Starting phenix.real_space_refine on Sat Sep 28 23:41:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnc_19394/09_2024/8rnc_19394.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnc_19394/09_2024/8rnc_19394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnc_19394/09_2024/8rnc_19394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnc_19394/09_2024/8rnc_19394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnc_19394/09_2024/8rnc_19394.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnc_19394/09_2024/8rnc_19394.cif" } resolution = 3.52 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 269 5.16 5 C 22579 2.51 5 N 6110 2.21 5 O 6680 1.98 5 H 35901 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 71539 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 11470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11470 Classifications: {'peptide': 716} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 689} Chain: "B" Number of atoms: 11272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11272 Classifications: {'peptide': 718} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 684} Chain breaks: 4 Chain: "C" Number of atoms: 12335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 12335 Classifications: {'peptide': 760} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 731} Chain breaks: 1 Chain: "Y" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 379 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "X" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 446 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "D" Number of atoms: 11270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 11270 Classifications: {'peptide': 703} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 676} Chain breaks: 1 Chain: "E" Number of atoms: 11310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11310 Classifications: {'peptide': 720} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 685} Chain breaks: 2 Chain: "F" Number of atoms: 10555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 10555 Classifications: {'peptide': 653} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 631} Chain breaks: 2 Chain: "G" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2502 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Time building chain proxies: 24.63, per 1000 atoms: 0.34 Number of scatterers: 71539 At special positions: 0 Unit cell: (131.88, 159.6, 212.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 269 16.00 O 6680 8.00 N 6110 7.00 C 22579 6.00 H 35901 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: 13.66 Conformation dependent library (CDL) restraints added in 4.2 seconds 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8340 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 51 sheets defined 49.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 163 through 184 Processing helix chain 'A' and resid 185 through 190 removed outlier: 4.194A pdb=" N VAL A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.627A pdb=" N ARG A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.852A pdb=" N TRP A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.617A pdb=" N ALA A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 429 through 447 removed outlier: 3.807A pdb=" N GLU A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.697A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 4.279A pdb=" N SER A 530 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY A 531 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 572 removed outlier: 4.000A pdb=" N MET A 571 " --> pdb=" O MET A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 595 removed outlier: 4.144A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 removed outlier: 3.537A pdb=" N PHE A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 3.572A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.355A 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 714 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.917A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.986A pdb=" N THR B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 22' Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.734A pdb=" N SER B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) 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 124 Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.917A pdb=" N LEU B 152 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.813A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 266 removed outlier: 3.597A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 removed outlier: 3.542A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.589A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.598A pdb=" N VAL B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 376 removed outlier: 4.794A pdb=" N PHE B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) 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 471 Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.835A pdb=" N GLY B 537 " --> pdb=" O MET B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 558 Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.951A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 removed outlier: 3.702A pdb=" N GLY B 593 " --> pdb=" O VAL B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.694A pdb=" N LEU B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 632 through 639 removed outlier: 3.950A pdb=" N GLU B 637 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY B 638 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 699 Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 735 through 750 Processing helix chain 'C' and resid 2 through 15 removed outlier: 4.065A pdb=" N ASP C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 44 through 55 removed outlier: 3.590A pdb=" N CYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.655A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 116 removed outlier: 4.225A pdb=" N ARG C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 201 through 214 removed outlier: 3.585A pdb=" N LEU C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.029A pdb=" N MET C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 257 through 275 removed outlier: 3.767A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 289 removed outlier: 3.970A pdb=" N LEU C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 317 Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.548A pdb=" N GLN C 408 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 446 through 452 removed outlier: 4.282A pdb=" N GLN C 450 " --> pdb=" O ASP C 446 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY C 452 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 557 Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.570A pdb=" N LEU C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 566 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 573 Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'C' and resid 578 through 583 Processing helix chain 'C' and resid 586 through 608 removed outlier: 4.718A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 608 " --> pdb=" O MET C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 623 removed outlier: 3.721A pdb=" N PHE