc_start: 0.9172 (t) cc_final: 0.8865 (t) REVERT: F 215 THR cc_start: 0.7679 (t) cc_final: 0.7474 (t) REVERT: F 244 ILE cc_start: 0.8924 (mt) cc_final: 0.8719 (mt) REVERT: F 278 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8339 (mt-10) REVERT: F 295 LEU cc_start: 0.8815 (tp) cc_final: 0.8603 (tp) REVERT: F 297 LYS cc_start: 0.8712 (mppt) cc_final: 0.8507 (mppt) REVERT: F 301 LEU cc_start: 0.8245 (mp) cc_final: 0.7867 (mp) REVERT: G 341 ASP cc_start: 0.8706 (m-30) cc_final: 0.8443 (m-30) REVERT: G 368 ARG cc_start: 0.8462 (mmm160) cc_final: 0.8219 (mmm-85) REVERT: G 369 LEU cc_start: 0.7959 (tp) cc_final: 0.7723 (tp) REVERT: G 370 MET cc_start: 0.6780 (tpt) cc_final: 0.5911 (tpt) REVERT: G 378 ASP cc_start: 0.7614 (m-30) cc_final: 0.6990 (m-30) REVERT: G 408 ARG cc_start: 0.6737 (tpm170) cc_final: 0.6289 (mmm-85) REVERT: G 432 ILE cc_start: 0.9306 (tt) cc_final: 0.8994 (tt) REVERT: G 480 ASN cc_start: 0.8725 (t0) cc_final: 0.8523 (t0) REVERT: G 489 HIS cc_start: 0.8207 (m170) cc_final: 0.7573 (m170) REVERT: G 504 ARG cc_start: 0.8558 (ttm110) cc_final: 0.7821 (ttp80) REVERT: G 508 LEU cc_start: 0.8799 (tp) cc_final: 0.8570 (tp) REVERT: G 509 MET cc_start: 0.8664 (ppp) cc_final: 0.7989 (ppp) REVERT: G 524 LEU cc_start: 0.9161 (mt) cc_final: 0.8811 (mt) REVERT: G 531 LEU cc_start: 0.8431 (tp) cc_final: 0.8098 (tp) REVERT: G 543 MET cc_start: 0.6913 (tpt) cc_final: 0.6683 (tpt) REVERT: N 436 MET cc_start: 0.7989 (tpt) cc_final: 0.7303 (tpt) REVERT: N 673 MET cc_start: 0.8668 (ppp) cc_final: 0.8387 (ppp) REVERT: N 677 LYS cc_start: 0.7750 (ptpp) cc_final: 0.7407 (ptpp) REVERT: N 681 TYR cc_start: 0.8318 (t80) cc_final: 0.7662 (t80) REVERT: N 890 TYR cc_start: 0.7485 (t80) cc_final: 0.6818 (t80) REVERT: N 1077 GLU cc_start: 0.8035 (pm20) cc_final: 0.7827 (pm20) REVERT: N 1085 VAL cc_start: 0.8176 (m) cc_final: 0.7849 (p) REVERT: N 1120 MET cc_start: 0.5914 (tpt) cc_final: 0.5473 (tpt) REVERT: N 1145 ARG cc_start: 0.8360 (mtm110) cc_final: 0.7575 (mtm180) REVERT: N 1155 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8254 (mtmm) REVERT: N 1243 PHE cc_start: 0.8152 (t80) cc_final: 0.7266 (t80) REVERT: N 1245 LEU cc_start: 0.9122 (mt) cc_final: 0.8440 (tp) outliers start: 6 outliers final: 0 residues processed: 783 average time/residue: 0.1536 time to fit residues: 182.7465 Evaluate side-chains 743 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 742 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 295 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 62 optimal weight: 0.0050 chunk 21 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 HIS C 52 GLN C 100 HIS ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS F 134 HIS F 296 ASN N 554 HIS N 734 GLN ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.166609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132045 restraints weight = 50156.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137460 restraints weight = 31858.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141443 restraints weight = 22137.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144364 restraints weight = 16381.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.146461 restraints weight = 12824.507| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24416 Z= 0.134 Angle : 0.575 8.795 33218 Z= 0.301 Chirality : 0.043 0.169 3709 Planarity : 0.005 0.082 4359 Dihedral : 7.445 78.178 3443 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.24 % Allowed : 3.35 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3010 helix: -0.19 (0.14), residues: 1315 sheet: -0.80 (0.27), residues: 353 loop : -1.03 (0.18), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 483 TYR 0.019 0.001 TYR B 219 PHE 0.038 0.002 PHE C 61 TRP 0.019 0.001 TRP N1156 HIS 0.013 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (24416) covalent geometry : angle 0.57487 / 0.30 (33218) hydrogen bonds : bond 0.03987 / 2.70 ( 1003) hydrogen bonds : angle 5.84924 / 4.16 ( 2877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 780 time to evaluate : 0.733 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7389 (m-80) cc_final: 0.7163 (m-80) REVERT: A 94 ARG cc_start: 0.7413 (ptm-80) cc_final: 0.7020 (ptm-80) REVERT: A 150 VAL cc_start: 0.8626 (p) cc_final: 0.7850 (p) REVERT: A 151 MET cc_start: 0.8359 (mmp) cc_final: 0.7854 (mmp) REVERT: A 159 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 174 ARG cc_start: 0.8009 (mmp80) cc_final: 0.7477 (mmp80) REVERT: A 182 PHE cc_start: 0.7958 (m-10) cc_final: 0.7609 (m-10) REVERT: A 207 GLN cc_start: 0.6751 (pm20) cc_final: 0.6494 (pm20) REVERT: A 256 ARG cc_start: 0.8824 (ttm170) cc_final: 0.8370 (ttm170) REVERT: A 288 PHE cc_start: 0.8287 (t80) cc_final: 0.7801 (t80) REVERT: B 46 ASP cc_start: 0.8106 (m-30) cc_final: 0.7870 (m-30) REVERT: B 48 LEU cc_start: 0.8092 (tt) cc_final: 0.7870 (tt) REVERT: B 80 HIS cc_start: 0.8455 (t70) cc_final: 0.7988 (t70) REVERT: B 109 LYS cc_start: 0.8409 (mptt) cc_final: 0.7641 (mmtm) REVERT: B 135 ASN cc_start: 0.7751 (p0) cc_final: 0.7354 (p0) REVERT: B 141 ASP cc_start: 0.6668 (m-30) cc_final: 0.6464 (m-30) REVERT: B 169 GLN cc_start: 0.8473 (mm110) cc_final: 0.8214 (mm-40) REVERT: B 210 ARG cc_start: 0.8513 (mmp80) cc_final: 0.8287 (mmp80) REVERT: B 254 MET cc_start: 0.7923 (mpp) cc_final: 0.7376 (mpp) REVERT: B 268 MET cc_start: 0.7618 (mmp) cc_final: 0.7258 (mmp) REVERT: B 271 ARG cc_start: 0.8585 (ttt-90) cc_final: 0.8189 (ttt-90) REVERT: B 285 ASP cc_start: 0.7870 (p0) cc_final: 0.7562 (p0) REVERT: B 310 TYR cc_start: 0.7488 (t80) cc_final: 0.6958 (t80) REVERT: C 33 TYR cc_start: 0.6201 (m-80) cc_final: 0.5602 (m-80) REVERT: C 116 GLU cc_start: 0.8056 (tp30) cc_final: 0.7426 (tp30) REVERT: C 119 GLN cc_start: 0.8564 (pm20) cc_final: 0.8129 (pm20) REVERT: C 141 ASP cc_start: 0.7198 (t0) cc_final: 0.6732 (t0) REVERT: C 152 PHE cc_start: 0.7506 (m-80) cc_final: 0.7174 (m-80) REVERT: C 217 LEU cc_start: 0.8111 (mt) cc_final: 0.7907 (mt) REVERT: C 236 TYR cc_start: 0.6585 (m-10) cc_final: 0.6329 (m-10) REVERT: C 238 ASN cc_start: 0.8964 (p0) cc_final: 0.8649 (p0) REVERT: C 248 MET cc_start: 0.8840 (mtp) cc_final: 0.8579 (mtp) REVERT: C 257 GLN cc_start: 0.8666 (tp40) cc_final: 0.8217 (tp40) REVERT: C 288 PHE cc_start: 0.8300 (t80) cc_final: 0.7058 (t80) REVERT: C 292 LEU cc_start: 0.7980 (mt) cc_final: 0.7406 (mt) REVERT: D 37 ASP cc_start: 0.7182 (m-30) cc_final: 0.6834 (m-30) REVERT: D 44 ASP cc_start: 0.7503 (m-30) cc_final: 0.6912 (m-30) REVERT: D 50 ASP cc_start: 0.7699 (t70) cc_final: 0.7388 (t70) REVERT: D 53 THR cc_start: 0.8326 (p) cc_final: 0.8038 (p) REVERT: D 123 PHE cc_start: 0.7649 (t80) cc_final: 0.7237 (t80) REVERT: D 124 LYS cc_start: 0.7700 (mmpt) cc_final: 0.7319 (mmpt) REVERT: D 130 TRP cc_start: 0.8591 (t60) cc_final: 0.7821 (t60) REVERT: D 144 ASP cc_start: 0.7404 (p0) cc_final: 0.6970 (p0) REVERT: D 166 LEU cc_start: 0.7998 (mt) cc_final: 0.7790 (mt) REVERT: D 179 PHE cc_start: 0.8494 (t80) cc_final: 0.7742 (t80) REVERT: D 182 PHE cc_start: 0.7439 (m-80) cc_final: 0.7189 (m-80) REVERT: D 201 GLN cc_start: 0.6532 (mp-120) cc_final: 0.6115 (mp-120) REVERT: D 205 GLN cc_start: 0.7690 (mp10) cc_final: 0.7222 (mp10) REVERT: D 208 MET cc_start: 0.7856 (ptp) cc_final: 0.7073 (ptp) REVERT: D 209 ASP cc_start: 0.7780 (t0) cc_final: 0.7420 (t0) REVERT: D 224 ASN cc_start: 0.8079 (m110) cc_final: 0.7867 (m110) REVERT: D 227 ASN cc_start: 0.8744 (m110) cc_final: 0.8386 (m110) REVERT: D 248 MET cc_start: 0.8416 (ttm) cc_final: 0.8108 (ttm) REVERT: D 251 VAL cc_start: 0.8950 (t) cc_final: 0.8329 (t) REVERT: D 254 MET cc_start: 0.8719 (mtm) cc_final: 0.8189 (mtm) REVERT: D 257 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7353 (tp-100) REVERT: D 278 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8443 (mt-10) REVERT: E 29 MET cc_start: 0.6998 (mmp) cc_final: 0.6790 (mmp) REVERT: E 46 ASP cc_start: 0.7692 (t0) cc_final: 0.7277 (t0) REVERT: E 49 PHE cc_start: 0.7540 (m-10) cc_final: 0.7159 (m-10) REVERT: E 101 VAL cc_start: 0.8641 (p) cc_final: 0.8371 (m) REVERT: E 143 TYR cc_start: 0.8494 (t80) cc_final: 0.7422 (t80) REVERT: E 250 ARG cc_start: 0.8378 (mmt180) cc_final: 0.7935 (mmt180) REVERT: E 261 ASN cc_start: 0.8607 (m-40) cc_final: 0.8299 (m-40) REVERT: E 279 ASN cc_start: 0.8563 (m-40) cc_final: 0.8335 (m-40) REVERT: E 285 ASP cc_start: 0.8482 (t70) cc_final: 0.8191 (t0) REVERT: E 300 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7158 (mm-30) REVERT: E 309 PHE cc_start: 0.8121 (m-80) cc_final: 0.7629 (m-80) REVERT: E 317 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7526 (mm-30) REVERT: F 42 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7631 (tm-30) REVERT: F 63 TYR cc_start: 0.6991 (m-10) cc_final: 0.6715 (m-10) REVERT: F 64 ASN cc_start: 0.8261 (m-40) cc_final: 0.8032 (m-40) REVERT: F 68 MET cc_start: 0.7555 (tmm) cc_final: 0.7140 (tmm) REVERT: F 100 HIS cc_start: 0.8024 (m-70) cc_final: 0.7708 (m-70) REVERT: F 109 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7522 (mtpp) REVERT: F 123 PHE cc_start: 0.7948 (t80) cc_final: 0.7739 (t80) REVERT: F 133 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7804 (tm-30) REVERT: F 147 ARG cc_start: 0.7805 (ptp-170) cc_final: 0.7440 (ptp-170) REVERT: F 152 PHE cc_start: 0.7588 (m-10) cc_final: 0.7362 (m-10) REVERT: F 215 THR cc_start: 0.7682 (t) cc_final: 0.7455 (t) REVERT: F 278 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8270 (mt-10) REVERT: F 294 PHE cc_start: 0.6991 (t80) cc_final: 0.6747 (t80) REVERT: F 297 LYS cc_start: 0.8714 (mppt) cc_final: 0.8505 (mppt) REVERT: F 301 LEU cc_start: 0.8170 (mp) cc_final: 0.7832 (mp) REVERT: G 334 LEU cc_start: 0.8407 (mt) cc_final: 0.8175 (mt) REVERT: G 368 ARG cc_start: 0.8463 (mmm160) cc_final: 0.8187 (mmm-85) REVERT: G 369 LEU cc_start: 0.7993 (tp) cc_final: 0.7766 (tp) REVERT: G 370 MET cc_start: 0.6778 (tpt) cc_final: 0.6093 (tpt) REVERT: G 489 HIS cc_start: 0.8206 (m170) cc_final: 0.7613 (m170) REVERT: G 511 ARG cc_start: 0.8831 (ttm170) cc_final: 0.8435 (ttm170) REVERT: G 524 LEU cc_start: 0.9152 (mt) cc_final: 0.8804 (mt) REVERT: G 531 LEU cc_start: 0.8456 (tp) cc_final: 0.8100 (tp) REVERT: G 564 GLU cc_start: 0.6938 (tm-30) cc_final: 0.5704 (tm-30) REVERT: N 432 MET cc_start: 0.8357 (mmt) cc_final: 0.7677 (mmt) REVERT: N 436 MET cc_start: 0.8000 (tpt) cc_final: 0.7301 (tpt) REVERT: N 673 MET cc_start: 0.8679 (ppp) cc_final: 0.8344 (ppp) REVERT: N 677 LYS cc_start: 0.7727 (ptpp) cc_final: 0.7317 (ptpp) REVERT: N 681 TYR cc_start: 0.8326 (t80) cc_final: 0.7680 (t80) REVERT: N 819 MET cc_start: 0.7217 (mtm) cc_final: 0.7007 (mtm) REVERT: N 877 GLU cc_start: 0.9077 (pm20) cc_final: 0.8862 (pm20) REVERT: N 890 TYR cc_start: 0.7423 (t80) cc_final: 0.6807 (t80) REVERT: N 1085 VAL cc_start: 0.8194 (m) cc_final: 0.7883 (p) REVERT: N 1120 MET cc_start: 0.5932 (tpt) cc_final: 0.5476 (tpt) REVERT: N 1145 ARG cc_start: 0.8255 (mtm110) cc_final: 0.7454 (mtm180) REVERT: N 1155 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8239 (mtmm) REVERT: N 1243 PHE cc_start: 0.7954 (t80) cc_final: 0.7152 (t80) outliers start: 6 outliers final: 0 residues processed: 783 average time/residue: 0.1662 time to fit residues: 196.7073 Evaluate side-chains 748 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 748 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 155 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 137 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 119 optimal weight: 0.0870 chunk 267 optimal weight: 10.0000 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN C 100 HIS C 186 ASN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN F 134 HIS ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN G 406 GLN N 470 GLN N1091 ASN ** N1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.172178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136632 restraints weight = 49991.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141950 restraints weight = 32094.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145901 restraints weight = 22614.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.148782 restraints weight = 17007.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.150804 restraints weight = 13447.178| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24416 Z= 0.167 Angle : 0.582 8.258 33218 Z= 0.308 Chirality : 0.043 0.191 3709 Planarity : 0.005 0.081 4359 Dihedral : 7.160 75.239 3443 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.24 % Allowed : 3.19 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3010 helix: -0.15 (0.14), residues: 1311 sheet: -0.79 (0.27), residues: 353 loop : -1.11 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 94 TYR 0.019 0.001 TYR N1177 PHE 0.035 0.002 PHE C 61 TRP 0.020 0.001 TRP N1156 HIS 0.010 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (24416) covalent geometry : angle 0.58237 / 0.31 (33218) hydrogen bonds : bond 0.03960 / 2.68 ( 1003) hydrogen bonds : angle 5.81707 / 4.15 ( 2877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 788 time to evaluate : 0.673 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 revert: symmetry clash revert: 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 72 TYR cc_start: 0.7410 (m-80) cc_final: 0.7191 (m-80) REVERT: A 94 ARG cc_start: 0.7536 (ptm-80) cc_final: 0.7158 (ptm-80) REVERT: A 103 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7868 (ttm-80) REVERT: A 150 VAL cc_start: 0.8679 (p) cc_final: 0.7921 (p) REVERT: A 151 MET cc_start: 0.8434 (mmp) cc_final: 0.7911 (mmp) REVERT: A 159 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 174 ARG cc_start: 0.8103 (mmp80) cc_final: 0.7508 (mmp80) REVERT: A 207 GLN cc_start: 0.6797 (pm20) cc_final: 0.6497 (pm20) REVERT: A 243 GLU cc_start: 0.8476 (pp20) cc_final: 0.8265 (pp20) REVERT: A 245 VAL cc_start: 0.9244 (p) cc_final: 0.8875 (m) REVERT: A 248 MET cc_start: 0.8380 (ptp) cc_final: 0.7983 (ptp) REVERT: A 288 PHE cc_start: 0.8283 (t80) cc_final: 0.7824 (t80) REVERT: B 48 LEU cc_start: 0.8125 (tt) cc_final: 0.7847 (tt) REVERT: B 80 HIS cc_start: 0.8462 (t70) cc_final: 0.7977 (t70) REVERT: B 109 LYS cc_start: 0.8427 (mptt) cc_final: 0.7701 (mmtm) REVERT: B 138 LEU cc_start: 0.7834 (tp) cc_final: 0.7418 (tp) REVERT: B 141 ASP cc_start: 0.6762 (m-30) cc_final: 0.6512 (m-30) REVERT: B 167 LEU cc_start: 0.9032 (tp) cc_final: 0.8830 (tp) REVERT: B 169 GLN cc_start: 0.8439 (mm110) cc_final: 0.8235 (mm-40) REVERT: B 210 ARG cc_start: 0.8559 (mmp80) cc_final: 0.8312 (mmp80) REVERT: B 254 MET cc_start: 0.7859 (mpp) cc_final: 0.7407 (mpp) REVERT: B 268 MET cc_start: 0.7636 (mmp) cc_final: 0.7233 (mmp) REVERT: B 271 ARG cc_start: 0.8649 (ttt-90) cc_final: 0.8196 (ttt-90) REVERT: B 285 ASP cc_start: 0.7874 (p0) cc_final: 0.7586 (p0) REVERT: B 309 PHE cc_start: 0.8988 (m-10) cc_final: 0.8714 (m-80) REVERT: B 310 TYR cc_start: 0.7613 (t80) cc_final: 0.7105 (t80) REVERT: C 29 MET cc_start: 0.6816 (tpt) cc_final: 0.6600 (tpp) REVERT: C 33 TYR cc_start: 0.6500 (m-80) cc_final: 0.5868 (m-80) REVERT: C 52 GLN cc_start: 0.8775 (tp40) cc_final: 0.8358 (tp-100) REVERT: C 119 GLN cc_start: 0.8584 (pm20) cc_final: 0.8115 (pm20) REVERT: C 141 ASP cc_start: 0.7329 (t0) cc_final: 0.6957 (t0) REVERT: C 152 PHE cc_start: 0.7617 (m-80) cc_final: 0.7250 (m-80) REVERT: C 174 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7176 (mtt-85) REVERT: C 236 TYR cc_start: 0.6766 (m-10) cc_final: 0.6476 (m-10) REVERT: C 238 ASN cc_start: 0.8959 (p0) cc_final: 0.8738 (p0) REVERT: C 248 MET cc_start: 0.8799 (mtp) cc_final: 0.8531 (mtp) REVERT: C 257 GLN cc_start: 0.8686 (tp40) cc_final: 0.8200 (tp40) REVERT: C 288 PHE cc_start: 0.8363 (t80) cc_final: 0.7095 (t80) REVERT: C 292 LEU cc_start: 0.7959 (mt) cc_final: 0.7339 (mt) REVERT: C 309 PHE cc_start: 0.8678 (m-80) cc_final: 0.8350 (m-80) REVERT: D 37 ASP cc_start: 0.7284 (m-30) cc_final: 0.6932 (m-30) REVERT: D 44 ASP cc_start: 0.7506 (m-30) cc_final: 0.6897 (m-30) REVERT: D 50 ASP cc_start: 0.7690 (t70) cc_final: 0.7372 (t70) REVERT: D 53 THR cc_start: 0.8374 (p) cc_final: 0.8085 (p) REVERT: D 80 HIS cc_start: 0.8478 (m-70) cc_final: 0.8201 (m-70) REVERT: D 92 CYS cc_start: 0.7893 (t) cc_final: 0.7629 (t) REVERT: D 123 PHE cc_start: 0.7690 (t80) cc_final: 0.7272 (t80) REVERT: D 124 LYS cc_start: 0.7775 (mmpt) cc_final: 0.7410 (mmpt) REVERT: D 130 TRP cc_start: 0.8779 (t60) cc_final: 0.7771 (t60) REVERT: D 144 ASP cc_start: 0.7515 (p0) cc_final: 0.7119 (p0) REVERT: D 179 PHE cc_start: 0.8568 (t80) cc_final: 0.7750 (t80) REVERT: D 182 PHE cc_start: 0.7653 (m-80) cc_final: 0.7382 (m-80) REVERT: D 201 GLN cc_start: 0.6518 (mp-120) cc_final: 0.6132 (mp-120) REVERT: D 205 GLN cc_start: 0.7763 (mp10) cc_final: 0.7237 (mp10) REVERT: D 208 MET cc_start: 0.7873 (ptp) cc_final: 0.7083 (ptp) REVERT: D 209 ASP cc_start: 0.7888 (t0) cc_final: 0.7435 (t0) REVERT: D 224 ASN cc_start: 0.8117 (m110) cc_final: 0.7883 (m110) REVERT: D 227 ASN cc_start: 0.8773 (m110) cc_final: 0.8410 (m110) REVERT: D 248 MET cc_start: 0.8433 (ttm) cc_final: 0.8161 (ttm) REVERT: D 251 VAL cc_start: 0.8925 (t) cc_final: 0.8424 (t) REVERT: D 254 MET cc_start: 0.8808 (mtm) cc_final: 0.8283 (mtm) REVERT: D 257 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7223 (tp-100) REVERT: D 261 ASN cc_start: 0.8621 (m-40) cc_final: 0.7718 (m110) REVERT: D 278 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8485 (mt-10) REVERT: D 294 PHE cc_start: 0.7657 (t80) cc_final: 0.7415 (t80) REVERT: E 29 MET cc_start: 0.7139 (mmp) cc_final: 0.6903 (mmp) REVERT: E 46 ASP cc_start: 0.7790 (t0) cc_final: 0.7342 (t0) REVERT: E 49 PHE cc_start: 0.7599 (m-10) cc_final: 0.7230 (m-10) REVERT: E 101 VAL cc_start: 0.8620 (p) cc_final: 0.8418 (m) REVERT: E 143 TYR cc_start: 0.8427 (t80) cc_final: 0.7957 (t80) REVERT: E 166 LEU cc_start: 0.7897 (mt) cc_final: 0.7688 (mt) REVERT: E 202 GLN cc_start: 0.7811 (tp40) cc_final: 0.7532 (tp40) REVERT: E 204 ASN cc_start: 0.7457 (p0) cc_final: 0.7138 (p0) REVERT: E 248 MET cc_start: 0.7778 (tpt) cc_final: 0.7352 (mmm) REVERT: E 250 ARG cc_start: 0.8406 (mmt180) cc_final: 0.7948 (mmt180) REVERT: E 261 ASN cc_start: 0.8609 (m-40) cc_final: 0.8294 (m-40) REVERT: E 285 ASP cc_start: 0.8437 (t70) cc_final: 0.8092 (t0) REVERT: E 300 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7202 (mm-30) REVERT: E 309 PHE cc_start: 0.8138 (m-80) cc_final: 0.7669 (m-80) REVERT: E 317 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7533 (mm-30) REVERT: F 42 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7593 (tm-30) REVERT: F 63 TYR cc_start: 0.7161 (m-10) cc_final: 0.6715 (m-10) REVERT: F 64 ASN cc_start: 0.8107 (m-40) cc_final: 0.7884 (m-40) REVERT: F 68 MET cc_start: 0.7565 (tmm) cc_final: 0.7143 (tmm) REVERT: F 100 HIS cc_start: 0.8088 (m-70) cc_final: 0.7666 (m-70) REVERT: F 109 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7645 (mtpp) REVERT: F 123 PHE cc_start: 0.7982 (t80) cc_final: 0.7724 (t80) REVERT: F 133 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7757 (tm-30) REVERT: F 147 ARG cc_start: 0.7895 (ptp-170) cc_final: 0.7456 (ptp-170) REVERT: F 152 PHE cc_start: 0.7609 (m-10) cc_final: 0.7401 (m-10) REVERT: F 244 ILE cc_start: 0.8919 (mt) cc_final: 0.8719 (mt) REVERT: F 278 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8292 (mt-10) REVERT: F 295 LEU cc_start: 0.8818 (tp) cc_final: 0.8614 (tp) REVERT: F 297 LYS cc_start: 0.8782 (mppt) cc_final: 0.8573 (mppt) REVERT: F 301 LEU cc_start: 0.8239 (mp) cc_final: 0.7843 (mp) REVERT: G 369 LEU cc_start: 0.8013 (tp) cc_final: 0.7804 (tp) REVERT: G 370 MET cc_start: 0.6858 (tpt) cc_final: 0.6183 (tpt) REVERT: G 489 HIS cc_start: 0.8245 (m170) cc_final: 0.7680 (m170) REVERT: G 524 LEU cc_start: 0.9143 (mt) cc_final: 0.8830 (mt) REVERT: G 531 LEU cc_start: 0.8491 (tp) cc_final: 0.8132 (tp) REVERT: G 543 MET cc_start: 0.7011 (tpt) cc_final: 0.6740 (tpt) REVERT: N 432 MET cc_start: 0.8298 (mmt) cc_final: 0.7654 (mmt) REVERT: N 436 MET cc_start: 0.8022 (tpt) cc_final: 0.7357 (tpt) REVERT: N 681 TYR cc_start: 0.8350 (t80) cc_final: 0.7712 (t80) REVERT: N 819 MET cc_start: 0.7221 (mtm) cc_final: 0.6978 (mtm) REVERT: N 890 TYR cc_start: 0.7433 (t80) cc_final: 0.6838 (t80) REVERT: N 1077 GLU cc_start: 0.8076 (pm20) cc_final: 0.7860 (pm20) REVERT: N 1085 VAL cc_start: 0.8190 (m) cc_final: 0.7843 (p) REVERT: N 1120 MET cc_start: 0.5896 (tpt) cc_final: 0.5477 (tpt) REVERT: N 1145 ARG cc_start: 0.8242 (mtm110) cc_final: 0.7698 (mtm110) REVERT: N 1155 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8231 (mtmm) REVERT: N 1243 PHE cc_start: 0.8107 (t80) cc_final: 0.7373 (t80) outliers start: 6 outliers final: 1 residues processed: 791 average time/residue: 0.1609 time to fit residues: 193.1226 Evaluate side-chains 764 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 763 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 241 optimal weight: 5.9990 chunk 271 optimal weight: 50.