Starting phenix.real_space_refine on Tue Sep 24 13:13:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn8_19390/09_2024/8rn8_19390.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn8_19390/09_2024/8rn8_19390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn8_19390/09_2024/8rn8_19390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn8_19390/09_2024/8rn8_19390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn8_19390/09_2024/8rn8_19390.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn8_19390/09_2024/8rn8_19390.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.085 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: 6 Type Number sf(0) Gaussians Mg 5 5.21 5 S 197 5.16 5 C 16289 2.51 5 N 4376 2.21 5 O 4795 1.98 5 H 25704 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51366 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 11326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 11326 Classifications: {'peptide': 706} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 679} Chain breaks: 1 Chain: "B" Number of atoms: 9701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 9701 Classifications: {'peptide': 622} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 589} Chain breaks: 3 Chain: "C" Number of atoms: 9818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9818 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 21, 'TRANS': 591} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 8275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 8275 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 21, 'TRANS': 496} Chain: "E" Number of atoms: 10039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10039 Classifications: {'peptide': 640} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 607} Chain breaks: 3 Chain: "F" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2202 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.05, per 1000 atoms: 0.35 Number of scatterers: 51366 At special positions: 0 Unit cell: (105, 131.04, 201.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 197 16.00 Mg 5 11.99 O 4795 8.00 N 4376 7.00 C 16289 6.00 H 25704 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: 9.71 Conformation dependent library (CDL) restraints added in 3.0 seconds 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6002 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 37 sheets defined 49.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 25 removed outlier: 4.164A pdb=" N PHE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 30 Processing helix chain 'A' and resid 31 through 52 removed outlier: 3.633A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 163 through 184 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.502A pdb=" N ARG A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.842A pdb=" N TRP A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.278A pdb=" N GLN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 Processing helix chain 'A' and resid 449 through 468 removed outlier: 3.628A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 575 through 595 removed outlier: 3.713A pdb=" N ILE A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 628 through 646 Processing helix chain 'A' and resid 648 through 671 removed outlier: 3.855A pdb=" N ARG A 659 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 693 through 716 removed outlier: 3.650A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.992A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.703A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.939A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 4.182A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.508A pdb=" N LEU B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.384A pdb=" N ALA B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.581A pdb=" N ASN B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 454 through 473 Processing helix chain 'B' and resid 517 through 536 removed outlier: 3.899A pdb=" N MET B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.995A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.588A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.700A pdb=" N GLU C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 255 through 274 removed outlier: 3.919A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.580A pdb=" N LEU C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.817A pdb=" N ASP C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 318 Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.580A pdb=" N GLN C 408 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.707A pdb=" N GLN C 450 " --> pdb=" O ASP C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 534 through 541 removed outlier: 4.251A pdb=" N GLU C 539 " --> pdb=" O LYS C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 557 Processing helix chain 'C' and resid 557 through 566 Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 575 through 583 removed outlier: 3.641A pdb=" N SER C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 606 removed outlier: 4.653A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.760A pdb=" N PHE C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 624 " --> pdb=" O PHE C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 624' Processing helix chain 'C' and resid 689 through 694 removed outlier: 4.199A pdb=" N VAL C 694 " --> pdb=" O GLY C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 720 Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 237 through 246 Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 313 through 319 Processing helix chain 'D' and resid 332 through 349 Processing helix chain 'D' and resid 360 through 366 removed outlier: 3.986A pdb=" N TRP D 364 " --> pdb=" O ASN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.555A pdb=" N ALA D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 411 removed outlier: 4.084A pdb=" N GLN D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 411 " --> pdb=" O MET D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 447 Processing helix chain 'D' and resid 449 through 472 removed outlier: 3.655A pdb=" N THR D 453 " --> pdb=" O CYS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 Processing helix chain 'D' and resid 563 through 572 Processing helix chain 'D' and resid 574 through 595 removed outlier: 3.888A pdb=" N LEU D 578 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN D 583 " --> pdb=" O GLN D 579 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET D 584 " --> pdb=" O SER D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 605 Processing helix chain 'D' and resid 629 through 646 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.157A pdb=" N ARG D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 688 Processing helix chain 'D' and resid 693 through 716 removed outlier: 3.563A pdb=" N VAL D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.735A pdb=" N THR E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 22' Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 84 through 99 Processing helix chain 'E' and resid 101 through 117 Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'E' and resid 138 through 153 Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.857A pdb=" N PHE E 166 " --> pdb=" O GLY E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 222 Processing helix chain 'E' and resid 245 through 265 removed outlier: 4.093A pdb=" N GLY E 250 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE E 251 " --> pdb=" O GLN E 247 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN E 265 " --> pdb=" O ASN E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 293 removed outlier: 4.023A pdb=" N ALA E 280 " --> pdb=" O ASN E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 313 removed outlier: 3.573A pdb=" N LEU E 313 " --> pdb=" O TRP E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 Processing helix chain 'E' and resid 330 through 338 Processing helix chain 'E' and resid 338 through 346 removed outlier: 3.505A pdb=" N VAL E 342 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 394 through 396 No H-bonds generated for 'chain 'E' and resid 394 through 396' Processing helix chain 'E' and resid 413 through 426 removed outlier: 3.536A pdb=" N SER E 417 " --> pdb=" O PHE E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 472 removed outlier: 3.628A pdb=" N LEU E 472 " --> pdb=" O THR E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 536 removed outlier: 3.527A pdb=" N ILE E 529 " --> pdb=" O GLY E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 559 Processing helix chain 'E' and resid 569 through 582 removed outlier: 3.947A pdb=" N ILE E 574 " --> pdb=" O LYS E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 588 Processing helix chain 'E' and resid 589 through 593 Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.711A pdb=" N LEU E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 611 Processing helix chain 'E' and resid 616 through 624 Processing helix chain 'E' and resid 661 through 665 removed outlier: 3.891A pdb=" N TRP E 665 " --> pdb=" O THR E 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 54 removed outlier: 3.638A pdb=" N CYS F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 69 Processing helix chain 'F' and resid 94 through 104 removed outlier: 3.620A pdb=" N VAL F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 117 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 227 through 234 removed outlier: 3.894A pdb=" N MET F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.576A pdb=" N PHE A 118 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N MET A 146 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLU A 120 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A 148 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY A 122 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.772A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B 445 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.372A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.372A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 492 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN A 487 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP A 494 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 485 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASN A 483 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.793A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 623 through 627 removed outlier: 3.642A pdb=" N GLY A 618 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 627 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N SER A 616 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 186 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 244 removed outlier: 3.591A pdb=" N ARG B 350 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 61 removed outlier: 4.374A pdb=" N GLN C 91 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 137 removed outlier: 5.977A pdb=" N ILE C 245 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 