C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 623' Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 705 through 709 removed outlier: 3.622A pdb=" N LEU C 708 " --> pdb=" O ASP C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 720 removed outlier: 3.698A pdb=" N LYS C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 766 Processing helix chain 'Y' and resid 369 through 373 Processing helix chain 'X' and resid 360 through 366 removed outlier: 3.951A pdb=" N TRP X 364 " --> pdb=" O ASN X 360 " (cutoff:3.500A) Processing helix chain 'X' and resid 376 through 383 Processing helix chain 'D' and resid 2 through 9 removed outlier: 3.548A pdb=" N PHE D 9 " --> pdb=" O ILE D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 84 through 100 Processing helix chain 'D' and resid 127 through 140 removed outlier: 4.295A pdb=" N TYR D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 182 removed outlier: 3.691A pdb=" N SER D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 198 removed outlier: 3.734A pdb=" N VAL D 196 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 237 through 246 removed outlier: 3.677A pdb=" N ARG D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 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 318 Processing helix chain 'D' and resid 332 through 349 Processing helix chain 'D' and resid 358 through 366 removed outlier: 4.268A pdb=" N ALA D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.501A pdb=" N ALA D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 411 removed outlier: 4.462A pdb=" N GLN D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 447 Processing helix chain 'D' and resid 449 through 469 removed outlier: 3.547A pdb=" N THR D 453 " --> pdb=" O CYS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 533 removed outlier: 3.967A pdb=" N SER D 530 " --> pdb=" O ARG D 527 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY D 531 " --> pdb=" O VAL D 528 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP D 533 " --> pdb=" O SER D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 573 Processing helix chain 'D' and resid 575 through 595 removed outlier: 3.606A pdb=" N GLN D 595 " --> pdb=" O GLU D 591 " (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: 3.959A pdb=" N ARG D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 688 Processing helix chain 'D' and resid 693 through 715 removed outlier: 3.950A pdb=" N LYS D 715 " --> pdb=" O LYS D 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.992A pdb=" N ASP E 11 " --> pdb=" O PHE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 18 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 removed outlier: 3.791A pdb=" N ALA E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'E' and resid 138 through 153 Processing helix chain 'E' and resid 156 through 161 removed outlier: 3.933A pdb=" N LYS E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY E 161 " --> pdb=" O GLY E 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 156 through 161' Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.563A 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 248 through 265 removed outlier: 4.112A pdb=" N ASN E 265 " --> pdb=" O ASN E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 292 removed outlier: 4.056A pdb=" N LYS E 279 " --> pdb=" O GLY E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 Processing helix chain 'E' and resid 330 through 346 removed outlier: 4.359A pdb=" N ALA E 340 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Proline residue: E 341 - end of helix Processing helix chain 'E' and resid 371 through 373 No H-bonds generated for 'chain 'E' and resid 371 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 413 through 426 Processing helix chain 'E' and resid 454 through 472 Processing helix chain 'E' and resid 477 through 480 removed outlier: 3.603A pdb=" N LYS E 480 " --> pdb=" O SER E 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 477 through 480' Processing helix chain 'E' and resid 517 through 536 Processing helix chain 'E' and resid 539 through 559 Processing helix chain 'E' and resid 569 through 582 removed outlier: 4.634A pdb=" N ILE E 574 " --> pdb=" O LYS E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 593 Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.521A pdb=" N LEU E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 612 Processing helix chain 'E' and resid 613 through 615 No H-bonds generated for 'chain 'E' and resid 613 through 615' Processing helix chain 'E' and resid 616 through 624 Processing helix chain 'E' and resid 675 through 684 Processing helix chain 'E' and resid 687 through 702 removed outlier: 3.617A pdb=" N ALA E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS E 698 " --> pdb=" O LEU E 694 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA E 702 " --> pdb=" O CYS E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 732 Processing helix chain 'E' and resid 735 through 750 removed outlier: 3.623A pdb=" N GLY E 750 " --> pdb=" O LEU E 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 15 removed outlier: 3.854A pdb=" N ASP F 15 " --> pdb=" O GLN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 25 removed outlier: 3.515A pdb=" N LYS F 19 " --> pdb=" O ASP F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 39 removed outlier: 3.561A pdb=" N ASN F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 32 " --> pdb=" O ASP F 28 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE F 33 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG F 34 " --> pdb=" O TYR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 55 removed outlier: 3.501A pdb=" N LYS F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER F 55 " --> pdb=" O TRP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 70 removed outlier: 3.694A pdb=" N ILE F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 105 removed outlier: 4.020A pdb=" N VAL F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 117 removed outlier: 3.563A pdb=" N VAL F 116 " --> pdb=" O GLY F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 removed outlier: 3.614A pdb=" N PHE F 121 " --> pdb=" O TYR F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 removed outlier: 4.040A pdb=" N GLU F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 228 through 232' Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 255 through 275 removed outlier: 4.101A pdb=" N VAL F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL F 274 " --> pdb=" O ARG F 270 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 288 removed outlier: 4.168A pdb=" N LEU F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 Processing helix chain 'F' and resid 308 through 318 Processing helix chain 'F' and resid 392 through 408 removed outlier: 3.577A pdb=" N MET F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 415 Processing helix chain 'F' and resid 431 through 443 Processing helix chain 'F' and resid 444 through 452 removed outlier: 4.021A pdb=" N GLY F 452 " --> pdb=" O PHE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 541 removed outlier: 4.013A pdb=" N MET F 537 " --> pdb=" O THR F 534 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU F 539 " --> pdb=" O LYS