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 100 HIS ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS F 207 GLN F 296 ASN ** N 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.165239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130619 restraints weight = 49963.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135951 restraints weight = 31990.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139892 restraints weight = 22324.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142695 restraints weight = 16654.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.145016 restraints weight = 13048.728| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24416 Z= 0.162 Angle : 0.588 8.613 33218 Z= 0.309 Chirality : 0.044 0.205 3709 Planarity : 0.005 0.091 4359 Dihedral : 6.953 79.065 3443 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.08 % Allowed : 2.31 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 3010 helix: -0.14 (0.14), residues: 1310 sheet: -0.82 (0.27), residues: 350 loop : -1.11 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 94 TYR 0.020 0.001 TYR N1177 PHE 0.035 0.002 PHE C 61 TRP 0.020 0.001 TRP N1156 HIS 0.008 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (24416) covalent geometry : angle 0.58752 / 0.31 (33218) hydrogen bonds : bond 0.03834 / 2.60 ( 1003) hydrogen bonds : angle 5.81633 / 4.14 ( 2877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 785 time to evaluate : 0.629 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 revert: symmetry clash revert: 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 72 TYR cc_start: 0.7403 (m-80) cc_final: 0.7174 (m-80) REVERT: A 94 ARG cc_start: 0.7499 (ptm-80) cc_final: 0.7097 (ptm-80) REVERT: A 103 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7787 (ttm-80) REVERT: A 150 VAL cc_start: 0.8698 (p) cc_final: 0.7940 (p) REVERT: A 151 MET cc_start: 0.8447 (mmp) cc_final: 0.7927 (mmp) REVERT: A 159 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7338 (mt-10) REVERT: A 174 ARG cc_start: 0.8099 (mmp80) cc_final: 0.7453 (mmp80) REVERT: A 207 GLN cc_start: 0.6782 (pm20) cc_final: 0.6513 (pm20) REVERT: A 248 MET cc_start: 0.8319 (ptp) cc_final: 0.8033 (ptp) REVERT: A 288 PHE cc_start: 0.8348 (t80) cc_final: 0.7856 (t80) REVERT: B 48 LEU cc_start: 0.8136 (tt) cc_final: 0.7827 (tt) REVERT: B 80 HIS cc_start: 0.8482 (t70) cc_final: 0.8005 (t70) REVERT: B 109 LYS cc_start: 0.8455 (mptt) cc_final: 0.7751 (mmtm) REVERT: B 138 LEU cc_start: 0.7802 (tp) cc_final: 0.7402 (tp) REVERT: B 141 ASP cc_start: 0.6751 (m-30) cc_final: 0.6486 (m-30) REVERT: B 169 GLN cc_start: 0.8487 (mm110) cc_final: 0.8252 (mm-40) REVERT: B 210 ARG cc_start: 0.8561 (mmp80) cc_final: 0.8308 (mmp80) REVERT: B 254 MET cc_start: 0.7871 (mpp) cc_final: 0.7400 (mpp) REVERT: B 268 MET cc_start: 0.7658 (mmp) cc_final: 0.7161 (mmp) REVERT: B 271 ARG cc_start: 0.8674 (ttt-90) cc_final: 0.8204 (ttt-90) REVERT: B 285 ASP cc_start: 0.7789 (p0) cc_final: 0.7587 (p0) REVERT: B 310 TYR cc_start: 0.7639 (t80) cc_final: 0.7150 (t80) REVERT: C 52 GLN cc_start: 0.8737 (tp40) cc_final: 0.8404 (tp-100) REVERT: C 119 GLN cc_start: 0.8596 (pm20) cc_final: 0.8167 (pm20) REVERT: C 141 ASP cc_start: 0.7221 (t0) cc_final: 0.6857 (t0) REVERT: C 152 PHE cc_start: 0.7643 (m-80) cc_final: 0.7315 (m-80) REVERT: C 174 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7175 (mtt-85) REVERT: C 236 TYR cc_start: 0.6759 (m-10) cc_final: 0.6442 (m-10) REVERT: C 238 ASN cc_start: 0.8960 (p0) cc_final: 0.8737 (p0) REVERT: C 248 MET cc_start: 0.8754 (mtp) cc_final: 0.8448 (mtp) REVERT: C 257 GLN cc_start: 0.8712 (tp40) cc_final: 0.8240 (tp40) REVERT: C 268 MET cc_start: 0.7678 (mmp) cc_final: 0.7430 (mmp) REVERT: C 288 PHE cc_start: 0.8340 (t80) cc_final: 0.7040 (t80) REVERT: C 292 LEU cc_start: 0.7998 (mt) cc_final: 0.7375 (mt) REVERT: C 309 PHE cc_start: 0.8591 (m-80) cc_final: 0.8328 (m-80) REVERT: D 37 ASP cc_start: 0.7286 (m-30) cc_final: 0.6909 (m-30) REVERT: D 44 ASP cc_start: 0.7495 (m-30) cc_final: 0.6888 (m-30) REVERT: D 50 ASP cc_start: 0.7677 (t70) cc_final: 0.7350 (t70) REVERT: D 53 THR cc_start: 0.8345 (p) cc_final: 0.8053 (p) REVERT: D 80 HIS cc_start: 0.8472 (m-70) cc_final: 0.8141 (m-70) REVERT: D 92 CYS cc_start: 0.7473 (t) cc_final: 0.7267 (t) REVERT: D 123 PHE cc_start: 0.7719 (t80) cc_final: 0.7296 (t80) REVERT: D 124 LYS cc_start: 0.7754 (mmpt) cc_final: 0.7391 (mmpt) REVERT: D 130 TRP cc_start: 0.8814 (t60) cc_final: 0.8149 (t60) REVERT: D 144 ASP cc_start: 0.7499 (p0) cc_final: 0.7108 (p0) REVERT: D 155 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7483 (tm-30) REVERT: D 179 PHE cc_start: 0.8580 (t80) cc_final: 0.7721 (t80) REVERT: D 182 PHE cc_start: 0.7656 (m-80) cc_final: 0.7340 (m-80) REVERT: D 201 GLN cc_start: 0.6521 (mp-120) cc_final: 0.6107 (mp-120) REVERT: D 205 GLN cc_start: 0.7760 (mp10) cc_final: 0.7177 (mp10) REVERT: D 208 MET cc_start: 0.7842 (ptp) cc_final: 0.7073 (ptp) REVERT: D 209 ASP cc_start: 0.7890 (t0) cc_final: 0.7418 (t0) REVERT: D 224 ASN cc_start: 0.8111 (m110) cc_final: 0.7881 (m110) REVERT: D 227 ASN cc_start: 0.8785 (m110) cc_final: 0.8433 (m110) REVERT: D 248 MET cc_start: 0.8432 (ttm) cc_final: 0.8198 (ttm) REVERT: D 251 VAL cc_start: 0.8991 (t) cc_final: 0.8377 (t) REVERT: D 254 MET cc_start: 0.8838 (mtm) cc_final: 0.8229 (mtm) REVERT: D 256 ARG cc_start: 0.8666 (mtt90) cc_final: 0.8009 (mtt90) REVERT: D 257 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7168 (tp-100) REVERT: D 261 ASN cc_start: 0.8606 (m-40) cc_final: 0.7664 (m110) REVERT: D 278 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8498 (mt-10) REVERT: D 294 PHE cc_start: 0.7830 (t80) cc_final: 0.7582 (t80) REVERT: D 297 LYS cc_start: 0.8502 (ptmt) cc_final: 0.8285 (ptmt) REVERT: E 29 MET cc_start: 0.7134 (mmp) cc_final: 0.6926 (mmp) REVERT: E 46 ASP cc_start: 0.7765 (t0) cc_final: 0.7322 (t0) REVERT: E 49 PHE cc_start: 0.7628 (m-10) cc_final: 0.7267 (m-10) REVERT: E 151 MET cc_start: 0.7845 (tpp) cc_final: 0.7557 (tpp) REVERT: E 166 LEU cc_start: 0.7914 (mt) cc_final: 0.7705 (mt) REVERT: E 169 GLN cc_start: 0.8298 (pp30) cc_final: 0.8040 (pp30) REVERT: E 202 GLN cc_start: 0.7806 (tp40) cc_final: 0.7485 (tp40) REVERT: E 248 MET cc_start: 0.7792 (tpt) cc_final: 0.7322 (mmm) REVERT: E 261 ASN cc_start: 0.8618 (m-40) cc_final: 0.8312 (m-40) REVERT: E 285 ASP cc_start: 0.8468 (t70) cc_final: 0.8130 (t0) REVERT: E 300 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7178 (mm-30) REVERT: E 309 PHE cc_start: 0.8108 (m-80) cc_final: 0.7698 (m-80) REVERT: E 317 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7635 (mm-30) REVERT: F 63 TYR cc_start: 0.7159 (m-10) cc_final: 0.6658 (m-10) REVERT: F 68 MET cc_start: 0.7647 (tmm) cc_final: 0.7170 (tmm) REVERT: F 100 HIS cc_start: 0.8084 (m-70) cc_final: 0.7682 (m-70) REVERT: F 109 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7537 (mttp) REVERT: F 123 PHE cc_start: 0.8039 (t80) cc_final: 0.7781 (t80) REVERT: F 147 ARG cc_start: 0.7909 (ptp-170) cc_final: 0.7473 (ptp-170) REVERT: F 244 ILE cc_start: 0.8910 (mt) cc_final: 0.8709 (mt) REVERT: F 278 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8287 (mt-10) REVERT: F 295 LEU cc_start: 0.8797 (tp) cc_final: 0.8594 (tp) REVERT: F 301 LEU cc_start: 0.8274 (mp) cc_final: 0.7753 (mp) REVERT: G 369 LEU cc_start: 0.8018 (tp) cc_final: 0.7812 (tp) REVERT: G 370 MET cc_start: 0.6843 (tpt) cc_final: 0.6117 (tpt) REVERT: G 430 ARG cc_start: 0.9162 (tmt-80) cc_final: 0.8903 (tpt90) REVERT: G 432 ILE cc_start: 0.9279 (tt) cc_final: 0.9014 (tt) REVERT: G 480 ASN cc_start: 0.8679 (t0) cc_final: 0.8449 (t0) REVERT: G 489 HIS cc_start: 0.8210 (m170) cc_final: 0.7599 (m170) REVERT: G 509 MET cc_start: 0.8539 (ppp) cc_final: 0.7754 (ppp) REVERT: G 524 LEU cc_start: 0.9178 (mt) cc_final: 0.8863 (mt) REVERT: G 531 LEU cc_start: 0.8548 (tp) cc_final: 0.8291 (tp) REVERT: G 543 MET cc_start: 0.6955 (tpt) cc_final: 0.6674 (tpt) REVERT: N 432 MET cc_start: 0.8227 (mmt) cc_final: 0.7578 (mmt) REVERT: N 436 MET cc_start: 0.8003 (tpt) cc_final: 0.7343 (tpt) REVERT: N 498 MET cc_start: 0.4560 (mmm) cc_final: 0.4160 (mmm) REVERT: N 681 TYR cc_start: 0.8357 (t80) cc_final: 0.7756 (t80) REVERT: N 819 MET cc_start: 0.7230 (mtm) cc_final: 0.6999 (mtm) REVERT: N 849 THR cc_start: 0.7291 (t) cc_final: 0.6596 (m) REVERT: N 890 TYR cc_start: 0.7489 (t80) cc_final: 0.6891 (t80) REVERT: N 911 MET cc_start: 0.7925 (mtp) cc_final: 0.7485 (mtp) REVERT: N 1077 GLU cc_start: 0.8100 (pm20) cc_final: 0.7871 (pm20) REVERT: N 1085 VAL cc_start: 0.8240 (m) cc_final: 0.7899 (p) REVERT: N 1120 MET cc_start: 0.5858 (tpt) cc_final: 0.5448 (tpt) REVERT: N 1145 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7703 (mtm110) REVERT: N 1155 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8248 (mtmm) REVERT: N 1209 PHE cc_start: 0.8498 (t80) cc_final: 0.8286 (t80) REVERT: N 1239 ASN cc_start: 0.6161 (m-40) cc_final: 0.5853 (m-40) REVERT: N 1243 PHE cc_start: 0.8130 (t80) cc_final: 0.7204 (t80) outliers start: 2 outliers final: 0 residues processed: 786 average time/residue: 0.1650 time to fit residues: 195.2468 Evaluate side-chains 760 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 760 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 163 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 219 optimal weight: 0.0270 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 171 optimal weight: 0.0570 chunk 293 optimal weight: 4.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 HIS C 100 HIS ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS F 296 ASN N 892 GLN ** N1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.165696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131388 restraints weight = 49882.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136726 restraints weight = 31596.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.140641 restraints weight = 21983.