135 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG C 243 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AB7, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.465A pdb=" N LEU C 332 " --> pdb=" O ARG C 368 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ARG C 368 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ARG C 334 " --> pdb=" O HIS C 366 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N HIS C 366 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG C 373 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE C 388 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 375 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU C 386 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS C 377 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL C 480 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU C 386 " --> pdb=" O VAL C 480 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 482 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE C 388 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 340 through 347 removed outlier: 3.776A pdb=" N PHE C 340 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 360 " --> pdb=" O PHE C 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 453 through 455 Processing sheet with id=AC1, first strand: chain 'C' and resid 498 through 499 removed outlier: 6.871A pdb=" N LEU C 505 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC3, first strand: chain 'C' and resid 660 through 662 removed outlier: 3.797A pdb=" N VAL C 667 " --> pdb=" O ASN C 662 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AC5, first strand: chain 'D' and resid 255 through 256 Processing sheet with id=AC6, first strand: chain 'D' and resid 291 through 295 removed outlier: 4.227A pdb=" N SER D 492 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR D 497 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR D 515 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS D 551 " --> pdb=" O SER D 543 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER D 543 " --> pdb=" O LYS D 551 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D 553 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 538 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE D 323 " --> pdb=" O ARG D 540 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 291 through 295 removed outlier: 4.227A pdb=" N SER D 492 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE D 481 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU D 499 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE D 479 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL D 501 " --> pdb=" O LYS D 477 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS D 477 " --> pdb=" O VAL D 501 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 373 through 374 removed outlier: 5.852A pdb=" N GLN D 373 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLN E 367 " --> pdb=" O GLN D 373 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 623 through 628 removed outlier: 3.718A pdb=" N GLY D 618 " --> pdb=" O VAL D 625 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY D 627 " --> pdb=" O SER D 616 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER D 616 " --> pdb=" O GLY D 627 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AD2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AD3, first strand: chain 'E' and resid 178 through 188 Processing sheet with id=AD4, first strand: chain 'E' and resid 240 through 244 removed outlier: 3.830A pdb=" N THR E 226 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 488 through 491 Processing sheet with id=AD6, first strand: chain 'E' and resid 641 through 642 removed outlier: 3.923A pdb=" N MET E 654 " --> pdb=" O ALA E 642 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 59 through 60 removed outlier: 4.334A pdb=" N MET F 92 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR F 81 " --> pdb=" O MET F 92 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 73 through 74 Processing sheet with id=AD9, first strand: chain 'F' and resid 131 through 136 removed outlier: 5.829A pdb=" N TRP F 132 " --> pdb=" O HIS F 247 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS F 247 " --> pdb=" O TRP F 132 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ARG F 134 " --> pdb=" O ILE F 245 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 143 through 147 1273 hydrogen bonds defined for protein. 3492 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: 17.17 Time building geometry restraints manager: 11.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 25642 1.03 - 1.23: 126 1.23 - 1.42: 10656 1.42 - 1.62: 15116 1.62 - 1.82: 332 Bond restraints: 51872 Sorted by residual: bond pdb=" C ILE C 585 " pdb=" N PRO C 586 " ideal model delta sigma weight residual 1.330 1.343 -0.012 1.19e-02 7.06e+03 1.08e+00 bond pdb=" CA ASP A 321 " pdb=" CB ASP A 321 " ideal model delta sigma weight residual 1.534 1.550 -0.016 1.57e-02 4.06e+03 1.04e+00 bond pdb=" CB ASP A 321 " pdb=" CG ASP A 321 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.43e-01 bond pdb=" CG LYS A 551 " pdb=" CD LYS A 551 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.04e-01 bond pdb=" CB LYS A 605 " pdb=" CG LYS A 605 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.49e-01 ... (remaining 51867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 90347 1.22 - 2.44: 3239 2.44 - 3.67: 222 3.67 - 4.89: 50 4.89 - 6.11: 5 Bond angle restraints: 93863 Sorted by residual: angle pdb=" N MET B 412 " pdb=" CA MET B 412 " pdb=" C MET B 412 " ideal model delta sigma weight residual 114.62 109.68 4.94 1.14e+00 7.69e-01 1.88e+01 angle pdb=" N ASP A 129 " pdb=" CA ASP A 129 " pdb=" CB ASP A 129 " ideal model delta sigma weight residual 114.17 110.97 3.20 1.14e+00 7.69e-01 7.87e+00 angle pdb=" CA MET B 412 " pdb=" C MET B 412 " pdb=" N PHE B 413 " ideal model delta sigma weight residual 119.71 116.46 3.25 1.17e+00 7.31e-01 7.72e+00 angle pdb=" N GLY E 35 " pdb=" CA GLY E 35 " pdb=" C GLY E 35 " ideal model delta sigma weight residual 115.34 111.27 4.07 1.67e+00 3.59e-01 5.94e+00 angle pdb=" N ILE C 513 " pdb=" CA ILE C 513 " pdb=" C ILE C 513 " ideal model delta sigma weight residual 111.81 109.78 2.03 8.60e-01 1.35e+00 5.57e+00 ... (remaining 93858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 21234 17.97 - 35.94: 2096 35.94 - 53.90: 763 53.90 - 71.87: 171 71.87 - 89.84: 48 Dihedral angle restraints: 24312 sinusoidal: 13431 harmonic: 10881 Sorted by residual: dihedral pdb=" CA LYS D 327 " pdb=" C LYS D 327 " pdb=" N SER D 328 " pdb=" CA SER D 328 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA MET B 408 " pdb=" C MET B 408 " pdb=" N MET B 409 " pdb=" CA MET B 409 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASP E 372 " pdb=" CB ASP E 372 " pdb=" CG ASP E 372 " pdb=" OD1 ASP E 372 " ideal model delta sinusoidal sigma weight residual -30.00 -86.92 56.92 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 24309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2915 0.037 - 0.075: 688 0.075 - 0.112: 193 0.112 - 0.149: 63 0.149 - 0.187: 2 Chirality restraints: 3861 Sorted by residual: chirality pdb=" CB VAL D 443 " pdb=" CA VAL D 443 " pdb=" CG1 VAL D 443 " pdb=" CG2 VAL D 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CG LEU A 171 " pdb=" CB LEU A 171 " pdb=" CD1 LEU A 171 " pdb=" CD2 LEU A 171 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE D 393 " pdb=" N ILE D 393 " pdb=" C ILE D 393 " pdb=" CB ILE D 393 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 3858 not shown) Planarity restraints: 7608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 359 " 0.014 2.00e-02 2.50e+03 9.55e-03 3.65e+00 pdb=" CG TRP C 359 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP C 359 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 359 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 359 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 359 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 359 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 359 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 359 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 359 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP C 359 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP C 359 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP C 359 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 359 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 359 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP C 359 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 429 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO D 430 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 430 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 430 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 574 " 0.146 9.50e-02 1.11e+02 4.87e-02 2.79e+00 pdb=" NE ARG A 574 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 574 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 574 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 574 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 574 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 574 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 574 " 0.007 2.00e-02 2.50e+03 pdb="HH22 ARG A 574 " -0.001 2.00e-02 2.50e+03 ... (remaining 7605 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1816 2.14 - 2.76: 98181 2.76 - 3.37: 148650 3.37 - 3.99: 194555 3.99 - 4.60: 306316 Nonbonded interactions: 749518 Sorted by model distance: nonbonded pdb="HE21 GLN E 108 " pdb=" OE2 GLU E 112 " model vdw 1.531 2.450 nonbonded pdb=" OE1 GLU E 383 " pdb=" H GLU E 383 " model vdw 1.541 2.450 nonbonded pdb=" O CYS D 576 " pdb=" HG SER D 580 " model vdw 1.566 2.450 nonbonded pdb=" O GLU B 518 " pdb=" HH TYR B 554 " model vdw 1.568 2.450 nonbonded pdb=" OE1 GLU B 618 " pdb=" H GLU B 618 " model vdw 1.578 2.450 ... (remaining 749513 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 'B' and (resid 1 through 665 or resid 801 through 802)) selection = (chain 'E' and (resid 1 through 188 or resid 203 through 228 or (resid 229 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name C \ E or name NZ )) or (resid 240 and (name N or name CA or name C or name O or name \ CB or name HA )) or resid 241 through 638 or (resid 655 and (name N or name CA \ or name C or name O or name CB or name CG or name OD1 or name OD2 or name HA or \ name HB2 or name HB3)) or resid 656 through 665 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 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: 0.660 Extract box with map and model: 1.440 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 80.360 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26168 Z= 0.170 Angle : 0.496 6.110 35279 Z= 0.258 Chirality : 0.038 0.187 3861 Planarity : 0.003 0.064 4532 Dihedral : 17.765 89.838 9917 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 1.95 % Allowed : 25.69 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3202 helix: 1.66 (0.14), residues: 1387 sheet: -0.79 (0.26), residues: 373 loop : -0.49 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 359 HIS 0.003 0.001 HIS E 604 PHE 0.018 0.001 PHE D 442 TYR 0.013 0.001 TYR B 466 ARG 0.003 0.000 ARG F 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 336 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 48 residues processed: 386 average time/residue: 1.9886 time to fit residues: 926.3576 Evaluate side-chains 372 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 324 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 477 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 291 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN B 32 HIS B 581 ASN E 108 GLN E 168 GLN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 26168 Z= 0.398 Angle : 0.585 6.635 35279 Z= 0.311 Chirality : 0.042 0.156 3861 Planarity : 0.004 0.046 4532 Dihedral : 5.913 59.195 3555 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 3.26 % Allowed : 24.38 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3202 helix: 1.18 (0.14), residues: 1401 sheet: -1.03 (0.26), residues: 379 loop : -0.76 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 437 HIS 0.004 0.001 HIS C 235 PHE 0.017 0.002 PHE A 24 TYR 0.017 0.002 TYR E 466 ARG 0.004 0.000 ARG E 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 431 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 339 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 350 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 657 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: B 180 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7728 (p) REVERT: B 410 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7471 (mpt) REVERT: B 666 ARG cc_start: 0.7513 (mtm110) cc_final: 0.7313 (mtp180) REVERT: C 587 GLN cc_start: 0.7590 (mp10) cc_final: 0.7340 (tp-100) REVERT: C 610 MET cc_start: 0.5891 (OUTLIER) cc_final: 0.4721 (ttm) REVERT: D 520 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: E 383 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7446 (mp0) outliers start: 92 outliers final: 50 residues processed: 411 average time/residue: 2.0464 time to fit residues: 1004.2184 Evaluate side-chains 378 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 320 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 583 GLN Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain F residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 242 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 315 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 168 GLN B 581 ASN C 484 ASN D 610 ASN E 108 GLN E 306 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26168 Z= 0.233 Angle : 0.519 6.720 35279 Z= 0.271 Chirality : 0.039 0.162 3861 Planarity : 0.004 0.045 4532 Dihedral : 5.505 59.088 3536 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 2.91 % Allowed : 24.73 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3202 helix: 1.33 (0.14), residues: 1403 sheet: -1.03 (0.25), residues: 384 loop : -0.76 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 PHE 0.019 0.001 PHE A 24 TYR 0.014 0.001 TYR B 466 ARG 0.003 0.000 ARG F 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 333 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: A 350 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: A 657 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: B 410 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7339 (mpt) REVERT: B 666 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7306 (mtp180) REVERT: C 610 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.4727 (ttm) REVERT: D 520 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: E 383 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: E 494 MET cc_start: 0.7033 (ttm) cc_final: 0.6720 (ttp) REVERT: E 599 ASN cc_start: 0.5552 (OUTLIER) cc_final: 0.5233 (m-40) REVERT: F 92 MET cc_start: 0.2892 (mmp) cc_final: 0.0784 (pmm) outliers start: 82 outliers final: 52 residues processed: 395 average time/residue: 2.0485 time to fit residues: 969.2063 Evaluate side-chains 383 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 323 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 599 ASN Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 233 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 310 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 271 ASN B 32 HIS B 168 GLN B 581 ASN ** D 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN E 306 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 26168 Z= 0.396 Angle : 0.575 6.989 35279 Z= 0.304 Chirality : 0.042 0.152 3861 Planarity : 0.004 0.043 4532 Dihedral : 5.466 57.663 3523 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 3.62 % Allowed : 23.92 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3202 helix: 1.02 (0.14), residues: 1405 sheet: -1.08 (0.25), residues: 379 loop : -0.93 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 437 HIS 0.004 0.001 HIS C 235 PHE 0.020 0.002 PHE A 24 TYR 0.016 0.002 TYR E 466 ARG 0.003 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 331 time to evaluate : 2.975 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: A 43 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: A 236 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7859 (tmmt) REVERT: A 329 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6214 (pm20) REVERT: A 350 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: A 657 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: C 387 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7708 (tp) REVERT: C 395 