Starting phenix.real_space_refine on Tue Aug 26 10:26:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gae_29895/08_2025/8gae_29895_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gae_29895/08_2025/8gae_29895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gae_29895/08_2025/8gae_29895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gae_29895/08_2025/8gae_29895.map" model { file = "/net/cci-nas-00/data/ceres_data/8gae_29895/08_2025/8gae_29895_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gae_29895/08_2025/8gae_29895_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 2 8.98 5 Mn 2 7.51 5 P 6 5.49 5 Mg 2 5.21 5 S 93 5.16 5 C 11222 2.51 5 N 3003 2.21 5 O 3418 1.98 5 H 17634 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35382 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 10338 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 17, 'TRANS': 617} Chain breaks: 1 Chain: "B" Number of atoms: 10284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 10284 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 1 Chain: "C" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4307 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain: "D" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 3072 Classifications: {'peptide': 189} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "E" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7317 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 16, 'TRANS': 442} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.08, per 1000 atoms: 0.14 Number of scatterers: 35382 At special positions: 0 Unit cell: (148.63, 151.135, 153.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Mn 2 24.99 K 2 19.00 S 93 16.00 P 6 15.00 Mg 2 11.99 O 3418 8.00 N 3003 7.00 C 11222 6.00 H 17634 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4138 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 16 sheets defined 53.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 37 through 59 removed outlier: 3.726A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.804A pdb=" N MET A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.554A pdb=" N VAL A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.762A pdb=" N ASN A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.728A pdb=" N TYR A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.718A pdb=" N LEU A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.714A pdb=" N ASN A 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A 376 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 422 removed outlier: 3.598A pdb=" N ARG A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 4.679A pdb=" N LYS A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.569A pdb=" N ARG A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 496 removed outlier: 4.037A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.685A pdb=" N CYS A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 removed outlier: 4.067A pdb=" N LYS A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 571 removed outlier: 3.681A pdb=" N LYS A 568 " --> pdb=" O CYS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.010A pdb=" N MET A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 648 through 666 removed outlier: 3.569A pdb=" N VAL A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 688 removed outlier: 3.576A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.645A pdb=" N PHE B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 61 removed outlier: 3.873A pdb=" N ARG B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.571A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 187 through 193 removed outlier: 5.604A pdb=" N GLU B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.881A pdb=" N ILE B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 removed outlier: 3.828A pdb=" N SER B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 399 through 420 removed outlier: 3.649A pdb=" N ASN B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 442 removed outlier: 3.845A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.835A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 476 removed outlier: 3.617A pdb=" N VAL B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 515 through 523 removed outlier: 4.208A pdb=" N GLU B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 572 removed outlier: 4.087A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 561 " --> pdb=" O LYS B 557 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 613 through 620 removed outlier: 4.105A pdb=" N THR B 616 " --> pdb=" O ASP B 613 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY B 618 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR B 619 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.788A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 666 removed outlier: 3.517A pdb=" N PHE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 