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.143602 restraints weight = 16285.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.145783 restraints weight = 12595.172| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24416 Z= 0.144 Angle : 0.581 8.896 33218 Z= 0.304 Chirality : 0.043 0.212 3709 Planarity : 0.005 0.080 4359 Dihedral : 6.751 87.745 3443 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 3010 helix: -0.10 (0.14), residues: 1303 sheet: -0.65 (0.27), residues: 340 loop : -1.09 (0.18), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 TYR 0.019 0.001 TYR N1177 PHE 0.030 0.002 PHE A 309 TRP 0.021 0.001 TRP N1156 HIS 0.008 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (24416) covalent geometry : angle 0.58082 / 0.30 (33218) hydrogen bonds : bond 0.03657 / 2.48 ( 1003) hydrogen bonds : angle 5.73126 / 4.08 ( 2877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 794 time to evaluate : 0.733 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 72 TYR cc_start: 0.7373 (m-80) cc_final: 0.7138 (m-80) REVERT: A 94 ARG cc_start: 0.7523 (ptm-80) cc_final: 0.7093 (ptm-80) REVERT: A 103 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7760 (ttm-80) REVERT: A 150 VAL cc_start: 0.8673 (p) cc_final: 0.7860 (p) REVERT: A 151 MET cc_start: 0.8414 (mmp) cc_final: 0.7960 (mmp) REVERT: A 159 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7325 (mt-10) REVERT: A 174 ARG cc_start: 0.8084 (mmp80) cc_final: 0.7430 (mmp80) REVERT: A 207 GLN cc_start: 0.6811 (pm20) cc_final: 0.6572 (pm20) REVERT: A 248 MET cc_start: 0.8285 (ptp) cc_final: 0.7990 (ptp) REVERT: A 288 PHE cc_start: 0.8317 (t80) cc_final: 0.7838 (t80) REVERT: B 48 LEU cc_start: 0.8131 (tt) cc_final: 0.7815 (tt) REVERT: B 80 HIS cc_start: 0.8408 (t70) cc_final: 0.7951 (t70) REVERT: B 109 LYS cc_start: 0.8457 (mptt) cc_final: 0.7725 (mmtm) REVERT: B 141 ASP cc_start: 0.6612 (m-30) cc_final: 0.6396 (m-30) REVERT: B 169 GLN cc_start: 0.8459 (mm110) cc_final: 0.8235 (mm-40) REVERT: B 210 ARG cc_start: 0.8558 (mmp80) cc_final: 0.8293 (mmp80) REVERT: B 248 MET cc_start: 0.8331 (ptp) cc_final: 0.8101 (ptp) REVERT: B 254 MET cc_start: 0.7848 (mpp) cc_final: 0.7359 (mpp) REVERT: B 268 MET cc_start: 0.7551 (mmp) cc_final: 0.7032 (mmp) REVERT: B 271 ARG cc_start: 0.8660 (ttt-90) cc_final: 0.8192 (ttt-90) REVERT: B 285 ASP cc_start: 0.7773 (p0) cc_final: 0.7558 (p0) REVERT: B 310 TYR cc_start: 0.7553 (t80) cc_final: 0.7120 (t80) REVERT: C 116 GLU cc_start: 0.8066 (tp30) cc_final: 0.7406 (tp30) REVERT: C 119 GLN cc_start: 0.8562 (pm20) cc_final: 0.8113 (pm20) REVERT: C 141 ASP cc_start: 0.7175 (t0) cc_final: 0.6859 (t0) REVERT: C 152 PHE cc_start: 0.7531 (m-80) cc_final: 0.7234 (m-80) REVERT: C 174 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.7132 (mtt-85) REVERT: C 236 TYR cc_start: 0.6779 (m-10) cc_final: 0.6439 (m-10) REVERT: C 238 ASN cc_start: 0.8968 (p0) cc_final: 0.8725 (p0) REVERT: C 248 MET cc_start: 0.8689 (mtp) cc_final: 0.8373 (mtp) REVERT: C 257 GLN cc_start: 0.8672 (tp40) cc_final: 0.8341 (tp40) REVERT: C 268 MET cc_start: 0.7661 (mmp) cc_final: 0.7453 (mmp) REVERT: C 288 PHE cc_start: 0.8313 (t80) cc_final: 0.7009 (t80) REVERT: C 292 LEU cc_start: 0.7999 (mt) cc_final: 0.7374 (mt) REVERT: C 309 PHE cc_start: 0.8575 (m-80) cc_final: 0.8327 (m-80) REVERT: D 37 ASP cc_start: 0.7179 (m-30) cc_final: 0.6797 (m-30) REVERT: D 44 ASP cc_start: 0.7475 (m-30) cc_final: 0.6888 (m-30) REVERT: D 50 ASP cc_start: 0.7665 (t70) cc_final: 0.7340 (t70) REVERT: D 53 THR cc_start: 0.8388 (p) cc_final: 0.8099 (p) REVERT: D 80 HIS cc_start: 0.8474 (m-70) cc_final: 0.8143 (m-70) REVERT: D 92 CYS cc_start: 0.7750 (t) cc_final: 0.7510 (t) REVERT: D 103 ARG cc_start: 0.8451 (tmt170) cc_final: 0.8169 (ttp80) REVERT: D 123 PHE cc_start: 0.7743 (t80) cc_final: 0.7340 (t80) REVERT: D 124 LYS cc_start: 0.7765 (mmpt) cc_final: 0.7380 (mmpt) REVERT: D 130 TRP cc_start: 0.8817 (t60) cc_final: 0.8078 (t60) REVERT: D 144 ASP cc_start: 0.7433 (p0) cc_final: 0.7025 (p0) REVERT: D 179 PHE cc_start: 0.8564 (t80) cc_final: 0.7699 (t80) REVERT: D 182 PHE cc_start: 0.7745 (m-80) cc_final: 0.7457 (m-80) REVERT: D 201 GLN cc_start: 0.6500 (mp-120) cc_final: 0.6091 (mp-120) REVERT: D 205 GLN cc_start: 0.7712 (mp10) cc_final: 0.7129 (mp10) REVERT: D 208 MET cc_start: 0.7819 (ptp) cc_final: 0.7069 (ptp) REVERT: D 209 ASP cc_start: 0.7883 (t0) cc_final: 0.7381 (t0) REVERT: D 224 ASN cc_start: 0.8116 (m110) cc_final: 0.7874 (m110) REVERT: D 227 ASN cc_start: 0.8789 (m110) cc_final: 0.8436 (m110) REVERT: D 248 MET cc_start: 0.8408 (ttm) cc_final: 0.8194 (ttm) REVERT: D 251 VAL cc_start: 0.8896 (t) cc_final: 0.8363 (t) REVERT: D 254 MET cc_start: 0.8822 (mtm) cc_final: 0.8224 (mtm) REVERT: D 256 ARG cc_start: 0.8657 (mtt90) cc_final: 0.7987 (mtt90) REVERT: D 257 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7353 (tp-100) REVERT: D 268 MET cc_start: 0.7865 (mmp) cc_final: 0.7593 (mmp) REVERT: D 278 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8463 (mt-10) REVERT: D 294 PHE cc_start: 0.7694 (t80) cc_final: 0.7388 (t80) REVERT: E 46 ASP cc_start: 0.7733 (t0) cc_final: 0.7296 (t0) REVERT: E 49 PHE cc_start: 0.7576 (m-10) cc_final: 0.7241 (m-10) REVERT: E 68 MET cc_start: 0.6150 (tmm) cc_final: 0.5929 (tmm) REVERT: E 113 VAL cc_start: 0.8301 (m) cc_final: 0.7942 (p) REVERT: E 151 MET cc_start: 0.7840 (tpp) cc_final: 0.7515 (tpp) REVERT: E 155 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7648 (tp-100) REVERT: E 166 LEU cc_start: 0.7843 (mt) cc_final: 0.7536 (mt) REVERT: E 208 MET cc_start: 0.7973 (tpt) cc_final: 0.7701 (tpt) REVERT: E 248 MET cc_start: 0.7759 (tpt) cc_final: 0.7432 (tpt) REVERT: E 261 ASN cc_start: 0.8626 (m-40) cc_final: 0.8314 (m-40) REVERT: E 279 ASN cc_start: 0.8541 (m-40) cc_final: 0.8332 (m-40) REVERT: E 285 ASP cc_start: 0.8491 (t70) cc_final: 0.8159 (t0) REVERT: E 300 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7140 (mm-30) REVERT: E 309 PHE cc_start: 0.8064 (m-80) cc_final: 0.7661 (m-80) REVERT: E 317 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7627 (mm-30) REVERT: F 42 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7627 (tm-30) REVERT: F 51 ARG cc_start: 0.8423 (tpp80) cc_final: 0.7779 (tpp80) REVERT: F 58 LEU cc_start: 0.8903 (mt) cc_final: 0.8702 (mt) REVERT: F 63 TYR cc_start: 0.7015 (m-10) cc_final: 0.6662 (m-10) REVERT: F 68 MET cc_start: 0.7667 (tmm) cc_final: 0.7170 (tmm) REVERT: F 100 HIS cc_start: 0.8213 (m-70) cc_final: 0.7616 (m-70) REVERT: F 109 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7604 (mttm) REVERT: F 123 PHE cc_start: 0.8021 (t80) cc_final: 0.7774 (t80) REVERT: F 147 ARG cc_start: 0.7894 (ptp-170) cc_final: 0.7454 (ptp-170) REVERT: F 244 ILE cc_start: 0.8906 (mt) cc_final: 0.8701 (mt) REVERT: F 268 MET cc_start: 0.7832 (pmm) cc_final: 0.7625 (pmm) REVERT: F 278 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8288 (mt-10) REVERT: F 295 LEU cc_start: 0.8781 (tp) cc_final: 0.8567 (tp) REVERT: F 297 LYS cc_start: 0.8678 (mppt) cc_final: 0.8361 (mppt) REVERT: F 301 LEU cc_start: 0.8242 (mp) cc_final: 0.7712 (mp) REVERT: G 336 ASP cc_start: 0.8507 (p0) cc_final: 0.8144 (p0) REVERT: G 370 MET cc_start: 0.6753 (tpt) cc_final: 0.5995 (tpt) REVERT: G 432 ILE cc_start: 0.9248 (tt) cc_final: 0.8996 (tt) REVERT: G 480 ASN cc_start: 0.8699 (t0) cc_final: 0.8408 (t0) REVERT: G 489 HIS cc_start: 0.8213 (m170) cc_final: 0.7627 (m170) REVERT: G 508 LEU cc_start: 0.8721 (tp) cc_final: 0.8505 (tp) REVERT: G 509 MET cc_start: 0.8484 (ppp) cc_final: 0.7682 (ppp) REVERT: G 524 LEU cc_start: 0.9155 (mt) cc_final: 0.8843 (mt) REVERT: G 531 LEU cc_start: 0.8504 (tp) cc_final: 0.8230 (tp) REVERT: G 543 MET cc_start: 0.6927 (tpt) cc_final: 0.6697 (tpt) REVERT: G 564 GLU cc_start: 0.6915 (tm-30) cc_final: 0.5572 (tm-30) REVERT: N 432 MET cc_start: 0.8176 (mmt) cc_final: 0.7561 (mmt) REVERT: N 436 MET cc_start: 0.7940 (tpt) cc_final: 0.7237 (tpt) REVERT: N 598 LYS cc_start: 0.7182 (pttt) cc_final: 0.6853 (pttt) REVERT: N 681 TYR cc_start: 0.8286 (t80) cc_final: 0.7689 (t80) REVERT: N 819 MET cc_start: 0.7260 (mtm) cc_final: 0.7018 (mtm) REVERT: N 849 THR cc_start: 0.7212 (t) cc_final: 0.6474 (m) REVERT: N 890 TYR cc_start: 0.7416 (t80) cc_final: 0.6812 (t80) REVERT: N 911 MET cc_start: 0.7885 (mtp) cc_final: 0.7438 (mtp) REVERT: N 1085 VAL cc_start: 0.8226 (m) cc_final: 0.7881 (p) REVERT: N 1120 MET cc_start: 0.5799 (tpt) cc_final: 0.5462 (tpt) REVERT: N 1145 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7654 (mtm110) REVERT: N 1155 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8219 (mtmm) REVERT: N 1239 ASN cc_start: 0.6204 (m-40) cc_final: 0.5901 (m-40) REVERT: N 1243 PHE cc_start: 0.7986 (t80) cc_final: 0.7184 (t80) outliers start: 1 outliers final: 0 residues processed: 794 average time/residue: 0.1629 time to fit residues: 195.0967 Evaluate side-chains 762 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 762 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 94 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 231 optimal weight: 4.9990 chunk 284 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 235 HIS B 207 GLN ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 702 GLN ** N1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.167060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132041 restraints weight = 50089.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137164 restraints weight = 32302.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140953 restraints weight = 22901.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.143672 restraints weight = 17296.