F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 557 Processing helix chain 'F' and resid 557 through 568 removed outlier: 3.517A pdb=" N LEU F 567 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 574 removed outlier: 3.716A pdb=" N PHE F 573 " --> pdb=" O GLU F 570 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN F 574 " --> pdb=" O ASP F 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 570 through 574' Processing helix chain 'F' and resid 575 through 583 removed outlier: 3.975A pdb=" N SER F 583 " --> pdb=" O GLU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 607 removed outlier: 4.423A pdb=" N GLY F 591 " --> pdb=" O GLN F 587 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLN F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 619 Processing helix chain 'F' and resid 620 through 623 removed outlier: 3.762A pdb=" N PHE F 623 " --> pdb=" O PRO F 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 620 through 623' Processing helix chain 'F' and resid 682 through 686 removed outlier: 3.705A pdb=" N ARG F 686 " --> pdb=" O ASP F 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 709 Processing helix chain 'F' and resid 713 through 719 removed outlier: 3.524A pdb=" N LYS F 719 " --> pdb=" O GLU F 715 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 12 Processing helix chain 'G' and resid 81 through 87 removed outlier: 3.814A pdb=" N GLU G 85 " --> pdb=" O GLU G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Proline residue: G 108 - end of helix removed outlier: 3.861A pdb=" N LYS G 111 " --> pdb=" O PRO G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'A' and resid 255 through 256 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.569A pdb=" N THR A 295 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 417 removed outlier: 6.302A pdb=" N LYS A 477 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL A 501 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 479 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU A 499 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.040A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.173A pdb=" N LYS A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 619 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 188 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.512A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 491 removed outlier: 3.943A pdb=" N PHE B 495 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 641 through 642 Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.979A pdb=" N MET C 92 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB7, first strand: chain 'C' and resid 131 through 136 removed outlier: 5.945A pdb=" N TRP C 132 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS C 247 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG C 134 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 148 Processing sheet with id=AB9, first strand: chain 'C' and resid 290 through 291 Processing sheet with id=AC1, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.988A pdb=" N GLU C 364 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 340 through 347 Processing sheet with id=AC3, first strand: chain 'C' and resid 498 through 499 Processing sheet with id=AC4, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC5, first strand: chain 'C' and resid 659 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AC7, first strand: chain 'Y' and resid 355 through 359 Processing sheet with id=AC8, first strand: chain 'D' and resid 77 through 79 removed outlier: 3.741A pdb=" N ARG D 117 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE D 118 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N MET D 146 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU D 120 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE D 148 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY D 122 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 255 through 256 removed outlier: 3.851A pdb=" N ASP E 445 " --> pdb=" O SER E 442 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 294 through 295 removed outlier: 4.444A pdb=" N SER D 492 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE D 481 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU D 499 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE D 479 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL D 501 " --> pdb=" O LYS D 477 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS D 477 " --> pdb=" O VAL D 501 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 294 through 295 removed outlier: 4.444A pdb=" N SER D 492 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N TYR D 497 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR D 562 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS D 551 " --> pdb=" O SER D 543 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 543 " --> pdb=" O LYS D 551 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL D 553 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 373 through 374 removed outlier: 5.786A pdb=" N GLN D 373 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLN E 367 " --> pdb=" O GLN D 373 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 623 through 628 removed outlier: 3.734A pdb=" N GLY D 618 " --> pdb=" O VAL D 625 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY D 627 " --> pdb=" O SER D 616 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER D 616 " --> pdb=" O GLY D 627 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AD6, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AD7, first strand: chain 'E' and resid 178 through 188 Processing sheet with id=AD8, first strand: chain 'E' and resid 243 through 244 removed outlier: 4.004A pdb=" N THR E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 488 through 490 Processing sheet with id=AE1, first strand: chain 'F' and resid 59 through 60 Processing sheet with id=AE2, first strand: chain 'F' and resid 73 through 74 Processing sheet with id=AE3, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AE4, first strand: chain 'F' and resid 135 through 137 Processing sheet with id=AE5, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.704A pdb=" N GLU F 294 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'F' and resid 334 through 337 removed outlier: 6.915A pdb=" N GLU F 364 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS F 372 " --> pdb=" O CYS F 369 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 334 through 337 removed outlier: 6.915A pdb=" N GLU F 364 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS F 385 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 340 through 347 removed outlier: 3.969A pdb=" N ILE F 346 " --> pdb=" O GLN F 354 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN F 354 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 453 through 455 Processing sheet with id=AF2, first strand: chain 'F' and resid 498 through 499 removed outlier: 3.616A pdb=" N SER F 498 " --> pdb=" O ILE F 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET F 514 " --> pdb=" O LEU F 505 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 639 through 641 Processing sheet with id=AF4, first strand: chain 'F' and resid 660 through 662 Processing sheet with id=AF5, first strand: chain 'F' and resid 698 through 702 removed outlier: 7.314A pdb=" N LYS F 737 " --> pdb=" O SER F 701 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 24 through 25 removed outlier: 6.948A pdb=" N LEU G 24 " --> pdb=" O ILE G 50 " (cutoff:3.500A) 1703 hydrogen bonds defined for protein. 