688 removed outlier: 4.277A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.693A pdb=" N GLU C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR C 19 " --> pdb=" O GLU C 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 15 through 19' Processing helix chain 'C' and resid 24 through 73 removed outlier: 3.936A pdb=" N ARG C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 112 removed outlier: 3.513A pdb=" N GLN C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 162 removed outlier: 5.577A pdb=" N GLU C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.850A pdb=" N GLN C 172 " --> pdb=" O TRP C 168 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N SER C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.750A pdb=" N CYS C 183 " --> pdb=" O HIS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 202 through 226 removed outlier: 3.605A pdb=" N MET C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 removed outlier: 3.569A pdb=" N PHE C 237 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 239 " --> pdb=" O GLN C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 259 removed outlier: 3.847A pdb=" N ARG C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 434 Processing helix chain 'D' and resid 441 through 461 Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.672A pdb=" N ILE D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 544 Processing helix chain 'D' and resid 553 through 563 removed outlier: 3.714A pdb=" N VAL D 561 " --> pdb=" O ILE D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 591 Processing helix chain 'D' and resid 592 through 594 No H-bonds generated for 'chain 'D' and resid 592 through 594' Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 43 through 58 removed outlier: 3.757A pdb=" N ALA E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 77 through 92 removed outlier: 3.543A pdb=" N ALA E 81 " --> pdb=" O CYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 110 Processing helix chain 'E' and resid 111 through 126 removed outlier: 3.707A pdb=" N ALA E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 153 removed outlier: 3.591A pdb=" N GLN E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.545A pdb=" N ASP E 166 " --> pdb=" O VAL E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 removed outlier: 3.591A pdb=" N ASP E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 223 Processing helix chain 'E' and resid 246 through 257 Processing helix chain 'E' and resid 278 through 293 removed outlier: 3.835A pdb=" N ILE E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 313 removed outlier: 4.052A pdb=" N ASN E 310 " --> pdb=" O THR E 306 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN E 311 " --> pdb=" O ASP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 323 Processing helix chain 'E' and resid 324 through 338 removed outlier: 4.322A pdb=" N TYR E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 379 through 387 Processing helix chain 'E' and resid 407 through 418 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.520A pdb=" N GLU A 13 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 178 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 217 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 215 removed outlier: 6.423A pdb=" N ILE A 73 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 322 removed outlier: 3.786A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 321 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 467 through 468 removed outlier: 4.281A pdb=" N HIS A 458 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 577 through 580 removed outlier: 4.360A pdb=" N LYS A 577 " --> pdb=" O LYS A 624 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 364 removed outlier: 7.015A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASP B 364 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE B 353 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 321 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE C 124 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU B 324 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP C 122 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 456 through 457 Processing sheet with id=AA9, first strand: chain 'B' and resid 510 through 513 removed outlier: 9.087A pdb=" N VAL B 511 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR B 484 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N MET B 513 " --> pdb=" O TYR B 484 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 486 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 577 through 580 removed outlier: 6.607A pdb=" N LYS B 577 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ILE B 628 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR B 579 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 474 through 477 removed outlier: 4.351A pdb=" N THR D 481 " --> pdb=" O HIS D 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 227 through 229 removed outlier: 3.742A pdb=" N CYS E 343 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU E 349 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS E 442 " --> pdb=" O ALA E 437 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA E 437 " --> pdb=" O CYS E 442 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.508A pdb=" N TYR E 266 " --> pdb=" O HIS E 298 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU E 300 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE E 268 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE E 267 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR E 238 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN E 269 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS E 240 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 464 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL E 239 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE E 462 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER E 460 " --> pdb=" O GLY E 433 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.508A pdb=" N TYR E 266 " --> pdb=" O HIS E 298 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU E 300 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE E 268 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE E 267 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR E 238 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN E 269 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS E 240 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 464 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL E 239 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE E 462 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 472 " --> pdb=" O HIS E 463 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 388 through 389 removed outlier: 6.213A pdb=" N ASP E 388 " --> pdb=" O PHE E 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 450 through 452 removed outlier: 6.739A pdb=" N MET E 455 " --> pdb=" O TYR E 451 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2391 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: 8.02 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.55 - 0.81: 3 0.81 - 1.06: 4087 1.06 - 1.32: 17174 1.32 - 1.57: 14273 1.57 - 1.82: 163 Bond restraints: 35700 Sorted by residual: bond pdb=" N PHE A 39 " pdb=" H PHE A 39 " ideal model delta sigma weight residual 0.860 0.553 0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" CB SER E 378 " pdb=" OG SER E 378 " ideal model delta sigma weight residual 1.417 1.160 0.257 2.00e-02 2.50e+03 1.66e+02 bond pdb=" CZ ARG B 291 " pdb=" NH2 ARG B 291 " ideal model delta sigma weight residual 1.330 1.176 0.154 1.30e-02 5.92e+03 1.40e+02 bond pdb=" CZ ARG A 177 " pdb=" NH2 ARG A 177 " ideal model delta sigma weight residual 1.330 1.189 0.141 1.30e-02 5.92e+03 1.18e+02 bond pdb=" CA PHE A 39 " pdb=" HA PHE A 39 " ideal model delta sigma weight residual 0.970 0.756 0.214 2.00e-02 2.50e+03 1.15e+02 ... (remaining 35695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 62950 6.18 - 12.36: 1604 12.36 - 18.54: 45 18.54 - 24.72: 2 24.72 - 30.90: 2 Bond angle restraints: 64603 Sorted by residual: angle pdb=" PB ATP B 803 " pdb=" O3B ATP B 803 " pdb=" PG ATP B 803 " ideal model delta sigma weight residual 139.87 122.61 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PA ATP B 803 " pdb=" O3A ATP B 803 " pdb=" PB ATP B 803 " ideal model delta sigma weight residual 136.83 121.28 15.55 1.00e+00 1.00e+00 2.42e+02 angle pdb=" C THR A 190 " pdb=" N GLU A 191 " pdb=" CA GLU A 191 " ideal model delta sigma weight residual 120.38 139.59 -19.21 1.37e+00 5.33e-01 1.97e+02 angle pdb=" C THR A 60 " pdb=" N ASP A 61 " pdb=" CA ASP A 61 " ideal model delta sigma weight residual 122.28 131.81 -9.53 8.80e-01 1.29e+00 1.17e+02 angle pdb=" C LEU B 388 " pdb=" N ASN B 389 " pdb=" CA ASN B 389 " ideal model delta sigma weight residual 120.75 136.32 -15.57 1.51e+00 4.39e-01 1.06e+02 ... (remaining 64598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 15989 31.09 - 62.18: 552 62.18 - 93.28: 109 93.28 - 124.37: 2 124.37 - 155.46: 1 Dihedral angle restraints: 16653 sinusoidal: 9181 harmonic: 7472 Sorted by residual: dihedral pdb=" N ASP B 151 " pdb=" C ASP B 151 " pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " ideal model delta harmonic sigma weight residual 122.80 146.13 -23.33 0 2.50e+00 1.60e-01 8.71e+01 dihedral pdb=" C ASP B 151 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " ideal model delta harmonic sigma weight residual -122.60 -145.38 22.78 0 2.50e+00 1.60e-01 8.31e+01 dihedral pdb=" N TRP A 312 " pdb=" C TRP A 312 " pdb=" CA TRP A 312 " pdb=" CB TRP A 312 " ideal model delta harmonic sigma weight residual 122.80 143.28 -20.48 0 2.50e+00 1.60e-01 6.71e+01 ... (remaining 16650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 