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145879 restraints weight = 13794.800| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24416 Z= 0.289 Angle : 0.696 10.712 33218 Z= 0.376 Chirality : 0.047 0.268 3709 Planarity : 0.006 0.090 4359 Dihedral : 7.176 86.978 3443 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 3010 helix: -0.49 (0.14), residues: 1307 sheet: -0.94 (0.27), residues: 340 loop : -1.25 (0.18), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 312 TYR 0.028 0.002 TYR A 143 PHE 0.040 0.002 PHE C 61 TRP 0.036 0.002 TRP B 90 HIS 0.010 0.002 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.29 (24416) covalent geometry : angle 0.69590 / 0.38 (33218) hydrogen bonds : bond 0.04813 / 3.24 ( 1003) hydrogen bonds : angle 6.22858 / 4.43 ( 2877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 789 time to evaluate : 0.840 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 revert: 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 72 TYR cc_start: 0.7455 (m-80) cc_final: 0.7205 (m-80) REVERT: A 94 ARG cc_start: 0.7677 (ptm-80) cc_final: 0.7452 (ptm-80) REVERT: A 103 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: A 150 VAL cc_start: 0.8770 (p) cc_final: 0.8051 (p) REVERT: A 151 MET cc_start: 0.8536 (mmp) cc_final: 0.7973 (mmp) REVERT: A 155 GLN cc_start: 0.8435 (pp30) cc_final: 0.8096 (pp30) REVERT: A 159 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 174 ARG cc_start: 0.8198 (mmp80) cc_final: 0.7496 (mmp80) REVERT: A 207 GLN cc_start: 0.6851 (pm20) cc_final: 0.6579 (pm20) REVERT: A 248 MET cc_start: 0.8369 (ptp) cc_final: 0.8104 (ptp) REVERT: A 288 PHE cc_start: 0.8408 (t80) cc_final: 0.7901 (t80) REVERT: B 48 LEU cc_start: 0.8187 (tt) cc_final: 0.7893 (tt) REVERT: B 80 HIS cc_start: 0.8521 (t70) cc_final: 0.8063 (t70) REVERT: B 100 HIS cc_start: 0.6863 (m-70) cc_final: 0.6178 (m-70) REVERT: B 109 LYS cc_start: 0.8456 (mptt) cc_final: 0.7741 (mmtm) REVERT: B 135 ASN cc_start: 0.7684 (p0) cc_final: 0.7293 (p0) REVERT: B 138 LEU cc_start: 0.7967 (tp) cc_final: 0.7503 (tp) REVERT: B 169 GLN cc_start: 0.8469 (mm110) cc_final: 0.8220 (mm-40) REVERT: B 182 PHE cc_start: 0.7246 (m-10) cc_final: 0.6966 (m-10) REVERT: B 209 ASP cc_start: 0.8472 (m-30) cc_final: 0.8268 (m-30) REVERT: B 210 ARG cc_start: 0.8598 (mmp80) cc_final: 0.8269 (mmp80) REVERT: B 244 ILE cc_start: 0.9203 (mt) cc_final: 0.8994 (mt) REVERT: B 248 MET cc_start: 0.8409 (ptp) cc_final: 0.8150 (ptp) REVERT: B 254 MET cc_start: 0.8003 (mpp) cc_final: 0.7532 (mpp) REVERT: B 268 MET cc_start: 0.7805 (mmp) cc_final: 0.7209 (mmp) REVERT: B 285 ASP cc_start: 0.7815 (p0) cc_final: 0.7577 (p0) REVERT: B 309 PHE cc_start: 0.8991 (m-80) cc_final: 0.8731 (m-80) REVERT: C 33 TYR cc_start: 0.7356 (m-80) cc_final: 0.7038 (m-80) REVERT: C 52 GLN cc_start: 0.8997 (tp40) cc_final: 0.8557 (tp-100) REVERT: C 116 GLU cc_start: 0.8127 (tp30) cc_final: 0.7493 (tp30) REVERT: C 119 GLN cc_start: 0.8681 (pm20) cc_final: 0.8399 (pm20) REVERT: C 141 ASP cc_start: 0.7385 (t0) cc_final: 0.7077 (t0) REVERT: C 152 PHE cc_start: 0.7769 (m-80) cc_final: 0.7515 (m-80) REVERT: C 174 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7174 (mtt-85) REVERT: C 227 ASN cc_start: 0.9163 (m110) cc_final: 0.8869 (m110) REVERT: C 230 LEU cc_start: 0.8894 (mt) cc_final: 0.8661 (mt) REVERT: C 236 TYR cc_start: 0.6894 (m-10) cc_final: 0.6404 (m-10) REVERT: C 238 ASN cc_start: 0.8990 (p0) cc_final: 0.8777 (p0) REVERT: C 257 GLN cc_start: 0.8747 (tp40) cc_final: 0.8380 (tp40) REVERT: C 268 MET cc_start: 0.7802 (mmp) cc_final: 0.7597 (mmp) REVERT: C 288 PHE cc_start: 0.8489 (t80) cc_final: 0.7227 (t80) REVERT: C 292 LEU cc_start: 0.7980 (mt) cc_final: 0.7412 (mt) REVERT: C 309 PHE cc_start: 0.8727 (m-80) cc_final: 0.8411 (m-80) REVERT: D 21 VAL cc_start: 0.9216 (p) cc_final: 0.8945 (p) REVERT: D 29 MET cc_start: 0.7392 (tpt) cc_final: 0.7130 (tpp) REVERT: D 37 ASP cc_start: 0.7415 (m-30) cc_final: 0.7048 (m-30) REVERT: D 44 ASP cc_start: 0.7545 (m-30) cc_final: 0.6922 (m-30) REVERT: D 50 ASP cc_start: 0.7708 (t70) cc_final: 0.7384 (t70) REVERT: D 53 THR cc_start: 0.8411 (p) cc_final: 0.8179 (p) REVERT: D 80 HIS cc_start: 0.8519 (m-70) cc_final: 0.8129 (m-70) REVERT: D 92 CYS cc_start: 0.7833 (t) cc_final: 0.7620 (t) REVERT: D 123 PHE cc_start: 0.7649 (t80) cc_final: 0.7283 (t80) REVERT: D 124 LYS cc_start: 0.7857 (mmpt) cc_final: 0.7562 (mmpt) REVERT: D 130 TRP cc_start: 0.8907 (t60) cc_final: 0.8177 (t60) REVERT: D 144 ASP cc_start: 0.7633 (p0) cc_final: 0.7260 (p0) REVERT: D 155 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 179 PHE cc_start: 0.8509 (t80) cc_final: 0.7531 (t80) REVERT: D 201 GLN cc_start: 0.6542 (mp-120) cc_final: 0.6162 (mp-120) REVERT: D 205 GLN cc_start: 0.7887 (mp10) cc_final: 0.7357 (mp10) REVERT: D 208 MET cc_start: 0.7938 (ptp) cc_final: 0.7198 (ptp) REVERT: D 224 ASN cc_start: 0.8111 (m110) cc_final: 0.7877 (m110) REVERT: D 227 ASN cc_start: 0.8869 (m110) cc_final: 0.8528 (m110) REVERT: D 251 VAL cc_start: 0.9027 (t) cc_final: 0.8439 (t) REVERT: D 254 MET cc_start: 0.8849 (mtm) cc_final: 0.8327 (mtm) REVERT: D 256 ARG cc_start: 0.8759 (mtt90) cc_final: 0.8143 (mtt90) REVERT: D 257 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7356 (tp-100) REVERT: D 261 ASN cc_start: 0.8633 (m-40) cc_final: 0.7717 (m-40) REVERT: D 278 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8578 (mt-10) REVERT: E 46 ASP cc_start: 0.7934 (t0) cc_final: 0.7489 (t0) REVERT: E 49 PHE cc_start: 0.7639 (m-10) cc_final: 0.7272 (m-10) REVERT: E 64 ASN cc_start: 0.8821 (t0) cc_final: 0.8583 (t0) REVERT: E 113 VAL cc_start: 0.8351 (m) cc_final: 0.7972 (p) REVERT: E 138 LEU cc_start: 0.8629 (tp) cc_final: 0.8410 (tp) REVERT: E 151 MET cc_start: 0.7982 (tpp) cc_final: 0.7699 (tpp) REVERT: E 152 PHE cc_start: 0.8936 (m-80) cc_final: 0.8427 (m-80) REVERT: E 154 ILE cc_start: 0.8946 (pt) cc_final: 0.8700 (pt) REVERT: E 169 GLN cc_start: 0.8295 (pp30) cc_final: 0.8041 (pp30) REVERT: E 248 MET cc_start: 0.7760 (tpt) cc_final: 0.7382 (tpt) REVERT: E 250 ARG cc_start: 0.8460 (mmt180) cc_final: 0.8148 (mmt90) REVERT: E 253 ASP cc_start: 0.7567 (m-30) cc_final: 0.7120 (m-30) REVERT: E 257 GLN cc_start: 0.8177 (mp10) cc_final: 0.7533 (mp10) REVERT: E 261 ASN cc_start: 0.8659 (m-40) cc_final: 0.8327 (m-40) REVERT: E 283 PHE cc_start: 0.8207 (m-10) cc_final: 0.7814 (m-80) REVERT: E 285 ASP cc_start: 0.8453 (t70) cc_final: 0.8124 (t0) REVERT: E 300 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7277 (mm-30) REVERT: E 309 PHE cc_start: 0.8223 (m-80) cc_final: 0.7821 (m-80) REVERT: F 42 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7627 (tm-30) REVERT: F 58 LEU cc_start: 0.9017 (mt) cc_final: 0.8813 (mt) REVERT: F 63 TYR cc_start: 0.7102 (m-10) cc_final: 0.6518 (m-10) REVERT: F 68 MET cc_start: 0.7637 (tmm) cc_final: 0.7154 (tmm) REVERT: F 100 HIS cc_start: 0.8097 (m-70) cc_final: 0.7579 (m-70) REVERT: F 109 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7678 (mttm) REVERT: F 123 PHE cc_start: 0.8101 (t80) cc_final: 0.7795 (t80) REVERT: F 147 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7559 (ptp-170) REVERT: F 244 ILE cc_start: 0.8932 (mt) cc_final: 0.8723 (mt) REVERT: F 268 MET cc_start: 0.7941 (pmm) cc_final: 0.7709 (pmm) REVERT: F 278 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8273 (mt-10) REVERT: F 295 LEU cc_start: 0.8802 (tp) cc_final: 0.8578 (tp) REVERT: F 297 LYS cc_start: 0.8775 (mppt) cc_final: 0.8431 (mppt) REVERT: F 301 LEU cc_start: 0.8320 (mp) cc_final: 0.7729 (mp) REVERT: G 369 LEU cc_start: 0.8056 (tp) cc_final: 0.7845 (tp) REVERT: G 370 MET cc_start: 0.7038 (tpt) cc_final: 0.6223 (tpt) REVERT: G 432 ILE cc_start: 0.9333 (tt) cc_final: 0.9112 (tt) REVERT: G 489 HIS cc_start: 0.8235 (m170) cc_final: 0.7594 (m90) REVERT: G 501 ARG cc_start: 0.8313 (ppt170) cc_final: 0.7558 (ptm-80) REVERT: G 509 MET cc_start: 0.8532 (ppp) cc_final: 0.7868 (ppp) REVERT: G 511 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8120 (ttm170) REVERT: G 512 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8296 (mm-30) REVERT: G 524 LEU cc_start: 0.9189 (mt) cc_final: 0.8918 (mt) REVERT: G 531 LEU cc_start: 0.8621 (tp) cc_final: 0.8353 (tp) REVERT: G 543 MET cc_start: 0.7001 (tpt) cc_final: 0.6742 (tpt) REVERT: N 432 MET cc_start: 0.8251 (mmt) cc_final: 0.7588 (mmt) REVERT: N 436 MET cc_start: 0.8041 (tpt) cc_final: 0.7379 (tpt) REVERT: N 498 MET cc_start: 0.5081 (mmm) cc_final: 0.4707 (mmm) REVERT: N 586 PHE cc_start: 0.6965 (t80) cc_final: 0.6697 (t80) REVERT: N 681 TYR cc_start: 0.8411 (t80) cc_final: 0.7848 (t80) REVERT: N 819 MET cc_start: 0.7269 (mtm) cc_final: 0.7024 (mtm) REVERT: N 849 THR cc_start: 0.7369 (t) cc_final: 0.6841 (m) REVERT: N 855 VAL cc_start: 0.6702 (t) cc_final: 0.6326 (m) REVERT: N 890 TYR cc_start: 0.7564 (t80) cc_final: 0.6959 (t80) REVERT: N 911 MET cc_start: 0.7961 (mtp) cc_final: 0.7499 (mtp) REVERT: N 965 ARG cc_start: 0.8402 (ptt90) cc_final: 0.8132 (ptt90) REVERT: N 1042 ASN cc_start: 0.6591 (t0) cc_final: 0.6263 (t0) REVERT: N 1077 GLU cc_start: 0.8147 (pm20) cc_final: 0.7860 (pm20) REVERT: N 1085 VAL cc_start: 0.8223 (m) cc_final: 0.7910 (p) REVERT: N 1120 MET cc_start: 0.5800 (tpt) cc_final: 0.5482 (tpt) REVERT: N 1155 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8200 (mtmm) REVERT: N 1207 HIS cc_start: 0.9032 (t70) cc_final: 0.8832 (t70) REVERT: N 1209 PHE cc_start: 0.8571 (t80) cc_final: 0.8304 (t80) REVERT: N 1239 ASN cc_start: 0.6506 (m-40) cc_final: 0.6205 (m-40) REVERT: N 1243 PHE cc_start: 0.8274 (t80) cc_final: 0.7492 (t80) outliers start: 0 outliers final: 0 residues processed: 789 average time/residue: 0.1656 time to fit residues: 196.7262 Evaluate side-chains 761 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 761 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 130 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 235 optimal weight: 6.9990 chunk 3 optimal weight: 0.0970 chunk 56 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 203 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 235 HIS B 207 GLN C 100 HIS ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** F 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** N1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.174930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139468 restraints weight = 48938.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144769 restraints weight = 31604.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.148712 restraints weight = 22286.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.151666 restraints weight = 16806.