4752 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: 28.90 Time building geometry restraints manager: 17.08 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: 35816 1.03 - 1.23: 93 1.23 - 1.42: 14770 1.42 - 1.62: 21065 1.62 - 1.81: 454 Bond restraints: 72198 Sorted by residual: bond pdb=" N ILE B 752 " pdb=" H ILE B 752 " ideal model delta sigma weight residual 0.860 1.114 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" N ILE E 749 " pdb=" CA ILE E 749 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ILE B 749 " pdb=" CA ILE B 749 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.07e+00 bond pdb=" N TYR B 751 " pdb=" H TYR B 751 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" N ILE B 749 " pdb=" H ILE B 749 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.57e+00 ... (remaining 72193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.04: 130729 6.04 - 12.08: 6 12.08 - 18.12: 2 18.12 - 24.16: 1 24.16 - 30.20: 1 Bond angle restraints: 130739 Sorted by residual: angle pdb=" C TYR B 751 " pdb=" N ILE B 752 " pdb=" H ILE B 752 " ideal model delta sigma weight residual 124.30 94.10 30.20 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C TYR B 751 " pdb=" CA TYR B 751 " pdb=" CB TYR B 751 " ideal model delta sigma weight residual 109.29 120.41 -11.12 1.51e+00 4.39e-01 5.42e+01 angle pdb=" C TYR B 751 " pdb=" CA TYR B 751 " pdb=" HA TYR B 751 " ideal model delta sigma weight residual 109.00 88.50 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" N ILE B 752 " pdb=" CA ILE B 752 " pdb=" CB ILE B 752 " ideal model delta sigma weight residual 111.50 100.04 11.46 1.70e+00 3.46e-01 4.54e+01 angle pdb=" CB MET E 409 " pdb=" CG MET E 409 " pdb=" SD MET E 409 " ideal model delta sigma weight residual 112.70 127.76 -15.06 3.00e+00 1.11e-01 2.52e+01 ... (remaining 130734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 29603 17.70 - 35.39: 2909 35.39 - 53.09: 914 53.09 - 70.78: 231 70.78 - 88.48: 44 Dihedral angle restraints: 33701 sinusoidal: 18732 harmonic: 14969 Sorted by residual: dihedral pdb=" C TYR B 751 " pdb=" N TYR B 751 " pdb=" CA TYR B 751 " pdb=" CB TYR B 751 " ideal model delta harmonic sigma weight residual -122.60 -142.59 19.99 0 2.50e+00 1.60e-01 6.39e+01 dihedral pdb=" N TYR B 751 " pdb=" C TYR B 751 " pdb=" CA TYR B 751 " pdb=" CB TYR B 751 " ideal model delta harmonic sigma weight residual 122.80 138.69 -15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" CA LYS A 327 " pdb=" C LYS A 327 " pdb=" N SER A 328 " pdb=" CA SER A 328 " ideal model delta harmonic sigma weight residual -180.00 -157.17 -22.83 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 33698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 5364 0.147 - 0.294: 2 0.294 - 0.442: 0 0.442 - 0.589: 0 0.589 - 0.736: 1 Chirality restraints: 5367 Sorted by residual: chirality pdb=" CA TYR B 751 " pdb=" N TYR B 751 " pdb=" C TYR B 751 " pdb=" CB TYR B 751 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CB VAL A 443 " pdb=" CA VAL A 443 " pdb=" CG1 VAL A 443 " pdb=" CG2 VAL A 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE B 749 " pdb=" N ILE B 749 " pdb=" C ILE B 749 " pdb=" CB ILE B 749 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 5364 not shown) Planarity restraints: 10566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 751 " -0.131 2.00e-02 2.50e+03 2.09e-01 4.35e+02 pdb=" N ILE B 752 " 0.361 2.00e-02 2.50e+03 pdb=" CA ILE B 752 " -0.121 2.00e-02 2.50e+03 pdb=" H ILE B 752 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 749 " 0.028 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" N GLY E 750 " -0.094 2.00e-02 2.50e+03 pdb=" CA GLY E 750 " 0.024 2.00e-02 2.50e+03 pdb=" H GLY E 750 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 429 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 430 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " 0.023 5.00e-02 4.00e+02 ... (remaining 10563 not shown) Histogram of nonbonded interaction distances: 0.67 - 1.46: 4 1.46 - 2.24: 9443 2.24 - 3.03: 212556 3.03 - 3.81: 296540 3.81 - 4.60: 493512 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1012055 Sorted by model distance: nonbonded pdb=" HB2 ALA C 471 " pdb=" HA LYS E 197 " model vdw 0.675 2.440 nonbonded pdb=" HB3 LEU E 746 " pdb="HD13 ILE E 752 " model vdw 1.365 2.440 nonbonded pdb=" HD3 ARG C 134 " pdb=" O THR D 371 " model vdw 1.385 2.620 nonbonded pdb=" HG3 GLU E 715 " pdb=" CE1 TYR E 751 " model vdw 1.443 2.970 nonbonded pdb=" O ASN G 127 " pdb="HD21 ASN G 127 " model vdw 1.475 2.450 ... (remaining 1012050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 61 or resid 75 through 716)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 1 through 227 or (resid 239 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 240 through 633 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 H \ B3)) or resid 656 through 687 or (resid 688 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or \ name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 or n \ ame HD2 or name HE1 or name HE2)) or resid 689 through 751 or (resid 752 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ D1 or name H or name HA or name HB or name HG12 or name HG13 or name HG21 or nam \ e HG22 or name HG23 or name HD11 or name HD12 or name HD13)))) selection = (chain 'E' and (resid 1 through 31 or (resid 34 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 \ or name HG21 or name HG22 or name HG23)) or resid 35 through 189 or (resid 201 a \ nd (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG \ 22 or name HG23 or name HD11 or name HD12 or name HD13)) or resid 202 through 67 \ 0 or (resid 684 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name H \ G2 or name HG3)) or resid 685 through 752)) } ncs_group { reference = (chain 'C' and (resid 1 through 140 or (resid 227 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG \ )) or resid 228 through 488 or (resid 493 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3)) or resid 494 through 743)) selection = (chain 'F' and (resid 1 through 249 or (resid 256 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG \ )) or resid 257 through 743)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.500 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: 0.910 Extract box with map and model: 2.060 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 120.690 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.230 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.002 0.043 36297 Z= 0.162 Angle : 0.508 15.064 48868 Z= 0.272 Chirality : 0.039 0.736 5367 Planarity : 0.003 0.045 6282 Dihedral : 16.405 88.478 13886 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.33 % Allowed : 19.49 % Favored : 80.18 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.15 % 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: 0.38 (0.13), residues: 4439 helix: 1.73 (0.12), residues: 1940 sheet: -1.01 (0.23), residues: 511 loop : -0.88 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 437 HIS 0.003 0.001 HIS B 604 PHE 0.017 0.001 PHE B 504 TYR 0.020 0.001 TYR A 644 ARG 0.008 0.000 ARG D 549 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 1104 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1091 time to evaluate : 4.