ASP cc_start: 0.5641 (OUTLIER) cc_final: 0.5095 (t0) REVERT: C 610 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.4835 (ttm) REVERT: D 520 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: E 321 MET cc_start: 0.8220 (mtp) cc_final: 0.7601 (mtp) REVERT: E 383 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: F 92 MET cc_start: 0.2966 (mmp) cc_final: 0.0774 (pmm) outliers start: 102 outliers final: 59 residues processed: 412 average time/residue: 2.0932 time to fit residues: 1028.5155 Evaluate side-chains 392 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 323 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 583 GLN Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 610 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 242 ASN A 271 ASN B 581 ASN B 628 ASN C 692 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 26168 Z= 0.383 Angle : 0.575 7.161 35279 Z= 0.303 Chirality : 0.041 0.148 3861 Planarity : 0.004 0.043 4532 Dihedral : 5.463 58.202 3518 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 3.73 % Allowed : 24.38 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3202 helix: 0.88 (0.14), residues: 1407 sheet: -1.14 (0.26), residues: 369 loop : -1.04 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 51 HIS 0.004 0.001 HIS E 604 PHE 0.015 0.002 PHE B 182 TYR 0.015 0.002 TYR E 466 ARG 0.007 0.000 ARG C 741 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 440 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 335 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: A 210 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7529 (tpt-90) REVERT: A 236 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7838 (tmmt) REVERT: A 329 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6288 (pm20) REVERT: A 350 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 657 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: B 410 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7369 (mpt) REVERT: B 526 MET cc_start: 0.9148 (mmp) cc_final: 0.8507 (mmp) REVERT: C 243 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7462 (tmm-80) REVERT: C 395 ASP cc_start: 0.5707 (OUTLIER) cc_final: 0.5127 (t0) REVERT: C 540 MET cc_start: 0.6698 (mpt) cc_final: 0.6264 (mpm) REVERT: C 610 MET cc_start: 0.5807 (OUTLIER) cc_final: 0.4813 (ttm) REVERT: C 710 ASP cc_start: 0.6104 (OUTLIER) cc_final: 0.5727 (m-30) REVERT: D 520 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7147 (mm-30) REVERT: E 321 MET cc_start: 0.8210 (mtp) cc_final: 0.7621 (mtp) REVERT: E 383 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: F 92 MET cc_start: 0.2907 (mmp) cc_final: 0.0674 (pmm) outliers start: 105 outliers final: 65 residues processed: 420 average time/residue: 2.1016 time to fit residues: 1055.3823 Evaluate side-chains 403 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 326 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain F residue 233 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.7980 chunk 279 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 271 ASN B 581 ASN B 627 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26168 Z= 0.227 Angle : 0.521 7.593 35279 Z= 0.273 Chirality : 0.039 0.145 3861 Planarity : 0.004 0.045 4532 Dihedral : 5.164 54.606 3515 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 3.48 % Allowed : 24.56 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3202 helix: 1.18 (0.14), residues: 1406 sheet: -1.17 (0.25), residues: 370 loop : -0.93 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 437 HIS 0.004 0.001 HIS E 604 PHE 0.022 0.001 PHE A 24 TYR 0.014 0.001 TYR D 644 ARG 0.003 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 338 time to evaluate : 3.025 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: A 43 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: A 86 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 210 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7498 (tpt-90) REVERT: A 329 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6247 (pm20) REVERT: A 350 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: A 657 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: B 31 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7610 (m) REVERT: C 243 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7455 (tmm-80) REVERT: C 387 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7682 (tp) REVERT: C 540 MET cc_start: 0.6752 (mpt) cc_final: 0.6340 (mpm) REVERT: C 610 MET cc_start: 0.5758 (OUTLIER) cc_final: 0.4711 (ttm) REVERT: C 666 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6629 (mm-30) REVERT: C 710 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5725 (m-30) REVERT: D 520 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7031 (tp30) REVERT: E 321 MET cc_start: 0.8091 (mtp) cc_final: 0.7441 (mtp) REVERT: E 383 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: F 92 MET cc_start: 0.2779 (mmp) cc_final: 0.0526 (pmm) outliers start: 98 outliers final: 61 residues processed: 413 average time/residue: 2.1640 time to fit residues: 1075.5963 Evaluate side-chains 404 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 329 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 618 GLU Chi-restraints excluded: chain F residue 233 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 309 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 242 ASN A 271 ASN B 581 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26168 Z= 0.352 Angle : 0.564 7.838 35279 Z= 0.296 Chirality : 0.041 0.149 3861 Planarity : 