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153833 restraints weight = 13260.932| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24416 Z= 0.124 Angle : 0.602 9.532 33218 Z= 0.313 Chirality : 0.044 0.222 3709 Planarity : 0.005 0.086 4359 Dihedral : 6.578 78.339 3443 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 3010 helix: -0.21 (0.14), residues: 1319 sheet: -0.64 (0.28), residues: 339 loop : -1.14 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 94 TYR 0.033 0.001 TYR A 236 PHE 0.037 0.002 PHE A 179 TRP 0.025 0.002 TRP D 130 HIS 0.010 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (24416) covalent geometry : angle 0.60175 / 0.31 (33218) hydrogen bonds : bond 0.03620 / 2.44 ( 1003) hydrogen bonds : angle 5.74999 / 4.10 ( 2877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 775 time to evaluate : 0.616 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7785 (mpt180) cc_final: 0.7572 (mpt180) REVERT: A 66 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7271 (ttm170) REVERT: A 68 MET cc_start: 0.6604 (ttp) cc_final: 0.6151 (ttp) REVERT: A 72 TYR cc_start: 0.7416 (m-80) cc_final: 0.7172 (m-80) REVERT: A 94 ARG cc_start: 0.7603 (ptm-80) cc_final: 0.7171 (ptm-80) REVERT: A 103 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7725 (ttm-80) REVERT: A 150 VAL cc_start: 0.8687 (p) cc_final: 0.7872 (p) REVERT: A 151 MET cc_start: 0.8433 (mmp) cc_final: 0.7905 (mmp) REVERT: A 174 ARG cc_start: 0.8148 (mmp80) cc_final: 0.7405 (mmp80) REVERT: A 210 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7307 (mmm160) REVERT: A 248 MET cc_start: 0.8223 (ptp) cc_final: 0.7954 (ptp) REVERT: A 288 PHE cc_start: 0.8315 (t80) cc_final: 0.7823 (t80) REVERT: B 48 LEU cc_start: 0.8133 (tt) cc_final: 0.7754 (tt) REVERT: B 67 VAL cc_start: 0.7412 (t) cc_final: 0.7189 (t) REVERT: B 68 MET cc_start: 0.6060 (ttt) cc_final: 0.5805 (ttt) REVERT: B 80 HIS cc_start: 0.8521 (t70) cc_final: 0.8054 (t70) REVERT: B 109 LYS cc_start: 0.8361 (mptt) cc_final: 0.7683 (mptt) REVERT: B 135 ASN cc_start: 0.7585 (p0) cc_final: 0.7212 (p0) REVERT: B 138 LEU cc_start: 0.7846 (tp) cc_final: 0.7450 (tp) REVERT: B 167 LEU cc_start: 0.9022 (tp) cc_final: 0.8764 (tp) REVERT: B 182 PHE cc_start: 0.7113 (m-10) cc_final: 0.6798 (m-10) REVERT: B 209 ASP cc_start: 0.8467 (m-30) cc_final: 0.8261 (m-30) REVERT: B 210 ARG cc_start: 0.8599 (mmp80) cc_final: 0.8338 (mmp80) REVERT: B 248 MET cc_start: 0.8291 (ptp) cc_final: 0.8051 (ptp) REVERT: B 254 MET cc_start: 0.7832 (mpp) cc_final: 0.7321 (mpp) REVERT: B 268 MET cc_start: 0.7656 (mmp) cc_final: 0.7032 (mmp) REVERT: B 285 ASP cc_start: 0.7754 (p0) cc_final: 0.7518 (p0) REVERT: B 309 PHE cc_start: 0.8883 (m-80) cc_final: 0.8666 (m-80) REVERT: B 310 TYR cc_start: 0.7755 (t80) cc_final: 0.7365 (t80) REVERT: C 29 MET cc_start: 0.6938 (tpt) cc_final: 0.6692 (tpt) REVERT: C 52 GLN cc_start: 0.8911 (tp40) cc_final: 0.8519 (tp-100) REVERT: C 116 GLU cc_start: 0.8091 (tp30) cc_final: 0.7468 (tp30) REVERT: C 119 GLN cc_start: 0.8550 (pm20) cc_final: 0.8080 (pm20) REVERT: C 141 ASP cc_start: 0.7219 (t0) cc_final: 0.6939 (t0) REVERT: C 152 PHE cc_start: 0.7513 (m-80) cc_final: 0.7292 (m-80) REVERT: C 158 LEU cc_start: 0.8654 (mt) cc_final: 0.8437 (mt) REVERT: C 174 ARG cc_start: 0.7849 (mtt-85) cc_final: 0.7113 (mtt-85) REVERT: C 236 TYR cc_start: 0.6693 (m-10) cc_final: 0.6280 (m-10) REVERT: C 238 ASN cc_start: 0.8973 (p0) cc_final: 0.8746 (p0) REVERT: C 248 MET cc_start: 0.8874 (mtp) cc_final: 0.8157 (mtp) REVERT: C 257 GLN cc_start: 0.8675 (tp40) cc_final: 0.8324 (tp40) REVERT: C 288 PHE cc_start: 0.8349 (t80) cc_final: 0.7043 (t80) REVERT: C 292 LEU cc_start: 0.7984 (mt) cc_final: 0.7278 (mt) REVERT: C 309 PHE cc_start: 0.8605 (m-80) cc_final: 0.8342 (m-80) REVERT: D 37 ASP cc_start: 0.7210 (m-30) cc_final: 0.6867 (m-30) REVERT: D 44 ASP cc_start: 0.7461 (m-30) cc_final: 0.6890 (m-30) REVERT: D 50 ASP cc_start: 0.7630 (t70) cc_final: 0.7270 (t70) REVERT: D 53 THR cc_start: 0.8379 (p) cc_final: 0.8165 (p) REVERT: D 72 TYR cc_start: 0.7348 (m-10) cc_final: 0.7085 (m-10) REVERT: D 73 HIS cc_start: 0.8302 (p-80) cc_final: 0.7979 (p-80) REVERT: D 80 HIS cc_start: 0.8422 (m-70) cc_final: 0.8197 (m-70) REVERT: D 123 PHE cc_start: 0.7628 (t80) cc_final: 0.7298 (t80) REVERT: D 124 LYS cc_start: 0.7761 (mmpt) cc_final: 0.7402 (mmpt) REVERT: D 130 TRP cc_start: 0.8882 (t60) cc_final: 0.7998 (t60) REVERT: D 138 LEU cc_start: 0.8443 (tp) cc_final: 0.8241 (tp) REVERT: D 144 ASP cc_start: 0.7345 (p0) cc_final: 0.7037 (p0) REVERT: D 179 PHE cc_start: 0.8432 (t80) cc_final: 0.7549 (t80) REVERT: D 208 MET cc_start: 0.7858 (ptp) cc_final: 0.7084 (ptp) REVERT: D 209 ASP cc_start: 0.7808 (t0) cc_final: 0.7372 (t0) REVERT: D 224 ASN cc_start: 0.8111 (m110) cc_final: 0.7896 (m110) REVERT: D 227 ASN cc_start: 0.8774 (m110) cc_final: 0.8433 (m110) REVERT: D 248 MET cc_start: 0.8420 (ttm) cc_final: 0.8072 (ttm) REVERT: D 251 VAL cc_start: 0.8892 (t) cc_final: 0.8369 (t) REVERT: D 254 MET cc_start: 0.8845 (mtm) cc_final: 0.8263 (mtm) REVERT: D 256 ARG cc_start: 0.8634 (mtt90) cc_final: 0.8001 (mtt90) REVERT: D 268 MET cc_start: 0.7918 (mmp) cc_final: 0.7612 (mmp) REVERT: D 278 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8492 (mt-10) REVERT: D 294 PHE cc_start: 0.7669 (t80) cc_final: 0.7440 (t80) REVERT: E 29 MET cc_start: 0.7026 (mmp) cc_final: 0.6753 (mmp) REVERT: E 46 ASP cc_start: 0.7741 (t0) cc_final: 0.7306 (t0) REVERT: E 49 PHE cc_start: 0.7602 (m-10) cc_final: 0.7251 (m-10) REVERT: E 89 ASN cc_start: 0.7506 (t0) cc_final: 0.7048 (t0) REVERT: E 113 VAL cc_start: 0.8346 (m) cc_final: 0.7977 (p) REVERT: E 149 ASP cc_start: 0.7900 (t70) cc_final: 0.7526 (t70) REVERT: E 151 MET cc_start: 0.8020 (tpp) cc_final: 0.7581 (tpp) REVERT: E 154 ILE cc_start: 0.8862 (pt) cc_final: 0.8631 (pt) REVERT: E 155 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7631 (tp-100) REVERT: E 166 LEU cc_start: 0.7898 (mt) cc_final: 0.7691 (mt) REVERT: E 248 MET cc_start: 0.7734 (tpt) cc_final: 0.7405 (tpt) REVERT: E 261 ASN cc_start: 0.8624 (m-40) cc_final: 0.8306 (m-40) REVERT: E 279 ASN cc_start: 0.8586 (m-40) cc_final: 0.8355 (m-40) REVERT: E 285 ASP cc_start: 0.8473 (t70) cc_final: 0.8127 (t0) REVERT: E 300 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7099 (mm-30) REVERT: E 309 PHE cc_start: 0.8096 (m-80) cc_final: 0.7749 (m-80) REVERT: E 310 TYR cc_start: 0.8613 (t80) cc_final: 0.8090 (t80) REVERT: F 42 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7663 (tm-30) REVERT: F 51 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7612 (tpp80) REVERT: F 58 LEU cc_start: 0.8874 (mt) cc_final: 0.8643 (mt) REVERT: F 63 TYR cc_start: 0.6982 (m-10) cc_final: 0.6583 (m-10) REVERT: F 68 MET cc_start: 0.7643 (tmm) cc_final: 0.7173 (tmm) REVERT: F 100 HIS cc_start: 0.8075 (m-70) cc_final: 0.7585 (m-70) REVERT: F 109 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7641 (mttm) REVERT: F 123 PHE cc_start: 0.8034 (t80) cc_final: 0.7766 (t80) REVERT: F 147 ARG cc_start: 0.7790 (ptp-170) cc_final: 0.7394 (ptp-170) REVERT: F 244 ILE cc_start: 0.8889 (mt) cc_final: 0.8682 (mt) REVERT: F 268 MET cc_start: 0.7705 (pmm) cc_final: 0.7481 (pmm) REVERT: F 278 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8188 (mt-10) REVERT: F 295 LEU cc_start: 0.8818 (tp) cc_final: 0.8608 (tp) REVERT: F 301 LEU cc_start: 0.8211 (mp) cc_final: 0.7760 (mp) REVERT: G 336 ASP cc_start: 0.8493 (p0) cc_final: 0.8173 (p0) REVERT: G 370 MET cc_start: 0.6808 (tpt) cc_final: 0.6060 (tpt) REVERT: G 480 ASN cc_start: 0.8677 (t0) cc_final: 0.8391 (t0) REVERT: G 489 HIS cc_start: 0.8212 (m170) cc_final: 0.7632 (m170) REVERT: G 524 LEU cc_start: 0.9129 (mt) cc_final: 0.8835 (mt) REVERT: G 531 LEU cc_start: 0.8499 (tp) cc_final: 0.8216 (tp) REVERT: G 543 MET cc_start: 0.6976 (tpt) cc_final: 0.6687 (tpt) REVERT: N 432 MET cc_start: 0.8115 (mmt) cc_final: 0.7525 (mmt) REVERT: N 436 MET cc_start: 0.7958 (tpt) cc_final: 0.7329 (tpt) REVERT: N 498 MET cc_start: 0.4509 (mmm) cc_final: 0.4230 (mmm) REVERT: N 598 LYS cc_start: 0.7246 (pttt) cc_final: 0.6906 (pttt) REVERT: N 681 TYR cc_start: 0.8269 (t80) cc_final: 0.7705 (t80) REVERT: N 819 MET cc_start: 0.7235 (mtm) cc_final: 0.6988 (mtm) REVERT: N 849 THR cc_start: 0.7255 (t) cc_final: 0.6721 (m) REVERT: N 855 VAL cc_start: 0.6506 (t) cc_final: 0.6175 (m) REVERT: N 890 TYR cc_start: 0.7331 (t80) cc_final: 0.6768 (t80) REVERT: N 911 MET cc_start: 0.7909 (mtp) cc_final: 0.7468 (mtp) REVERT: N 1085 VAL cc_start: 0.8161 (m) cc_final: 0.7783 (p) REVERT: N 1120 MET cc_start: 0.5767 (tpt) cc_final: 0.5473 (tpt) REVERT: N 1145 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7541 (mtm110) REVERT: N 1155 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8280 (mtmm) REVERT: N 1166 LYS cc_start: 0.8330 (pttm) cc_final: 0.8016 (pttm) REVERT: N 1209 PHE cc_start: 0.8416 (t80) cc_final: 0.8172 (t80) REVERT: N 1212 GLU cc_start: 0.8072 (pp20) cc_final: 0.7539 (tm-30) REVERT: N 1243 PHE cc_start: 0.7914 (t80) cc_final: 0.7399 (t80) outliers start: 1 outliers final: 1 residues processed: 775 average time/residue: 0.1618 time to fit residues: 188.0126 Evaluate side-chains 762 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 761 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 226 optimal weight: 0.0170 chunk 76 optimal weight: 0.0670 chunk 223 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 224 ASN B 207 GLN C 100 HIS C 186 ASN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN N 810 GLN ** N1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.173371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137738 restraints weight = 49124.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142997 restraints weight = 31690.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.146950 restraints weight = 22448.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.149887 restraints weight = 16873.