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 185 ASN cc_start: 0.8510 (m110) cc_final: 0.7938 (t0) REVERT: A 568 LYS cc_start: 0.8282 (tttm) cc_final: 0.7936 (tttt) REVERT: B 364 LEU cc_start: 0.7208 (mt) cc_final: 0.6849 (mt) REVERT: C 456 SER cc_start: 0.5945 (OUTLIER) cc_final: 0.5716 (m) REVERT: C 521 GLU cc_start: 0.6299 (mm-30) cc_final: 0.6084 (pm20) REVERT: C 548 GLN cc_start: 0.8728 (tt0) cc_final: 0.8514 (tp-100) REVERT: C 610 MET cc_start: 0.4155 (tmm) cc_final: 0.3861 (tpp) REVERT: C 640 LEU cc_start: 0.8695 (mt) cc_final: 0.8491 (mt) REVERT: D 51 MET cc_start: 0.3397 (pmm) cc_final: 0.3172 (pmm) REVERT: D 592 SER cc_start: 0.8665 (m) cc_final: 0.8323 (t) REVERT: D 661 LEU cc_start: 0.8766 (tp) cc_final: 0.8525 (mp) REVERT: E 93 ASP cc_start: 0.7557 (t0) cc_final: 0.7015 (t0) REVERT: F 448 PHE cc_start: 0.6820 (m-10) cc_final: 0.6529 (m-10) REVERT: G 152 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.3836 (p0) outliers start: 13 outliers final: 2 residues processed: 1097 average time/residue: 1.1313 time to fit residues: 1913.6848 Evaluate side-chains 690 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 686 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain G residue 152 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 8.9990 chunk 336 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 403 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN D 334 ASN E 314 ASN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 662 ASN G 94 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 36297 Z= 0.370 Angle : 0.630 7.549 48868 Z= 0.340 Chirality : 0.041 0.161 5367 Planarity : 0.005 0.070 6282 Dihedral : 4.386 54.571 4839 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 2.17 % Allowed : 21.84 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.13), residues: 4439 helix: 1.19 (0.12), residues: 1946 sheet: -1.04 (0.24), residues: 494 loop : -1.16 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 553 HIS 0.006 0.001 HIS C 366 PHE 0.030 0.002 PHE B 504 TYR 0.020 0.002 TYR E 554 ARG 0.007 0.001 ARG E 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 763 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 678 time to evaluate : 4.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 185 ASN cc_start: 0.8666 (m110) cc_final: 0.8298 (t0) REVERT: A 383 ASP cc_start: 0.6983 (t70) cc_final: 0.6538 (p0) REVERT: B 502 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7521 (m) REVERT: B 691 CYS cc_start: 0.7974 (m) cc_final: 0.7675 (m) REVERT: C 521 GLU cc_start: 0.6386 (mm-30) cc_final: 0.5827 (pm20) REVERT: C 604 MET cc_start: 0.7878 (tpp) cc_final: 0.7317 (tpp) REVERT: C 637 PHE cc_start: 0.5997 (m-10) cc_final: 0.5573 (m-10) REVERT: D 21 MET cc_start: 0.6253 (tmm) cc_final: 0.5698 (tpp) REVERT: E 415 MET cc_start: 0.8452 (mmp) cc_final: 0.8247 (mmm) REVERT: F 22 LEU cc_start: 0.8747 (mt) cc_final: 0.8411 (mt) REVERT: F 253 LEU cc_start: 0.6892 (mt) cc_final: 0.6401 (tp) REVERT: F 320 LYS cc_start: 0.7417 (mmmm) cc_final: 0.7142 (mmtm) REVERT: F 448 PHE cc_start: 0.7083 (m-10) cc_final: 0.6744 (m-10) REVERT: F 614 GLN cc_start: 0.8186 (mm110) cc_final: 0.6884 (pp30) REVERT: G 101 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7742 (tppt) REVERT: G 152 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.3952 (p0) outliers start: 85 outliers final: 45 residues processed: 742 average time/residue: 1.0436 time to fit residues: 1222.3402 Evaluate side-chains 628 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 581 time to evaluate : 4.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 152 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 335 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 403 optimal weight: 5.9990 chunk 436 optimal weight: 10.0000 chunk 359 optimal weight: 9.9990 chunk 400 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 324 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 104 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN E 55 GLN F 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36297 Z= 0.256 Angle : 0.553 7.595 48868 Z= 0.294 Chirality : 0.039 0.148 5367 Planarity : 0.004 0.058 6282 Dihedral : 4.313 55.424 4836 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 2.22 % Allowed : 22.47 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -0.15 (0.13), residues: 4439 helix: 1.24 (0.12), residues: 1949 sheet: -1.03 (0.24), residues: 484 loop : -1.19 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 553 HIS 0.005 0.001 HIS G 8 PHE 0.019 0.001 PHE B 504 TYR 0.016 0.001 TYR E 554 ARG 0.008 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 704 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 617 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 185 ASN cc_start: 0.8631 (m110) cc_final: 0.8245 (t0) REVERT: A 386 MET cc_start: 0.7137 (mtp) cc_final: 0.6740 (mtp) REVERT: A 579 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: B 691 CYS cc_start: 0.8027 (m) cc_final: 0.7678 (m) REVERT: C 51 TRP cc_start: 0.7699 (m-10) cc_final: 0.7179 (m-10) REVERT: C 521 GLU cc_start: 0.6456 (mm-30) cc_final: 0.5828 (pm20) REVERT: C 548 GLN cc_start: 0.9020 (tt0) cc_final: 0.8521 (tp-100) REVERT: C 624 SER cc_start: 0.7579 (OUTLIER) cc_final: 0.7147 (t) REVERT: D 21 MET cc_start: 0.6285 (tmm) cc_final: 0.5736 (tpp) REVERT: E 227 MET cc_start: 0.6682 (pmm) cc_final: 0.5142 (mmm) REVERT: F 448 PHE cc_start: 0.7172 (m-10) cc_final: 0.6842 (m-10) REVERT: F 614 GLN cc_start: 0.8242 (mm110) cc_final: 0.6781 (pp30) REVERT: G 101 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7762 (tppt) REVERT: G 149 ASP cc_start: 0.3477 (t0) cc_final: 0.3200 (t0) REVERT: G 152 ASP cc_start: 0.6559 (OUTLIER) cc_final: 0.3820 (p0) outliers start: 87 outliers final: 57 residues processed: 681 average time/residue: 1.0487 time to fit residues: 1150.4781 Evaluate side-chains 630 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 570 time to evaluate : 4.