2450 0.204 - 0.408: 170 0.408 - 0.612: 20 0.612 - 0.816: 2 0.816 - 1.020: 2 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CA ASP B 151 " pdb=" N ASP B 151 " pdb=" C ASP B 151 " pdb=" CB ASP B 151 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA TRP A 312 " pdb=" N TRP A 312 " pdb=" C TRP A 312 " pdb=" CB TRP A 312 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA LYS C 160 " pdb=" N LYS C 160 " pdb=" C LYS C 160 " pdb=" CB LYS C 160 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2641 not shown) Planarity restraints: 5226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 612 " 0.202 9.50e-02 1.11e+02 1.81e-01 6.42e+02 pdb=" NE ARG B 612 " 0.111 2.00e-02 2.50e+03 pdb=" CZ ARG B 612 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG B 612 " 0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG B 612 " 0.144 2.00e-02 2.50e+03 pdb="HH11 ARG B 612 " -0.155 2.00e-02 2.50e+03 pdb="HH12 ARG B 612 " -0.094 2.00e-02 2.50e+03 pdb="HH21 ARG B 612 " -0.368 2.00e-02 2.50e+03 pdb="HH22 ARG B 612 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 539 " 0.296 2.00e-02 2.50e+03 1.26e-01 4.75e+02 pdb=" CG TYR D 539 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR D 539 " -0.081 2.00e-02 2.50e+03 pdb=" CD2 TYR D 539 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 TYR D 539 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR D 539 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR D 539 " 0.043 2.00e-02 2.50e+03 pdb=" OH TYR D 539 " 0.248 2.00e-02 2.50e+03 pdb=" HD1 TYR D 539 " -0.061 2.00e-02 2.50e+03 pdb=" HD2 TYR D 539 " -0.080 2.00e-02 2.50e+03 pdb=" HE1 TYR D 539 " -0.065 2.00e-02 2.50e+03 pdb=" HE2 TYR D 539 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 425 " -0.195 9.50e-02 1.11e+02 1.43e-01 3.67e+02 pdb=" NE ARG E 425 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG E 425 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG E 425 " -0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG E 425 " -0.042 2.00e-02 2.50e+03 pdb="HH11 ARG E 425 " -0.236 2.00e-02 2.50e+03 pdb="HH12 ARG E 425 " 0.232 2.00e-02 2.50e+03 pdb="HH21 ARG E 425 " 0.023 2.00e-02 2.50e+03 pdb="HH22 ARG E 425 " 0.164 2.00e-02 2.50e+03 ... (remaining 5223 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.26: 3549 2.26 - 2.98: 90545 2.98 - 3.70: 127067 3.70 - 4.42: 188888 4.42 - 5.14: 297598 Nonbonded interactions: 707647 Sorted by model distance: nonbonded pdb=" HA LEU B 333 " pdb="HD22 LEU B 333 " model vdw 1.540 2.440 nonbonded pdb=" OE1 GLU A 70 " pdb=" H GLU A 70 " model vdw 1.565 2.450 nonbonded pdb=" H THR A 297 " pdb=" HG1 THR A 297 " model vdw 1.596 2.100 nonbonded pdb=" OE1 GLN A 326 " pdb=" H GLN A 326 " model vdw 1.631 2.450 nonbonded pdb=" OE1 GLU A 11 " pdb=" H GLU A 11 " model vdw 1.645 2.450 ... (remaining 707642 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 10 through 220 or resid 273 through 319 or (resid 320 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD2 or name HE1 or name HE2)) or resid 321 through 802)) selection = (chain 'B' and (resid 10 through 691 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.310 Find NCS groups from input model: 0.350 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.016 0.257 18066 Z= 0.967 Angle : 2.114 19.205 24304 Z= 1.431 Chirality : 0.122 1.020 2644 Planarity : 0.017 0.281 3120 Dihedral : 14.874 155.461 6975 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 0.05 % Allowed : 0.56 % Favored : 99.38 % Cbeta Deviations : 1.30 % 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 aren not related in a simple way. whole: -1.76 (0.16), residues: 2156 helix: -1.44 (0.14), residues: 968 sheet: 0.21 (0.32), residues: 249 loop : -1.08 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 291 TYR 0.261 0.025 TYR D 539 PHE 0.117 0.014 PHE E 476 TRP 0.139 0.026 TRP D 511 HIS 0.034 0.005 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.01559 (18066) covalent geometry : angle 2.11408 (24304) hydrogen bonds : bond 0.20181 ( 855) hydrogen bonds : angle 7.64026 ( 2391) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.798 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 553 MET cc_start: 0.9380 (ttp) cc_final: 0.9143 (tmm) REVERT: A 602 MET cc_start: 0.9408 (tpt) cc_final: 0.9077 (tpt) REVERT: A 617 MET cc_start: 0.8923 (ptm) cc_final: 0.8710 (ptm) REVERT: A 620 MET cc_start: 0.8472 (tpt) cc_final: 0.8190 (tpp) REVERT: D 553 ASN cc_start: 0.9242 (t0) cc_final: 0.8869 (t0) outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 0.3587 time to fit residues: 74.1959 Evaluate side-chains 114 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 266 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN B 396 GLN D 454 GLN E 211 GLN ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 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 = 0.3858 r_free = 0.3858 target = 