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151951 restraints weight = 13348.064| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24416 Z= 0.149 Angle : 0.610 9.083 33218 Z= 0.319 Chirality : 0.044 0.193 3709 Planarity : 0.005 0.085 4359 Dihedral : 6.431 81.612 3443 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.08 % Allowed : 0.64 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3010 helix: -0.18 (0.14), residues: 1311 sheet: -0.64 (0.28), residues: 340 loop : -1.09 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 271 TYR 0.022 0.001 TYR N1177 PHE 0.032 0.002 PHE A 309 TRP 0.026 0.002 TRP B 276 HIS 0.009 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (24416) covalent geometry : angle 0.60984 / 0.32 (33218) hydrogen bonds : bond 0.03758 / 2.55 ( 1003) hydrogen bonds : angle 5.80124 / 4.13 ( 2877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 777 time to evaluate : 0.824 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 revert: 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 65 ARG cc_start: 0.7778 (mpt180) cc_final: 0.7575 (mpt180) REVERT: A 68 MET cc_start: 0.6516 (ttp) cc_final: 0.5792 (ttp) REVERT: A 72 TYR cc_start: 0.7429 (m-80) cc_final: 0.7180 (m-80) REVERT: A 94 ARG cc_start: 0.7625 (ptm-80) cc_final: 0.7215 (ptm-80) REVERT: A 103 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7801 (ttm-80) REVERT: A 150 VAL cc_start: 0.8720 (p) cc_final: 0.7940 (p) REVERT: A 151 MET cc_start: 0.8473 (mmp) cc_final: 0.7924 (mmp) REVERT: A 174 ARG cc_start: 0.8149 (mmp80) cc_final: 0.7415 (mmp80) REVERT: A 210 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7254 (mmm160) REVERT: A 211 TRP cc_start: 0.8499 (m100) cc_final: 0.7879 (m100) REVERT: A 248 MET cc_start: 0.8375 (ptp) cc_final: 0.7981 (ptp) REVERT: A 288 PHE cc_start: 0.8358 (t80) cc_final: 0.7880 (t80) REVERT: B 48 LEU cc_start: 0.8153 (tt) cc_final: 0.7778 (tt) REVERT: B 67 VAL cc_start: 0.7449 (t) cc_final: 0.7197 (t) REVERT: B 68 MET cc_start: 0.6098 (ttt) cc_final: 0.5813 (ttt) REVERT: B 80 HIS cc_start: 0.8554 (t70) cc_final: 0.8092 (t70) REVERT: B 109 LYS cc_start: 0.8395 (mptt) cc_final: 0.7747 (mptt) REVERT: B 135 ASN cc_start: 0.7651 (p0) cc_final: 0.7229 (p0) REVERT: B 182 PHE cc_start: 0.7104 (m-10) cc_final: 0.6791 (m-10) REVERT: B 210 ARG cc_start: 0.8641 (mmp80) cc_final: 0.8375 (mmp80) REVERT: B 248 MET cc_start: 0.8314 (ptp) cc_final: 0.8091 (ptp) REVERT: B 254 MET cc_start: 0.7819 (mpp) cc_final: 0.7397 (mpp) REVERT: B 268 MET cc_start: 0.7715 (mmp) cc_final: 0.7071 (mmp) REVERT: B 271 ARG cc_start: 0.8732 (ttt-90) cc_final: 0.7728 (ttt180) REVERT: B 285 ASP cc_start: 0.7748 (p0) cc_final: 0.7527 (p0) REVERT: B 309 PHE cc_start: 0.8902 (m-80) cc_final: 0.8682 (m-80) REVERT: B 310 TYR cc_start: 0.7779 (t80) cc_final: 0.7424 (t80) REVERT: C 52 GLN cc_start: 0.8992 (tp40) cc_final: 0.8507 (tp-100) REVERT: C 116 GLU cc_start: 0.8135 (tp30) cc_final: 0.7502 (tp30) REVERT: C 119 GLN cc_start: 0.8600 (pm20) cc_final: 0.8136 (pm20) REVERT: C 141 ASP cc_start: 0.7287 (t0) cc_final: 0.7005 (t0) REVERT: C 158 LEU cc_start: 0.8702 (mt) cc_final: 0.8486 (mt) REVERT: C 174 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.7147 (mtt-85) REVERT: C 236 TYR cc_start: 0.6739 (m-10) cc_final: 0.6324 (m-10) REVERT: C 238 ASN cc_start: 0.8966 (p0) cc_final: 0.8754 (p0) REVERT: C 248 MET cc_start: 0.8874 (mtp) cc_final: 0.8281 (mtp) REVERT: C 257 GLN cc_start: 0.8697 (tp40) cc_final: 0.8373 (tp40) REVERT: C 292 LEU cc_start: 0.8038 (mt) cc_final: 0.7771 (mt) REVERT: C 309 PHE cc_start: 0.8600 (m-80) cc_final: 0.8360 (m-80) REVERT: D 29 MET cc_start: 0.7364 (tpt) cc_final: 0.7066 (tpp) REVERT: D 37 ASP cc_start: 0.7271 (m-30) cc_final: 0.6916 (m-30) REVERT: D 44 ASP cc_start: 0.7471 (m-30) cc_final: 0.6899 (m-30) REVERT: D 50 ASP cc_start: 0.7644 (t70) cc_final: 0.7290 (t70) REVERT: D 53 THR cc_start: 0.8403 (p) cc_final: 0.8179 (p) REVERT: D 73 HIS cc_start: 0.8323 (p-80) cc_final: 0.8031 (p-80) REVERT: D 80 HIS cc_start: 0.8474 (m-70) cc_final: 0.8137 (m-70) REVERT: D 123 PHE cc_start: 0.7673 (t80) cc_final: 0.7340 (t80) REVERT: D 124 LYS cc_start: 0.7768 (mmpt) cc_final: 0.7388 (mmpt) REVERT: D 130 TRP cc_start: 0.8909 (t60) cc_final: 0.7987 (t60) REVERT: D 138 LEU cc_start: 0.8462 (tp) cc_final: 0.8248 (tp) REVERT: D 144 ASP cc_start: 0.7427 (p0) cc_final: 0.7083 (p0) REVERT: D 179 PHE cc_start: 0.8431 (t80) cc_final: 0.7558 (t80) REVERT: D 208 MET cc_start: 0.7923 (ptp) cc_final: 0.7120 (ptp) REVERT: D 209 ASP cc_start: 0.7990 (t0) cc_final: 0.7467 (t0) REVERT: D 217 LEU cc_start: 0.7978 (tt) cc_final: 0.7774 (tt) REVERT: D 224 ASN cc_start: 0.8176 (m110) cc_final: 0.7927 (m110) REVERT: D 227 ASN cc_start: 0.8792 (m110) cc_final: 0.8448 (m110) REVERT: D 248 MET cc_start: 0.8474 (ttm) cc_final: 0.8145 (ttm) REVERT: D 251 VAL cc_start: 0.8998 (t) cc_final: 0.8408 (t) REVERT: D 254 MET cc_start: 0.8843 (mtm) cc_final: 0.8275 (mtm) REVERT: D 256 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8053 (mtt90) REVERT: D 268 MET cc_start: 0.7881 (mmp) cc_final: 0.7503 (mmp) REVERT: D 278 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8521 (mt-10) REVERT: D 294 PHE cc_start: 0.7709 (t80) cc_final: 0.7502 (t80) REVERT: E 29 MET cc_start: 0.7088 (mmp) cc_final: 0.6800 (mmp) REVERT: E 46 ASP cc_start: 0.7778 (t0) cc_final: 0.7345 (t0) REVERT: E 49 PHE cc_start: 0.7729 (m-10) cc_final: 0.7333 (m-10) REVERT: E 113 VAL cc_start: 0.8295 (m) cc_final: 0.7940 (p) REVERT: E 149 ASP cc_start: 0.7889 (t70) cc_final: 0.7568 (t0) REVERT: E 151 MET cc_start: 0.8024 (tpp) cc_final: 0.7614 (tpp) REVERT: E 152 PHE cc_start: 0.8920 (m-80) cc_final: 0.8531 (m-80) REVERT: E 154 ILE cc_start: 0.8901 (pt) cc_final: 0.8666 (pt) REVERT: E 248 MET cc_start: 0.7754 (tpt) cc_final: 0.7414 (tpt) REVERT: E 261 ASN cc_start: 0.8626 (m-40) cc_final: 0.8317 (m-40) REVERT: E 285 ASP cc_start: 0.8443 (t70) cc_final: 0.8092 (t0) REVERT: E 300 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7102 (mm-30) REVERT: E 309 PHE cc_start: 0.8109 (m-80) cc_final: 0.7738 (m-80) REVERT: E 310 TYR cc_start: 0.8651 (t80) cc_final: 0.8151 (t80) REVERT: F 42 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7670 (tm-30) REVERT: F 51 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7612 (tpp80) REVERT: F 58 LEU cc_start: 0.8913 (mt) cc_final: 0.8677 (mt) REVERT: F 63 TYR cc_start: 0.6945 (m-10) cc_final: 0.6562 (m-10) REVERT: F 68 MET cc_start: 0.7565 (tmm) cc_final: 0.7114 (tmm) REVERT: F 83 GLN cc_start: 0.8178 (mp10) cc_final: 0.7868 (mp10) REVERT: F 100 HIS cc_start: 0.8029 (m-70) cc_final: 0.7507 (m-70) REVERT: F 109 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7683 (mttm) REVERT: F 123 PHE cc_start: 0.8037 (t80) cc_final: 0.7768 (t80) REVERT: F 147 ARG cc_start: 0.7877 (ptp-170) cc_final: 0.7487 (ptp-170) REVERT: F 232 LYS cc_start: 0.8494 (tppt) cc_final: 0.8286 (tppp) REVERT: F 248 MET cc_start: 0.8003 (mtm) cc_final: 0.7587 (mtm) REVERT: F 268 MET cc_start: 0.7758 (pmm) cc_final: 0.7512 (pmm) REVERT: F 278 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8278 (mt-10) REVERT: F 295 LEU cc_start: 0.8827 (tp) cc_final: 0.8615 (tp) REVERT: F 297 LYS cc_start: 0.8734 (mppt) cc_final: 0.8499 (mppt) REVERT: F 301 LEU cc_start: 0.8267 (mp) cc_final: 0.7783 (mp) REVERT: G 336 ASP cc_start: 0.8564 (p0) cc_final: 0.8281 (p0) REVERT: G 341 ASP cc_start: 0.8782 (m-30) cc_final: 0.8569 (m-30) REVERT: G 370 MET cc_start: 0.6902 (tpt) cc_final: 0.6079 (tpt) REVERT: G 432 ILE cc_start: 0.9263 (tt) cc_final: 0.9022 (tt) REVERT: G 480 ASN cc_start: 0.8681 (t0) cc_final: 0.8392 (t0) REVERT: G 489 HIS cc_start: 0.8235 (m170) cc_final: 0.7622 (m90) REVERT: G 509 MET cc_start: 0.8412 (ppp) cc_final: 0.7673 (ppp) REVERT: G 511 ARG cc_start: 0.8878 (ttm170) cc_final: 0.8126 (ttm170) REVERT: G 524 LEU cc_start: 0.9156 (mt) cc_final: 0.8881 (mt) REVERT: G 531 LEU cc_start: 0.8529 (tp) cc_final: 0.8254 (tp) REVERT: N 432 MET cc_start: 0.8104 (mmt) cc_final: 0.7497 (mmt) REVERT: N 436 MET cc_start: 0.7975 (tpt) cc_final: 0.7310 (tpt) REVERT: N 498 MET cc_start: 0.4549 (mmm) cc_final: 0.4231 (mmm) REVERT: N 598 LYS cc_start: 0.7212 (pttt) cc_final: 0.6863 (pttt) REVERT: N 622 LEU cc_start: 0.8912 (mt) cc_final: 0.8637 (tt) REVERT: N 681 TYR cc_start: 0.8304 (t80) cc_final: 0.7747 (t80) REVERT: N 819 MET cc_start: 0.7241 (mtm) cc_final: 0.6995 (mtm) REVERT: N 849 THR cc_start: 0.7340 (t) cc_final: 0.6825 (m) REVERT: N 855 VAL cc_start: 0.6525 (t) cc_final: 0.6183 (m) REVERT: N 890 TYR cc_start: 0.7395 (t80) cc_final: 0.6844 (t80) REVERT: N 892 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8827 (mp10) REVERT: N 911 MET cc_start: 0.7932 (mtp) cc_final: 0.7510 (mtp) REVERT: N 1085 VAL cc_start: 0.8168 (m) cc_final: 0.7773 (p) REVERT: N 1120 MET cc_start: 0.5782 (tpt) cc_final: 0.5486 (tpt) REVERT: N 1155 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8219 (mtmm) REVERT: N 1166 LYS cc_start: 0.8334 (pttm) cc_final: 0.8050 (pttm) REVERT: N 1207 HIS cc_start: 0.9005 (t70) cc_final: 0.8798 (t70) REVERT: N 1209 PHE cc_start: 0.8471 (t80) cc_final: 0.8183 (t80) REVERT: N 1212 GLU cc_start: 0.8157 (pp20) cc_final: 0.7610 (tm-30) REVERT: N 1243 PHE cc_start: 0.8160 (t80) cc_final: 0.7368 (t80) outliers start: 2 outliers final: 1 residues processed: 777 average time/residue: 0.1622 time to fit residues: 189.4241 Evaluate side-chains 753 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 752 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 282 optimal weight: 0.3980 chunk 62 optimal weight: 0.0060 chunk 148 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 134 optimal weight: 0.0970 chunk 206 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 235 HIS B 207 GLN C 100 HIS ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS E 202 GLN ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN N 810 GLN ** N1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.175703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140007 restraints weight = 49224.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.145399 restraints weight = 31528.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.149340 restraints weight = 22214.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152398 restraints weight = 16706.