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 344 PHE Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain F residue 713 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 152 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 209 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 405 optimal weight: 0.9980 chunk 429 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 384 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36297 Z= 0.271 Angle : 0.557 8.367 48868 Z= 0.295 Chirality : 0.039 0.149 5367 Planarity : 0.004 0.051 6282 Dihedral : 4.360 57.154 4836 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 2.45 % Allowed : 22.73 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -0.25 (0.13), residues: 4439 helix: 1.20 (0.12), residues: 1941 sheet: -1.13 (0.24), residues: 471 loop : -1.28 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 553 HIS 0.005 0.001 HIS G 8 PHE 0.019 0.001 PHE C 596 TYR 0.019 0.001 TYR D 361 ARG 0.008 0.000 ARG G 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 693 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 597 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 185 ASN cc_start: 0.8567 (m110) cc_final: 0.8275 (t0) REVERT: A 386 MET cc_start: 0.7239 (mtp) cc_final: 0.6823 (mtp) REVERT: A 579 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: A 642 MET cc_start: 0.8694 (mmp) cc_final: 0.8482 (mmm) REVERT: B 256 GLU cc_start: 0.8196 (tp30) cc_final: 0.7979 (mm-30) REVERT: B 538 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7557 (ttm) REVERT: B 630 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: B 691 CYS cc_start: 0.8084 (m) cc_final: 0.7712 (m) REVERT: C 51 TRP cc_start: 0.7643 (m-10) cc_final: 0.6939 (m-10) REVERT: C 397 ARG cc_start: 0.8657 (tmm-80) cc_final: 0.8337 (tmm-80) REVERT: C 521 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6146 (pm20) REVERT: C 548 GLN cc_start: 0.8976 (tt0) cc_final: 0.8378 (tp-100) REVERT: C 649 PHE cc_start: 0.9083 (p90) cc_final: 0.8797 (p90) REVERT: D 21 MET cc_start: 0.6256 (tmm) cc_final: 0.5710 (tpp) REVERT: D 98 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6007 (mt-10) REVERT: D 143 MET cc_start: 0.3675 (mpp) cc_final: 0.3396 (mpp) REVERT: D 415 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8462 (t) REVERT: F 1 MET cc_start: 0.7353 (mmm) cc_final: 0.6988 (mmm) REVERT: F 404 MET cc_start: 0.7084 (mmt) cc_final: 0.6879 (mmt) REVERT: F 448 PHE cc_start: 0.7276 (m-10) cc_final: 0.6942 (m-10) REVERT: F 532 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.4307 (m-80) REVERT: F 610 MET cc_start: 0.8342 (tpt) cc_final: 0.7711 (tpt) REVERT: F 614 GLN cc_start: 0.8258 (mm110) cc_final: 0.6814 (pp30) REVERT: F 631 ASN cc_start: 0.8345 (m-40) cc_final: 0.7560 (m110) REVERT: F 633 GLU cc_start: 0.7546 (mp0) cc_final: 0.6764 (mm-30) REVERT: G 21 GLU cc_start: 0.8609 (pt0) cc_final: 0.8012 (tm-30) REVERT: G 101 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7788 (tppt) REVERT: G 149 ASP cc_start: 0.3415 (t0) cc_final: 0.3129 (t0) REVERT: G 152 ASP cc_start: 0.6470 (OUTLIER) cc_final: 0.3696 (p0) outliers start: 96 outliers final: 65 residues processed: 668 average time/residue: 1.0217 time to fit residues: 1107.8893 Evaluate side-chains 639 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 567 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 658 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 344 PHE Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 532 TYR Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain F residue 713 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 152 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 319 optimal weight: 0.4980 chunk 177 optimal weight: 8.9990 chunk 366 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 385 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 ASN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36297 Z= 0.292 Angle : 0.556 7.414 48868 Z= 0.297 Chirality : 0.039 0.160 5367 Planarity : 0.004 0.049 6282 Dihedral : 4.443 59.055 4836 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 2.60 % Allowed : 22.93 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -0.38 (0.12), residues: 4439 helix: 1.08 (0.12), residues: 1946 sheet: -1.21 (0.23), residues: 488 loop : -1.34 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 553 HIS 0.005 0.001 HIS G 8 PHE 0.020 0.001 PHE D 132 TYR 0.022 0.001 TYR F 635 ARG 0.005 0.000 ARG G 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 683 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 581 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 TYR cc_start: 0.5859 (t80) cc_final: 0.4338 (t80) REVERT: A 185 ASN cc_start: 0.8622 (m110) cc_final: 0.8285 (t0) REVERT: A 386 MET cc_start: 0.7373 (mtp) cc_final: 0.7034 (mtp) REVERT: A 579 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: B 256 GLU cc_start: 0.8216 (tp30) cc_final: 0.7854 (mm-30) REVERT: B 364 LEU cc_start: 0.7134 (mt) cc_final: 0.6828 (mt) REVERT: B 538 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7640 (ttm) REVERT: B 630 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: B 691 CYS cc_start: 0.8092 (m) cc_final: 0.7713 (m) REVERT: C 397 ARG cc_start: 0.8626 (tmm-80) cc_final: 0.8340 (tmm-80) REVERT: C 521 GLU cc_start: 0.6244 (mm-30) cc_final: 0.6020 (pm20) REVERT: C 649 PHE cc_start: 0.8991 (p90) cc_final: 0.8772 (p90) REVERT: D 21 MET cc_start: 0.6255 (tmm) cc_final: 0.5741 (tpp) REVERT: D 98 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6106 (mt-10) REVERT: D 143 MET cc_start: 0.3744 (mpp) cc_final: 0.3430 (mpp) REVERT: D 415 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8473 (t) REVERT: F 22 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8496 (mt) REVERT: F 448 PHE cc_start: 0.7332 (m-10) cc_final: 0.6814 (m-10) REVERT: G 21 GLU cc_start: 0.8571 (pt0) cc_final: 0.8006 (tm-30) REVERT: G 101 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7848 (tppt) REVERT: G 149 ASP cc_start: 0.3552 (t0) cc_final: 0.3351 (t0) outliers start: 102 outliers final: 77 residues processed: 654 average time/residue: 0.9615 time to fit residues: 1002.6722 Evaluate side-chains 638 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 555 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 658 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 344 PHE Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 532 ASN Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 323 GLN Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 6.9990 chunk 386 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 429 optimal weight: 8.9990 chunk 356 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 76 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN E 109 ASN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 36297 Z= 0.520 Angle : 0.680 7.452 48868 Z= 0.374 Chirality : 0.043 0.234 5367 Planarity : 0.005 0.055 6282 Dihedral : 4.915 59.595 4834 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 3.49 % Allowed : 22.73 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4439 helix: 0.35 (0.11), residues: 1946 sheet: -1.45 (0.24), residues: 459 loop : -1.72 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 569 HIS 0.008 0.002 HIS E 47 PHE 0.022 0.002 PHE D 132 TYR 0.025 0.002 TYR E 554 ARG 0.007 0.001 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 682 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 545 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 TYR cc_start: 0.5831 (t80) cc_final: 0.4298 (t80) REVERT: A 185 ASN cc_start: 0.8721 (m110) cc_final: 0.8390 (t0) REVERT: A 386 MET cc_start: 0.7555 (mtp) cc_final: 0.7240 (mtp) REVERT: A 571 MET cc_start: 0.7114 (tmm) cc_final: 0.6767 (tmm) REVERT: A 579 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: B 256 GLU cc_start: 0.8247 (tp30) cc_final: 0.8018 (mm-30) REVERT: B 364 LEU cc_start: 0.7291 (mt) cc_final: 0.7000 (mt) REVERT: B 538 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7953 (ttm) REVERT: B 630 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.6191 (m-80) REVERT: B 691 CYS cc_start: 0.8129 (m) cc_final: 0.7810 (m) REVERT: C 397 ARG cc_start: 0.8633 (tmm-80) cc_final: 0.8249 (tmm-80) REVERT: C 453 TYR cc_start: 0.7849 (m-80) cc_final: 0.7303 (m-80) REVERT: C 521 GLU cc_start: 0.6331 (mm-30) cc_final: 0.6040 (pm20) REVERT: D 21 MET