0.004 0.044 4532 Dihedral : 5.186 58.114 3511 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.72 % Rotamer: Outliers : 3.55 % Allowed : 24.80 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3202 helix: 1.04 (0.14), residues: 1406 sheet: -1.19 (0.26), residues: 367 loop : -1.03 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 437 HIS 0.004 0.001 HIS C 235 PHE 0.023 0.002 PHE A 24 TYR 0.015 0.002 TYR A 313 ARG 0.004 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 432 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 332 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: A 86 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8258 (p) REVERT: A 210 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7515 (tpt-90) REVERT: A 296 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: A 329 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6260 (pm20) REVERT: A 350 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: A 657 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: B 31 SER cc_start: 0.8079 (OUTLIER) cc_final: 0.7644 (m) REVERT: C 243 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7457 (tmm-80) REVERT: C 387 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7765 (tp) REVERT: C 610 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.4866 (ttm) REVERT: C 666 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: C 710 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5703 (m-30) REVERT: D 520 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7151 (tp30) REVERT: D 671 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6321 (mtm180) REVERT: E 321 MET cc_start: 0.8151 (mtp) cc_final: 0.7563 (mtp) REVERT: E 383 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: E 494 MET cc_start: 0.7207 (ttm) cc_final: 0.6898 (ttp) REVERT: F 92 MET cc_start: 0.2810 (mmp) cc_final: 0.0512 (pmm) outliers start: 100 outliers final: 63 residues processed: 409 average time/residue: 2.0461 time to fit residues: 998.5730 Evaluate side-chains 401 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 322 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 671 ARG Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 618 GLU Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 233 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN A 271 ASN B 581 ASN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26168 Z= 0.223 Angle : 0.529 8.074 35279 Z= 0.276 Chirality : 0.039 0.146 3861 Planarity : 0.004 0.045 4532 Dihedral : 5.046 55.038 3508 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.56 % Favored : 95.38 % Rotamer: Outliers : 3.23 % Allowed : 25.20 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3202 helix: 1.21 (0.14), residues: 1407 sheet: -1.13 (0.26), residues: 359 loop : -0.94 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 437 HIS 0.004 0.001 HIS D 643 PHE 0.015 0.001 PHE B 550 TYR 0.016 0.001 TYR D 644 ARG 0.004 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 429 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 338 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: A 86 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8324 (p) REVERT: A 210 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7496 (tpt-90) REVERT: A 329 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6249 (pm20) REVERT: A 350 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: A 657 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: B 31 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7666 (m) REVERT: B 410 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7338 (mpt) REVERT: C 243 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7444 (tmm-80) REVERT: C 610 MET cc_start: 0.5812 (OUTLIER) cc_final: 0.4735 (ttm) REVERT: C 666 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6745 (mm-30) REVERT: C 710 ASP cc_start: 0.6144 (OUTLIER) cc_final: 0.5782 (m-30) REVERT: D 520 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7044 (tp30) REVERT: E 163 LEU cc_start: 0.7920 (mt) cc_final: 0.7596 (mp) REVERT: E 321 MET cc_start: 0.8074 (mtp) cc_final: 0.7433 (mtp) REVERT: E 383 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: E 494 MET cc_start: 0.7115 (ttm) cc_final: 0.6884 (ttm) REVERT: F 92 MET cc_start: 0.2826 (mmp) cc_final: 0.0404 (pmm) outliers start: 91 outliers final: 58 residues processed: 409 average time/residue: 2.1068 time to fit residues: 1037.9483 Evaluate side-chains 403 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 331 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 618 GLU Chi-restraints excluded: chain F residue 124 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.5980 chunk 296 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 chunk 287 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 178 GLN A 271 ASN B 581 ASN F 247 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26168 Z= 0.224 Angle : 0.529 7.857 35279 Z= 0.275 Chirality : 0.039 0.148 3861 Planarity : 0.004 0.045 4532 Dihedral : 4.892 54.093 3504 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 2.91 % Allowed : 25.98 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3202 helix: 1.30 (0.14), residues: 1408 sheet: -1.15 (0.26), residues: 370 loop : -0.90 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 359 HIS 0.004 0.001 HIS D 643 PHE 0.021 0.001 PHE C 440 TYR 0.014 0.001 TYR D 644 ARG 0.004 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 414 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 332 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: A 