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154520 restraints weight = 13126.185| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24416 Z= 0.115 Angle : 0.598 9.279 33218 Z= 0.310 Chirality : 0.044 0.176 3709 Planarity : 0.005 0.082 4359 Dihedral : 6.151 74.222 3443 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 3010 helix: -0.11 (0.14), residues: 1304 sheet: -0.53 (0.29), residues: 335 loop : -1.03 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 271 TYR 0.020 0.001 TYR N 532 PHE 0.033 0.002 PHE A 309 TRP 0.031 0.002 TRP B 276 HIS 0.008 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (24416) covalent geometry : angle 0.59837 / 0.31 (33218) hydrogen bonds : bond 0.03458 / 2.35 ( 1003) hydrogen bonds : angle 5.64963 / 4.02 ( 2877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 786 time to evaluate : 0.647 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7072 (mtt90) cc_final: 0.6867 (ttm170) REVERT: A 68 MET cc_start: 0.6520 (ttp) cc_final: 0.6095 (ttp) REVERT: A 72 TYR cc_start: 0.7365 (m-80) cc_final: 0.7143 (m-80) REVERT: A 103 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7699 (ttm-80) REVERT: A 150 VAL cc_start: 0.8634 (p) cc_final: 0.7887 (p) REVERT: A 151 MET cc_start: 0.8348 (mmp) cc_final: 0.7898 (mmp) REVERT: A 155 GLN cc_start: 0.8341 (pp30) cc_final: 0.8048 (pp30) REVERT: A 174 ARG cc_start: 0.8091 (mmp80) cc_final: 0.7343 (mmp80) REVERT: A 210 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7228 (mmm160) REVERT: A 248 MET cc_start: 0.8237 (ptp) cc_final: 0.8005 (ptp) REVERT: A 288 PHE cc_start: 0.8432 (t80) cc_final: 0.7926 (t80) REVERT: B 48 LEU cc_start: 0.8135 (tt) cc_final: 0.7747 (tt) REVERT: B 67 VAL cc_start: 0.7405 (t) cc_final: 0.7114 (t) REVERT: B 68 MET cc_start: 0.6062 (ttt) cc_final: 0.5785 (ttt) REVERT: B 80 HIS cc_start: 0.8538 (t70) cc_final: 0.8075 (t70) REVERT: B 135 ASN cc_start: 0.7630 (p0) cc_final: 0.7249 (p0) REVERT: B 138 LEU cc_start: 0.7818 (tp) cc_final: 0.7443 (tp) REVERT: B 167 LEU cc_start: 0.8965 (tp) cc_final: 0.8753 (tp) REVERT: B 182 PHE cc_start: 0.7028 (m-10) cc_final: 0.6802 (m-10) REVERT: B 210 ARG cc_start: 0.8622 (mmp80) cc_final: 0.8380 (mmp80) REVERT: B 254 MET cc_start: 0.7818 (mpp) cc_final: 0.7394 (mpp) REVERT: B 268 MET cc_start: 0.7585 (mmp) cc_final: 0.6964 (mmp) REVERT: B 271 ARG cc_start: 0.8657 (ttt-90) cc_final: 0.7530 (ttt180) REVERT: B 285 ASP cc_start: 0.7726 (p0) cc_final: 0.7484 (p0) REVERT: B 310 TYR cc_start: 0.7800 (t80) cc_final: 0.7450 (t80) REVERT: C 52 GLN cc_start: 0.8924 (tp40) cc_final: 0.8510 (tp-100) REVERT: C 116 GLU cc_start: 0.8165 (tp30) cc_final: 0.7549 (tp30) REVERT: C 141 ASP cc_start: 0.7187 (t0) cc_final: 0.6884 (t0) REVERT: C 174 ARG cc_start: 0.7839 (mtt-85) cc_final: 0.7096 (mtt-85) REVERT: C 209 ASP cc_start: 0.8449 (m-30) cc_final: 0.8245 (m-30) REVERT: C 236 TYR cc_start: 0.6692 (m-10) cc_final: 0.6265 (m-10) REVERT: C 238 ASN cc_start: 0.8973 (p0) cc_final: 0.8653 (p0) REVERT: C 244 ILE cc_start: 0.8757 (mp) cc_final: 0.8461 (mp) REVERT: C 248 MET cc_start: 0.8877 (mtp) cc_final: 0.8249 (mtp) REVERT: C 257 GLN cc_start: 0.8663 (tp40) cc_final: 0.8354 (tp40) REVERT: C 268 MET cc_start: 0.7691 (mmp) cc_final: 0.7391 (mmp) REVERT: C 292 LEU cc_start: 0.8030 (mt) cc_final: 0.7758 (mt) REVERT: C 309 PHE cc_start: 0.8564 (m-80) cc_final: 0.8317 (m-80) REVERT: D 10 ASN cc_start: 0.8331 (m-40) cc_final: 0.7794 (t0) REVERT: D 33 TYR cc_start: 0.6898 (m-80) cc_final: 0.6467 (m-80) REVERT: D 37 ASP cc_start: 0.7159 (m-30) cc_final: 0.6800 (m-30) REVERT: D 44 ASP cc_start: 0.7432 (m-30) cc_final: 0.6855 (m-30) REVERT: D 50 ASP cc_start: 0.7612 (t70) cc_final: 0.7284 (t70) REVERT: D 53 THR cc_start: 0.8355 (p) cc_final: 0.8143 (p) REVERT: D 73 HIS cc_start: 0.8204 (p-80) cc_final: 0.7957 (p-80) REVERT: D 80 HIS cc_start: 0.8439 (m-70) cc_final: 0.8143 (m-70) REVERT: D 123 PHE cc_start: 0.7670 (t80) cc_final: 0.7346 (t80) REVERT: D 124 LYS cc_start: 0.7681 (mmpt) cc_final: 0.7214 (mmpt) REVERT: D 130 TRP cc_start: 0.8885 (t60) cc_final: 0.8149 (t60) REVERT: D 138 LEU cc_start: 0.8452 (tp) cc_final: 0.8237 (tp) REVERT: D 179 PHE cc_start: 0.8416 (t80) cc_final: 0.7570 (t80) REVERT: D 184 THR cc_start: 0.8795 (t) cc_final: 0.8278 (p) REVERT: D 201 GLN cc_start: 0.6501 (mp-120) cc_final: 0.6095 (mp-120) REVERT: D 205 GLN cc_start: 0.7605 (mp10) cc_final: 0.7158 (mp10) REVERT: D 208 MET cc_start: 0.7842 (ptp) cc_final: 0.6977 (ptp) REVERT: D 209 ASP cc_start: 0.7789 (t0) cc_final: 0.7342 (t0) REVERT: D 224 ASN cc_start: 0.8168 (m110) cc_final: 0.7926 (m110) REVERT: D 227 ASN cc_start: 0.8726 (m110) cc_final: 0.8382 (m110) REVERT: D 248 MET cc_start: 0.8447 (ttm) cc_final: 0.8083 (ttm) REVERT: D 251 VAL cc_start: 0.8889 (t) cc_final: 0.8377 (t) REVERT: D 254 MET cc_start: 0.8797 (mtm) cc_final: 0.8225 (mtm) REVERT: D 257 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7233 (tp-100) REVERT: D 261 ASN cc_start: 0.8529 (m110) cc_final: 0.7369 (m110) REVERT: D 268 MET cc_start: 0.7933 (mmp) cc_final: 0.7432 (mmp) REVERT: D 278 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8498 (mt-10) REVERT: D 294 PHE cc_start: 0.7567 (t80) cc_final: 0.7363 (t80) REVERT: E 46 ASP cc_start: 0.7693 (t0) cc_final: 0.7250 (t0) REVERT: E 49 PHE cc_start: 0.7720 (m-10) cc_final: 0.7295 (m-10) REVERT: E 113 VAL cc_start: 0.8294 (m) cc_final: 0.7950 (p) REVERT: E 149 ASP cc_start: 0.7834 (t70) cc_final: 0.7553 (t0) REVERT: E 151 MET cc_start: 0.8030 (tpp) cc_final: 0.7513 (tpp) REVERT: E 154 ILE cc_start: 0.8864 (pt) cc_final: 0.8577 (pt) REVERT: E 155 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7725 (tp-100) REVERT: E 166 LEU cc_start: 0.7854 (mt) cc_final: 0.7500 (mt) REVERT: E 248 MET cc_start: 0.7771 (tpt) cc_final: 0.7442 (tpt) REVERT: E 261 ASN cc_start: 0.8572 (m-40) cc_final: 0.8260 (m-40) REVERT: E 279 ASN cc_start: 0.8639 (m-40) cc_final: 0.8420 (m-40) REVERT: E 285 ASP cc_start: 0.8477 (t70) cc_final: 0.8110 (t0) REVERT: E 309 PHE cc_start: 0.8042 (m-80) cc_final: 0.7668 (m-80) REVERT: E 310 TYR cc_start: 0.8568 (t80) cc_final: 0.8078 (t80) REVERT: F 42 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7672 (tm-30) REVERT: F 51 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7615 (tpp80) REVERT: F 58 LEU cc_start: 0.8884 (mt) cc_final: 0.8654 (mt) REVERT: F 63 TYR cc_start: 0.6837 (m-10) cc_final: 0.6529 (m-10) REVERT: F 68 MET cc_start: 0.7584 (tmm) cc_final: 0.7113 (tmm) REVERT: F 83 GLN cc_start: 0.8146 (mp10) cc_final: 0.7834 (mp10) REVERT: F 100 HIS cc_start: 0.7922 (m-70) cc_final: 0.7488 (m-70) REVERT: F 123 PHE cc_start: 0.7976 (t80) cc_final: 0.7749 (t80) REVERT: F 147 ARG cc_start: 0.7680 (ptp-170) cc_final: 0.7429 (ptp-170) REVERT: F 157 VAL cc_start: 0.9115 (t) cc_final: 0.8776 (t) REVERT: F 244 ILE cc_start: 0.8866 (mt) cc_final: 0.8625 (mt) REVERT: F 268 MET cc_start: 0.7589 (pmm) cc_final: 0.7345 (pmm) REVERT: F 278 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8291 (mt-10) REVERT: F 290 PHE cc_start: 0.7572 (t80) cc_final: 0.7120 (t80) REVERT: F 295 LEU cc_start: 0.8825 (tp) cc_final: 0.8624 (tp) REVERT: F 297 LYS cc_start: 0.8700 (mppt) cc_final: 0.8469 (mppt) REVERT: F 301 LEU cc_start: 0.8206 (mp) cc_final: 0.7831 (mp) REVERT: G 336 ASP cc_start: 0.8511 (p0) cc_final: 0.8233 (p0) REVERT: G 341 ASP cc_start: 0.8763 (m-30) cc_final: 0.8554 (m-30) REVERT: G 347 LEU cc_start: 0.8458 (tp) cc_final: 0.8239 (tp) REVERT: G 370 MET cc_start: 0.6781 (tpt) cc_final: 0.6096 (tpt) REVERT: G 480 ASN cc_start: 0.8683 (t0) cc_final: 0.8368 (t0) REVERT: G 489 HIS cc_start: 0.8185 (m170) cc_final: 0.7603 (m170) REVERT: G 510 MET cc_start: 0.8079 (mmp) cc_final: 0.7530 (mmp) REVERT: G 511 ARG cc_start: 0.8872 (ttm170) cc_final: 0.8111 (ttm170) REVERT: G 524 LEU cc_start: 0.9132 (mt) cc_final: 0.8850 (mt) REVERT: G 531 LEU cc_start: 0.8484 (tp) cc_final: 0.8210 (tp) REVERT: G 564 GLU cc_start: 0.6870 (tm-30) cc_final: 0.5855 (tm-30) REVERT: N 432 MET cc_start: 0.8014 (mmt) cc_final: 0.7457 (mmt) REVERT: N 436 MET cc_start: 0.7919 (tpt) cc_final: 0.7274 (tpt) REVERT: N 498 MET cc_start: 0.4359 (mmm) cc_final: 0.4082 (mmm) REVERT: N 598 LYS cc_start: 0.7200 (pttt) cc_final: 0.6867 (pttt) REVERT: N 681 TYR cc_start: 0.8273 (t80) cc_final: 0.7714 (t80) REVERT: N 819 MET cc_start: 0.7292 (mtm) cc_final: 0.7027 (mtm) REVERT: N 849 THR cc_start: 0.7312 (t) cc_final: 0.6806 (m) REVERT: N 855 VAL cc_start: 0.6416 (t) cc_final: 0.6052 (m) REVERT: N 884 GLU cc_start: 0.9138 (mp0) cc_final: 0.8901 (mp0) REVERT: N 890 TYR cc_start: 0.7278 (t80) cc_final: 0.6750 (t80) REVERT: N 911 MET cc_start: 0.7898 (mtp) cc_final: 0.7481 (mtp) REVERT: N 1085 VAL cc_start: 0.8202 (m) cc_final: 0.7798 (p) REVERT: N 1120 MET cc_start: 0.5795 (tpt) cc_final: 0.5493 (tpt) REVERT: N 1155 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8204 (mtmm) REVERT: N 1166 LYS cc_start: 0.8552 (pttp) cc_final: 0.8267 (pttp) REVERT: N 1209 PHE cc_start: 0.8397 (t80) cc_final: 0.8140 (t80) REVERT: N 1212 GLU cc_start: 0.8180 (pp20) cc_final: 0.7643 (tm-30) REVERT: N 1243 PHE cc_start: 0.8057 (t80) cc_final: 0.7325 (t80) outliers start: 1 outliers final: 0 residues processed: 787 average time/residue: 0.1685 time to fit residues: 199.2905 Evaluate side-chains 751 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 751 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 249 optimal weight: 0.0170 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 133 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN B 207 GLN C 100 HIS C 186 ASN ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN N 810 GLN ** N1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.175530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138958 restraints weight = 48764.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.144229 restraints weight = 31762.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.148114 restraints weight = 22684.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151052 restraints weight = 17243.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.153458 restraints weight = 13735.476| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24416 Z= 0.117 Angle : 0.597 9.028 33218 Z= 0.309 Chirality : 0.044 0.175 3709 Planarity : 0.005 0.079 4359 Dihedral : 6.051 75.841 3443 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.12 % Allowed : 0.28 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.16), residues: 3010 helix: -0.09 (0.14), residues: 1314 sheet: -0.51 (0.29), residues: 338 loop : -0.97 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 156 TYR 0.019 0.001 TYR N1177 PHE 0.034 0.002 PHE A 309 TRP 0.037 0.002 TRP B 276 HIS 0.008 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (24416) covalent geometry : angle 0.59667 / 0.31 (33218) hydrogen bonds : bond 0.03428 / 2.32 ( 1003) hydrogen bonds : angle 5.61757 / 3.99 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4449.03 seconds wall clock time: 77 minutes 19.09 seconds (4639.09 seconds total)