0.055136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.038051 restraints weight = 347264.076| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.62 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18066 Z= 0.238 Angle : 0.680 7.406 24304 Z= 0.380 Chirality : 0.041 0.153 2644 Planarity : 0.005 0.094 3120 Dihedral : 8.575 119.959 2412 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.46 % Allowed : 3.79 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.17), residues: 2156 helix: -0.16 (0.15), residues: 1005 sheet: -0.06 (0.32), residues: 252 loop : -1.05 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 301 TYR 0.038 0.002 TYR D 539 PHE 0.027 0.002 PHE E 278 TRP 0.022 0.002 TRP E 197 HIS 0.011 0.002 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00507 (18066) covalent geometry : angle 0.68022 (24304) hydrogen bonds : bond 0.05251 ( 855) hydrogen bonds : angle 5.34940 ( 2391) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.633 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: A 553 MET cc_start: 0.9663 (ttp) cc_final: 0.9224 (tmm) REVERT: A 567 MET cc_start: 0.9367 (mtp) cc_final: 0.9144 (mpp) REVERT: B 114 MET cc_start: 0.9439 (tpp) cc_final: 0.9104 (tmm) REVERT: D 581 MET cc_start: 0.9223 (mtp) cc_final: 0.8745 (mmm) REVERT: E 141 LYS cc_start: 0.9156 (tppt) cc_final: 0.8824 (tptt) REVERT: E 327 MET cc_start: 0.9334 (mmt) cc_final: 0.8778 (mmm) outliers start: 9 outliers final: 5 residues processed: 112 average time/residue: 0.3903 time to fit residues: 61.1383 Evaluate side-chains 105 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain E residue 351 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 202 optimal weight: 40.0000 chunk 100 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 352 ASN E 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.053578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.037513 restraints weight = 365953.235| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 5.61 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18066 Z= 0.178 Angle : 0.581 6.270 24304 Z= 0.321 Chirality : 0.038 0.145 2644 Planarity : 0.004 0.053 3120 Dihedral : 7.662 105.320 2412 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.56 % Allowed : 5.33 % Favored : 94.11 % 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 aren not related in a simple way. whole: -0.25 (0.17), residues: 2156 helix: 0.55 (0.16), residues: 1001 sheet: -0.01 (0.33), residues: 245 loop : -0.95 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 301 TYR 0.029 0.002 TYR D 539 PHE 0.021 0.001 PHE E 278 TRP 0.018 0.002 TRP E 197 HIS 0.009 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00375 (18066) covalent geometry : angle 0.58142 (24304) hydrogen bonds : bond 0.04515 ( 855) hydrogen bonds : angle 4.90800 ( 2391) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.772 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: A 553 MET cc_start: 0.9664 (ttp) cc_final: 0.9242 (tmm) REVERT: A 567 MET cc_start: 0.9399 (mtp) cc_final: 0.9158 (mpp) REVERT: A 621 MET cc_start: 0.9217 (ppp) cc_final: 0.8486 (ppp) REVERT: B 114 MET cc_start: 0.9453 (tpp) cc_final: 0.9133 (tmm) REVERT: B 683 MET cc_start: 0.9094 (mmp) cc_final: 0.8886 (mmp) REVERT: D 581 MET cc_start: 0.9352 (mtp) cc_final: 0.8819 (mmm) REVERT: E 141 LYS cc_start: 0.9193 (tppt) cc_final: 0.8793 (tptt) REVERT: E 273 VAL cc_start: 0.9368 (OUTLIER) cc_final: 0.8961 (p) REVERT: E 327 MET cc_start: 0.9442 (mmt) cc_final: 0.8863 (mmm) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.3708 time to fit residues: 56.2492 Evaluate side-chains 103 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 351 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 117 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 187 optimal weight: 0.7980 chunk 211 optimal weight: 50.0000 chunk 182 optimal weight: 30.0000 chunk 71 optimal weight: 6.9990 chunk 146 optimal weight: 40.0000 chunk 206 optimal weight: 20.0000 chunk 203 optimal weight: 30.0000 chunk 11 optimal weight: 0.9980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.050627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.035033 restraints weight = 413944.945| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 5.35 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18066 Z= 0.241 Angle : 0.599 7.029 24304 Z= 0.330 Chirality : 0.039 0.143 2644 Planarity : 0.004 0.053 3120 Dihedral : 7.155 95.364 2410 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.56 % Allowed : 6.51 % Favored : 92.93 % 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 aren not related in a simple way. whole: -0.22 (0.17), residues: 2156 helix: 0.72 (0.16), residues: 1008 sheet: -0.08 (0.33), residues: 250 loop : -1.12 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 301 TYR 0.025 0.002 TYR D 539 PHE 0.018 0.001 PHE C 237 TRP 0.015 0.002 TRP E 197 HIS 0.006 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00504 (18066) covalent geometry : angle 0.59887 (24304) hydrogen bonds : bond 0.04297 ( 855) hydrogen bonds : angle 4.91517 ( 2391) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.936 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: A 125 MET cc_start: 0.8831 (mtp) cc_final: 0.7981 (mtp) REVERT: A 553 MET cc_start: 0.9675 (ttp) cc_final: 0.9244 (tmm) REVERT: A 567 MET cc_start: 0.9411 (mtp) cc_final: 0.9174 (mpp) REVERT: B 114 MET cc_start: 0.9418 (tpp) cc_final: 0.9097 (tmm) REVERT: C 206 MET cc_start: 0.4970 (ppp) cc_final: 0.4421 (ppp) REVERT: C 216 MET cc_start: 0.9369 (ptt) cc_final: 0.9015 (ppp) REVERT: D 469 MET cc_start: 0.8739 (tmm) cc_final: 0.8460 (tmm) REVERT: E 141 LYS cc_start: 0.9193 (tppt) cc_final: 0.8843 (tptt) REVERT: E 273 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.8921 (p) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.3609 time to fit residues: 53.8905 Evaluate side-chains 104 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 451 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 161 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 203 optimal weight: 30.0000 chunk 90 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.050191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.034766 restraints weight = 423857.685| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.35 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18066 Z= 0.233 Angle : 0.571 6.337 24304 Z= 0.314 Chirality : 0.038 0.143 2644 Planarity : 0.004 0.051 3120 Dihedral : 6.957 104.794 2410 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.03 % Allowed : 7.23 % Favored : 91.75 % 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 aren not related in a simple way. whole: -0.15 (0.18), residues: 2156 helix: 0.89 (0.16), residues: 1005 sheet: -0.12 (0.34), residues: 251 loop : -1.20 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 301 TYR 0.025 0.002 TYR D 539 PHE 0.015 0.001 PHE C 237 TRP 0.013 0.002 TRP E 197 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00484 (18066) covalent geometry : angle 0.57061 (24304) hydrogen bonds : bond 0.04101 ( 855) hydrogen bonds : angle 4.81819 ( 2391) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.633 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: A 125 MET cc_start: 0.8831 (mtp) cc_final: 0.8064 (mtp) REVERT: A 553 MET cc_start: 0.9687 (ttp) cc_final: 0.9261 (tmm) REVERT: A 567 MET cc_start: 0.9422 (mtp) cc_final: 0.9172 (mpp) REVERT: B 114 MET cc_start: 0.9421 (tpp) cc_final: 0.9118 (tmm) REVERT: B 188 ASP cc_start: 0.9361 (OUTLIER) cc_final: 0.8849 (p0) REVERT: C 206 MET cc_start: 0.5105 (ppp) cc_final: 0.4537 (ppp) REVERT: C 216 MET cc_start: 0.9338 (ptt) cc_final: 0.9001 (ppp) REVERT: D 469 MET cc_start: 0.8998 (tmm) cc_final: 0.8389 (tmm) REVERT: E 141 LYS cc_start: 0.9206 (tppt) cc_final: 0.8857 (tptt) REVERT: E 174 ASP cc_start: 0.8322 (m-30) cc_final: 0.8039 (t70) REVERT: E 198 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.7476 (m-10) REVERT: E 273 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9038 (p) REVERT: E 327 MET cc_start: 0.9520 (mmt) cc_final: 0.8961 (mmm) outliers start: 20 outliers final: 12 residues processed: 112 average time/residue: 0.3604 time to fit residues: 57.9221 Evaluate side-chains 110 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 451 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 212 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.050594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.035651 restraints weight = 397781.247| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 5.53 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18066 Z= 0.207 Angle : 0.559 9.572 24304 Z= 0.304 Chirality : 0.038 0.146 2644 Planarity : 0.003 0.037 3120 Dihedral : 6.841 105.465 2410 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.08 % Allowed : 8.20 % Favored : 90.72 % 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 aren not related in a simple way. whole: -0.13 (0.18), residues: 2156 helix: 0.95 (0.16), residues: 1006 sheet: -0.22 (0.34), residues: 253 loop : -1.20 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 301 TYR 0.023 0.001 TYR D 539 PHE 0.015 0.001 PHE E 287 TRP 0.014 0.002 TRP E 197 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00432 (18066) covalent geometry : angle 0.55884 (24304) hydrogen bonds : bond 0.03929 ( 855) hydrogen bonds : angle 4.73323 ( 2391) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.9667 (ttp) cc_final: 0.9246 (tmm) REVERT: A 567 MET cc_start: 0.9483 (mtp) cc_final: 0.9218 (mpp) REVERT: B 114 MET cc_start: 0.9428 (tpp) cc_final: 0.9147 (tmm) REVERT: C 206 MET cc_start: 0.4995 (ppp) cc_final: 0.4581 (ppp) REVERT: C 216 MET cc_start: 0.9411 (ptt) cc_final: 0.9077 (ppp) REVERT: D 469 MET cc_start: 0.9058 (tmm) cc_final: 0.8244 (tmm) REVERT: E 141 LYS cc_start: 0.9198 (tppt) cc_final: 0.8854 (tptt) REVERT: E 174 ASP cc_start: 0.8668 (m-30) cc_final: 0.8381 (t70) REVERT: E 198 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: E 240 CYS cc_start: 0.9629 (OUTLIER) cc_final: 0.9425 (p) REVERT: E 273 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.8962 (p) outliers start: 21 outliers final: 16 residues processed: 109 average time/residue: 0.3294 time to fit residues: 52.9885 Evaluate side-chains 111 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 451 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 207 optimal weight: 30.0000 chunk 148 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.050919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.035585 restraints weight = 390805.827| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 5.69 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18066 Z= 0.178 Angle : 0.543 8.499 24304 Z= 0.293 Chirality : 0.037 0.147 2644 Planarity : 0.003 0.035 3120 Dihedral : 6.719 106.808 2410 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.92 % Allowed : 8.97 % Favored : 90.11 % 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 aren not related in a simple way. whole: -0.03 (0.18), residues: 2156 helix: 1.06 (0.16), residues: 1008 sheet: -0.19 (0.34), residues: 253 loop : -1.19 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 301 TYR 0.022 0.001 TYR D 539 PHE 0.023 0.001 PHE E 287 TRP 0.014 0.001 TRP E 197 HIS 0.009 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00369 (18066) covalent geometry : angle 0.54275 (24304) hydrogen bonds : bond 0.03810 ( 855) hydrogen bonds : angle 4.64439 ( 2391) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.028 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: A 553 MET cc_start: 0.9666 (ttp) cc_final: 0.9238 (tmm) REVERT: A 567 MET cc_start: 0.9452 (mtp) cc_final: 0.9193 (mpp) REVERT: B 114 MET cc_start: 0.9401 (tpp) cc_final: 0.9117 (tmm) REVERT: C 112 MET cc_start: 0.7843 (ppp) cc_final: 0.7642 (ppp) REVERT: C 206 MET cc_start: 0.5092 (ppp) cc_final: 0.4763 (ppp) REVERT: C 216 MET cc_start: 0.9362 (ptt) cc_final: 0.9029 (ppp) REVERT: D 469 MET cc_start: 0.9058 (tmm) cc_final: 0.8153 (tmm) REVERT: E 141 LYS cc_start: 0.9201 (tppt) cc_final: 0.8850 (tptt) REVERT: E 174 ASP cc_start: 0.8613 (m-30) cc_final: 0.8364 (t70) REVERT: E 198 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: E 273 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.8933 (p) REVERT: E 327 MET cc_start: 0.9532 (mmt) cc_final: 0.8986 (mmm) outliers start: 18 outliers final: 13 residues processed: 104 average time/residue: 0.3281 time to fit residues: 50.4073 Evaluate side-chains 107 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 451 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 87 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 205 optimal weight: 0.0770 chunk 178 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.050553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.035666 restraints weight = 401134.229| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 5.76 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18066 Z= 0.179 Angle : 0.543 9.208 24304 Z= 0.292 Chirality : 0.037 0.139 2644 Planarity : 0.003 0.034 3120 Dihedral : 6.658 107.301 2410 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.92 % Allowed : 9.23 % Favored : 89.85 % 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 aren not related in a simple way. whole: 0.02 (0.18), residues: 2156 helix: 1.10 (0.16), residues: 1007 sheet: -0.20 (0.34), residues: 253 loop : -1.16 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 301 TYR 0.022 0.001 TYR D 539 PHE 0.013 0.001 PHE C 237 TRP 0.014 0.001 TRP E 197 HIS 0.008 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00373 (18066) covalent geometry : angle 0.54268 (24304) hydrogen bonds : bond 0.03749 ( 855) hydrogen bonds : angle 4.61178 ( 2391) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.9469 (mtp) cc_final: 0.9209 (mpp) REVERT: B 114 MET cc_start: 0.9414 (tpp) cc_final: 0.9128 (tmm) REVERT: C 112 MET cc_start: 0.7910 (ppp) cc_final: 0.7691 (ppp) REVERT: C 206 MET cc_start: 0.5103 (ppp) cc_final: 0.4825 (ppp) REVERT: C 216 MET cc_start: 0.9366 (ptt) cc_final: 0.9035 (ppp) REVERT: D 469 MET cc_start: 0.9032 (tmm) cc_final: 0.8064 (tmm) REVERT: E 141 LYS cc_start: 0.9210 (tppt) cc_final: 0.8859 (tptt) REVERT: E 174 ASP cc_start: 0.8706 (m-30) cc_final: 0.8456 (t70) REVERT: E 198 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: E 273 VAL cc_start: 0.9388 (OUTLIER) cc_final: 0.8968 (p) outliers start: 18 outliers final: 15 residues processed: 104 average time/residue: 0.3334 time to fit residues: 50.5072 Evaluate side-chains 108 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 457 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 209 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.052718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.036511 