cc_start: 0.6256 (tmm) cc_final: 0.5765 (tpp) REVERT: D 98 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6172 (mt-10) REVERT: D 143 MET cc_start: 0.3870 (mpp) cc_final: 0.3533 (mpp) REVERT: D 589 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: F 22 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8550 (mt) REVERT: F 448 PHE cc_start: 0.7333 (m-10) cc_final: 0.6953 (m-10) REVERT: G 21 GLU cc_start: 0.8587 (pt0) cc_final: 0.8001 (tm-30) REVERT: G 101 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7950 (tppt) outliers start: 137 outliers final: 100 residues processed: 642 average time/residue: 0.9651 time to fit residues: 996.0731 Evaluate side-chains 632 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 526 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 616 SER Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 658 SER Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 344 PHE Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 532 ASN Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 596 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 314 ARG Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 361 optimal weight: 10.0000 chunk 239 optimal weight: 0.7980 chunk 427 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 260 optimal weight: 0.5980 chunk 197 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 650 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 451 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36297 Z= 0.196 Angle : 0.550 7.882 48868 Z= 0.289 Chirality : 0.039 0.151 5367 Planarity : 0.004 0.047 6282 Dihedral : 4.527 58.242 4834 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.00 % Rotamer: Outliers : 2.22 % Allowed : 24.26 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.12), residues: 4439 helix: 0.96 (0.12), residues: 1935 sheet: -1.33 (0.24), residues: 463 loop : -1.50 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 437 HIS 0.006 0.001 HIS G 8 PHE 0.021 0.001 PHE D 132 TYR 0.019 0.001 TYR A 644 ARG 0.005 0.000 ARG F 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 648 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 561 time to evaluate : 4.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 TYR cc_start: 0.5691 (t80) cc_final: 0.4039 (t80) REVERT: A 185 ASN cc_start: 0.8621 (m110) cc_final: 0.8217 (t0) REVERT: A 386 MET cc_start: 0.7400 (mtp) cc_final: 0.7146 (mtp) REVERT: A 579 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7388 (mt0) REVERT: B 364 LEU cc_start: 0.7249 (mt) cc_final: 0.7000 (mt) REVERT: B 630 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.6095 (m-80) REVERT: B 691 CYS cc_start: 0.8126 (m) cc_final: 0.7777 (m) REVERT: C 453 TYR cc_start: 0.7752 (m-80) cc_final: 0.7216 (m-80) REVERT: C 521 GLU cc_start: 0.6266 (mm-30) cc_final: 0.5938 (pm20) REVERT: C 624 SER cc_start: 0.7796 (OUTLIER) cc_final: 0.7222 (t) REVERT: C 649 PHE cc_start: 0.8963 (p90) cc_final: 0.8697 (p90) REVERT: C 708 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6045 (tp) REVERT: D 21 MET cc_start: 0.6272 (tmm) cc_final: 0.5835 (tpp) REVERT: D 98 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6189 (mt-10) REVERT: D 143 MET cc_start: 0.3727 (mpp) cc_final: 0.3399 (mpp) REVERT: E 227 MET cc_start: 0.6518 (pmm) cc_final: 0.5315 (tpt) REVERT: F 22 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8513 (mt) REVERT: F 448 PHE cc_start: 0.7274 (m-10) cc_final: 0.6853 (m-10) REVERT: F 540 MET cc_start: 0.8243 (tmm) cc_final: 0.7896 (mmp) REVERT: F 575 TRP cc_start: 0.7485 (m100) cc_final: 0.7185 (m100) REVERT: F 610 MET cc_start: 0.8304 (tpt) cc_final: 0.7792 (tpt) REVERT: F 614 GLN cc_start: 0.8314 (mm110) cc_final: 0.6777 (pp30) REVERT: F 633 GLU cc_start: 0.7369 (mp0) cc_final: 0.6694 (mm-30) REVERT: G 21 GLU cc_start: 0.8606 (pt0) cc_final: 0.7939 (tm-30) REVERT: G 101 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7903 (tppt) REVERT: G 149 ASP cc_start: 0.3730 (t0) cc_final: 0.3451 (t0) outliers start: 87 outliers final: 67 residues processed: 619 average time/residue: 0.9749 time to fit residues: 962.5672 Evaluate side-chains 613 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 540 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 532 ASN Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 314 ARG Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 272 optimal weight: 0.7980 chunk 291 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** E 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36297 Z= 0.318 Angle : 0.585 9.687 48868 Z= 0.311 Chirality : 0.039 0.148 5367 Planarity : 0.004 0.060 6282 Dihedral : 4.585 56.760 4834 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 2.37 % Allowed : 24.54 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -0.72 (0.12), residues: 4439 helix: 0.87 (0.12), residues: 1927 sheet: -1.42 (0.24), residues: 461 loop : -1.57 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.006 0.001 HIS G 8 PHE 0.026 0.002 PHE C 596 TYR 0.018 0.002 TYR D 361 ARG 0.007 0.000 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 629 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 536 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 TYR cc_start: 0.5722 (t80) cc_final: 0.4194 (t80) REVERT: A 185 ASN cc_start: 0.8669 (m110) cc_final: 0.8295 (t0) REVERT: A 386 MET cc_start: 0.7436 (mtp) cc_final: 0.7220 (mtp) REVERT: A 579 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: B 364 LEU cc_start: 0.7299 (mt) cc_final: 0.7053 (mt) REVERT: B 630 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: B 691 CYS cc_start: 0.8211 (m) cc_final: 0.7835 (m) REVERT: C 453 TYR cc_start: 0.7771 (m-80) cc_final: 0.7276 (m-80) REVERT: C 521 GLU cc_start: 0.6248 (mm-30) cc_final: 0.5872 (pm20) REVERT: C 624 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7517 (t) REVERT: C 708 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6201 (tp) REVERT: D 21 MET cc_start: 0.6273 (tmm) cc_final: 0.5786 (tpp) REVERT: D 98 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6262 (mt-10) REVERT: D 143 MET cc_start: 0.3738 (mpp) cc_final: 0.3410 (mpp) REVERT: D 661 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8918 (mm) REVERT: F 22 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8534 (mt) REVERT: F 253 LEU cc_start: 0.6637 (mt) cc_final: 0.6111 (tp) REVERT: F 448 PHE cc_start: 0.7304 (m-10) cc_final: 0.6883 (m-10) REVERT: F 540 MET cc_start: 0.8292 (tmm) cc_final: 0.7981 (mmp) REVERT: G 21 GLU cc_start: 0.8612 (pt0) cc_final: 0.7958 (tm-30) REVERT: G 101 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7944 (tppt) REVERT: G 149 ASP cc_start: 0.3506 (t0) cc_final: 0.3217 (t0) outliers start: 93 outliers final: 77 residues processed: 603 average time/residue: 1.0159 time to fit residues: 988.9875 Evaluate side-chains 614 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 530 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 PHE Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 532 ASN Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 314 ARG Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 20.0000 chunk 409 optimal weight: 4.9990 chunk 374 optimal weight: 10.0000 chunk 398 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 360 optimal weight: 20.0000 chunk 377 optimal weight: 2.9990 chunk 397 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN E 686 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36297 Z= 0.312 Angle : 0.589 8.828 48868 Z= 0.313 Chirality : 0.040 0.174 5367 Planarity : 0.004 0.055 6282 Dihedral : 4.629 54.493 4834 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.65 % Favored : 93.29 % Rotamer: Outliers : 2.55 % Allowed : 24.41 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.77 (0.12), residues: 4439 helix: 0.81 (0.12), residues: 1928 sheet: -1.34 (0.25), residues: 429 loop : -1.62 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 364 HIS 0.005 0.001 HIS G 8 PHE 0.022 0.001 PHE D 132 TYR 0.017 0.001 TYR E 554 ARG 0.006 0.000 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 642 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 542 time to evaluate : 4.