86 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8320 (p) REVERT: A 210 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7482 (tpt-90) REVERT: A 350 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: A 657 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: B 31 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7667 (m) REVERT: C 243 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7447 (tmm-80) REVERT: C 545 GLU cc_start: 0.7255 (pt0) cc_final: 0.6822 (pm20) REVERT: C 610 MET cc_start: 0.5767 (OUTLIER) cc_final: 0.4730 (ttm) REVERT: C 666 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6753 (mm-30) REVERT: C 710 ASP cc_start: 0.6122 (OUTLIER) cc_final: 0.5753 (m-30) REVERT: D 520 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7025 (tp30) REVERT: E 24 TYR cc_start: 0.4618 (m-80) cc_final: 0.4417 (m-80) REVERT: E 130 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5887 (t70) REVERT: E 163 LEU cc_start: 0.7895 (mt) cc_final: 0.7607 (mp) REVERT: E 321 MET cc_start: 0.8065 (mtp) cc_final: 0.7437 (mtp) REVERT: E 383 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: E 494 MET cc_start: 0.7131 (ttm) cc_final: 0.6905 (ttm) REVERT: E 599 ASN cc_start: 0.5826 (OUTLIER) cc_final: 0.5604 (m110) outliers start: 82 outliers final: 53 residues processed: 394 average time/residue: 2.2491 time to fit residues: 1081.0492 Evaluate side-chains 395 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 328 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 475 LYS Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 599 ASN Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 618 GLU Chi-restraints excluded: chain F residue 124 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.0030 chunk 304 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 211 optimal weight: 0.9990 chunk 319 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 196 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 overall best weight: 0.7472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 178 GLN A 271 ASN B 581 ASN ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26168 Z= 0.188 Angle : 0.521 8.131 35279 Z= 0.269 Chirality : 0.038 0.150 3861 Planarity : 0.004 0.045 4532 Dihedral : 4.771 52.077 3502 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 2.31 % Allowed : 26.54 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3202 helix: 1.42 (0.14), residues: 1410 sheet: -1.07 (0.26), residues: 361 loop : -0.86 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 359 HIS 0.003 0.001 HIS D 643 PHE 0.022 0.001 PHE A 24 TYR 0.014 0.001 TYR B 466 ARG 0.005 0.000 ARG E 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 399 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 334 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 61 TYR cc_start: 0.4082 (OUTLIER) cc_final: 0.3253 (p90) REVERT: A 86 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8322 (p) REVERT: A 210 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7470 (tpt-90) REVERT: A 350 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: A 657 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: B 31 SER cc_start: 0.8055 (OUTLIER) cc_final: 0.7649 (m) REVERT: B 526 MET cc_start: 0.9069 (mmp) cc_final: 0.8438 (mmp) REVERT: C 243 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7459 (tmm-80) REVERT: C 610 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.4786 (ttm) REVERT: C 710 ASP cc_start: 0.6051 (OUTLIER) cc_final: 0.5680 (m-30) REVERT: D 495 MET cc_start: 0.8175 (mmm) cc_final: 0.7721 (mmt) REVERT: D 520 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7031 (tp30) REVERT: E 24 TYR cc_start: 0.4600 (m-80) cc_final: 0.4374 (m-80) REVERT: E 130 ASP cc_start: 0.6044 (OUTLIER) cc_final: 0.5838 (t70) REVERT: E 163 LEU cc_start: 0.7890 (mt) cc_final: 0.7633 (mp) REVERT: E 321 MET cc_start: 0.8016 (mtp) cc_final: 0.7408 (mtp) REVERT: E 383 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: E 492 THR cc_start: 0.8691 (t) cc_final: 0.8480 (m) REVERT: E 494 MET cc_start: 0.7094 (ttm) cc_final: 0.6868 (ttm) outliers start: 65 outliers final: 46 residues processed: 386 average time/residue: 2.1366 time to fit residues: 987.9009 Evaluate side-chains 383 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 324 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 618 GLU Chi-restraints excluded: chain F residue 124 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 0.9990 chunk 271 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 0.0030 chunk 255 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 271 ASN B 32 HIS B 137 GLN B 581 ASN ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.203170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151526 restraints weight = 85523.665| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.91 r_work: 0.3602 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 26168 Z= 0.234 Angle : 0.787 61.555 35279 Z= 0.418 Chirality : 0.038 0.295 3861 Planarity : 0.004 0.045 4532 Dihedral : 4.770 52.074 3502 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 2.31 % Allowed : 26.51 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3202 helix: 1.42 (0.14), residues: 1410 sheet: -1.06 (0.26), residues: 361 loop : -0.86 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 359 HIS 0.006 0.001 HIS C 366 PHE 0.021 0.001 PHE A 24 TYR 0.013 0.001 TYR B 466 ARG 0.003 0.000 ARG E 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16054.27 seconds wall clock time: 272 minutes 30.61 seconds (16350.61 seconds total)