restraints weight = 352141.676| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 5.30 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18066 Z= 0.229 Angle : 0.573 8.035 24304 Z= 0.311 Chirality : 0.038 0.138 2644 Planarity : 0.003 0.036 3120 Dihedral : 6.758 108.608 2410 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.03 % Allowed : 9.43 % Favored : 89.54 % 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 aren not related in a simple way. whole: -0.15 (0.18), residues: 2156 helix: 0.95 (0.16), residues: 1010 sheet: -0.28 (0.33), residues: 255 loop : -1.25 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 101 TYR 0.020 0.002 TYR D 539 PHE 0.019 0.001 PHE E 335 TRP 0.015 0.002 TRP C 31 HIS 0.008 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00476 (18066) covalent geometry : angle 0.57279 (24304) hydrogen bonds : bond 0.03933 ( 855) hydrogen bonds : angle 4.72356 ( 2391) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.075 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: B 114 MET cc_start: 0.9435 (tpp) cc_final: 0.9161 (tmm) REVERT: C 112 MET cc_start: 0.7907 (ppp) cc_final: 0.7696 (ppp) REVERT: C 216 MET cc_start: 0.9261 (ptt) cc_final: 0.8921 (ppp) REVERT: D 469 MET cc_start: 0.9019 (tmm) cc_final: 0.8156 (tmm) REVERT: E 141 LYS cc_start: 0.9233 (tppt) cc_final: 0.8899 (tptt) REVERT: E 174 ASP cc_start: 0.8500 (m-30) cc_final: 0.8250 (t70) REVERT: E 273 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.8922 (p) outliers start: 20 outliers final: 18 residues processed: 104 average time/residue: 0.4133 time to fit residues: 62.2783 Evaluate side-chains 108 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 457 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 176 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 211 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 207 optimal weight: 40.0000 chunk 27 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.048746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.033837 restraints weight = 552835.039| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 6.08 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18066 Z= 0.185 Angle : 0.558 11.069 24304 Z= 0.299 Chirality : 0.038 0.138 2644 Planarity : 0.003 0.037 3120 Dihedral : 6.670 108.441 2410 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.97 % Allowed : 9.69 % Favored : 89.34 % 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 aren not related in a simple way. whole: -0.08 (0.18), residues: 2156 helix: 1.02 (0.16), residues: 1013 sheet: -0.35 (0.33), residues: 265 loop : -1.19 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 301 TYR 0.022 0.001 TYR D 539 PHE 0.028 0.001 PHE C 218 TRP 0.015 0.002 TRP C 31 HIS 0.008 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00386 (18066) covalent geometry : angle 0.55791 (24304) hydrogen bonds : bond 0.03763 ( 855) hydrogen bonds : angle 4.62956 ( 2391) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.095 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: B 114 MET cc_start: 0.9395 (tpp) cc_final: 0.9114 (tmm) REVERT: C 112 MET cc_start: 0.8154 (ppp) cc_final: 0.7933 (ppp) REVERT: C 216 MET cc_start: 0.9456 (ptt) cc_final: 0.9206 (ppp) REVERT: D 469 MET cc_start: 0.9055 (tmm) cc_final: 0.8143 (tmm) REVERT: E 174 ASP cc_start: 0.9407 (m-30) cc_final: 0.9135 (t70) REVERT: E 273 VAL cc_start: 0.9453 (OUTLIER) cc_final: 0.9105 (p) REVERT: E 327 MET cc_start: 0.9668 (mmt) cc_final: 0.9371 (mmm) outliers start: 19 outliers final: 17 residues processed: 103 average time/residue: 0.3459 time to fit residues: 52.5205 Evaluate side-chains 107 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 457 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 3 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.051689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.036009 restraints weight = 379232.865| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 5.75 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18066 Z= 0.118 Angle : 0.528 9.873 24304 Z= 0.279 Chirality : 0.037 0.142 2644 Planarity : 0.003 0.037 3120 Dihedral : 6.386 107.569 2410 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.67 % Allowed : 9.99 % Favored : 89.34 % 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 aren not related in a simple way. whole: 0.14 (0.18), residues: 2156 helix: 1.22 (0.16), residues: 1023 sheet: -0.19 (0.33), residues: 265 loop : -1.16 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 301 TYR 0.024 0.001 TYR D 539 PHE 0.032 0.001 PHE E 287 TRP 0.015 0.001 TRP E 197 HIS 0.006 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00250 (18066) covalent geometry : angle 0.52770 (24304) hydrogen bonds : bond 0.03427 ( 855) hydrogen bonds : angle 4.40063 ( 2391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6372.94 seconds wall clock time: 109 minutes 10.61 seconds (6550.61 seconds total)