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 TYR cc_start: 0.5507 (t80) cc_final: 0.3983 (t80) REVERT: A 185 ASN cc_start: 0.8619 (m110) cc_final: 0.8267 (t0) REVERT: A 571 MET cc_start: 0.7049 (tmm) cc_final: 0.6730 (tmm) REVERT: A 579 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: B 130 ASP cc_start: 0.7562 (t0) cc_final: 0.7217 (t0) REVERT: B 364 LEU cc_start: 0.7294 (mt) cc_final: 0.7050 (mt) REVERT: B 630 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: B 691 CYS cc_start: 0.8348 (m) cc_final: 0.7992 (m) REVERT: C 453 TYR cc_start: 0.7854 (m-80) cc_final: 0.7401 (m-80) REVERT: C 521 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5800 (pm20) REVERT: C 708 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6240 (tp) REVERT: Y 363 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7538 (mtm-85) REVERT: D 98 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6290 (mt-10) REVERT: D 143 MET cc_start: 0.3735 (mpp) cc_final: 0.3404 (mpp) REVERT: D 661 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8939 (mm) REVERT: F 22 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8519 (mt) REVERT: F 253 LEU cc_start: 0.6513 (mt) cc_final: 0.5981 (tp) REVERT: F 448 PHE cc_start: 0.7337 (m-10) cc_final: 0.6899 (m-10) REVERT: F 540 MET cc_start: 0.8277 (tmm) cc_final: 0.8068 (mmp) REVERT: F 610 MET cc_start: 0.8195 (tpt) cc_final: 0.7782 (tpt) REVERT: G 21 GLU cc_start: 0.8613 (pt0) cc_final: 0.7934 (tm-30) REVERT: G 101 LYS cc_start: 0.8409 (ttmt) cc_final: 0.7923 (tppt) REVERT: G 149 ASP cc_start: 0.3918 (t0) cc_final: 0.3582 (t0) outliers start: 100 outliers final: 83 residues processed: 615 average time/residue: 0.9834 time to fit residues: 968.5897 Evaluate side-chains 621 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 532 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 658 SER Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 344 PHE Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 532 ASN Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 314 ARG Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 0.9980 chunk 421 optimal weight: 0.8980 chunk 257 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 442 optimal weight: 4.9990 chunk 407 optimal weight: 3.9990 chunk 352 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36297 Z= 0.177 Angle : 0.556 9.452 48868 Z= 0.287 Chirality : 0.039 0.159 5367 Planarity : 0.004 0.054 6282 Dihedral : 4.373 50.759 4834 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 1.96 % Allowed : 25.10 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -0.38 (0.12), residues: 4439 helix: 1.22 (0.12), residues: 1919 sheet: -1.28 (0.24), residues: 455 loop : -1.44 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 364 HIS 0.007 0.001 HIS G 8 PHE 0.023 0.001 PHE C 596 TYR 0.019 0.001 TYR A 644 ARG 0.007 0.000 ARG A 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 639 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 562 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 TYR cc_start: 0.5595 (t80) cc_final: 0.4051 (t80) REVERT: A 185 ASN cc_start: 0.8629 (m110) cc_final: 0.8200 (t0) REVERT: A 585 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7725 (tp30) REVERT: B 130 ASP cc_start: 0.7398 (t0) cc_final: 0.6793 (t0) REVERT: B 364 LEU cc_start: 0.7185 (mt) cc_final: 0.6953 (mt) REVERT: B 630 PHE cc_start: 0.6496 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: B 691 CYS cc_start: 0.8298 (m) cc_final: 0.7917 (m) REVERT: C 453 TYR cc_start: 0.7747 (m-80) cc_final: 0.7255 (m-80) REVERT: C 521 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5740 (pm20) REVERT: C 572 MET cc_start: 0.6797 (tmm) cc_final: 0.6512 (tmm) REVERT: C 708 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6209 (tp) REVERT: Y 363 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7538 (mtm-85) REVERT: D 98 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6293 (mt-10) REVERT: D 143 MET cc_start: 0.3670 (mpp) cc_final: 0.3336 (mpp) REVERT: D 415 SER cc_start: 0.8716 (p) cc_final: 0.8305 (t) REVERT: E 279 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8789 (tptm) REVERT: E 669 ARG cc_start: 0.6616 (mtt180) cc_final: 0.6406 (tmm160) REVERT: F 22 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8459 (mt) REVERT: F 397 ARG cc_start: 0.8123 (tpt170) cc_final: 0.7897 (tpt170) REVERT: F 448 PHE cc_start: 0.7254 (m-10) cc_final: 0.6917 (m-10) REVERT: F 614 GLN cc_start: 0.8328 (mm110) cc_final: 0.6748 (pp30) REVERT: F 675 MET cc_start: 0.6256 (mtm) cc_final: 0.5712 (mtp) REVERT: G 21 GLU cc_start: 0.8645 (pt0) cc_final: 0.7909 (tm-30) REVERT: G 101 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7919 (tppt) REVERT: G 149 ASP cc_start: 0.3705 (t0) cc_final: 0.3410 (t0) outliers start: 77 outliers final: 63 residues processed: 618 average time/residue: 0.9795 time to fit residues: 969.9881 Evaluate side-chains 607 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 539 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 658 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 344 PHE Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 532 ASN Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 3.9990 chunk 375 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 chunk 324 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 352 optimal weight: 0.9980 chunk 147 optimal weight: 0.4980 chunk 362 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.128482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100848 restraints weight = 283533.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.104528 restraints weight = 110665.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.106742 restraints weight = 63803.160| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36297 Z= 0.168 Angle : 0.546 9.413 48868 Z= 0.280 Chirality : 0.038 0.161 5367 Planarity : 0.004 0.065 6282 Dihedral : 4.225 46.091 4834 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 1.51 % Allowed : 25.43 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.13), residues: 4439 helix: 1.41 (0.12), residues: 1929 sheet: -1.16 (0.25), residues: 427 loop : -1.37 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 364 HIS 0.007 0.001 HIS G 8 PHE 0.020 0.001 PHE C 596 TYR 0.018 0.001 TYR A 644 ARG 0.009 0.000 ARG A 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17349.29 seconds wall clock time: 296 minutes 10.31 seconds (17770.31 seconds total)