Starting phenix.real_space_refine on Thu Jan 23 15:34:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rnc_19394/01_2025/8rnc_19394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rnc_19394/01_2025/8rnc_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/cci-nas-00/data/ceres_data/8rnc_19394/01_2025/8rnc_19394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rnc_19394/01_2025/8rnc_19394.map" model { file = "/net/cci-nas-00/data/ceres_data/8rnc_19394/01_2025/8rnc_19394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rnc_19394/01_2025/8rnc_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 25.78, per 1000 atoms: 0.36 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: 15.11 Conformation dependent library (CDL) restraints added in 4.3 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: 5.35 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: 27.74 Time building geometry restraints manager: 18.15 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: 12.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.930 Extract box with map and model: 2.330 Check model and map are aligned: 0.440 Set scattering table: 0.510 Process input model: 119.840 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.290 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.480 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 13 poor density : 1091 time to evaluate : 4.517 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: 1.1242 time to fit residues: 1892.9009 Evaluate side-chains 690 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 686 time to evaluate : 4.537 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.131142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103174 restraints weight = 282292.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106896 restraints weight = 110834.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.109127 restraints weight = 64175.458| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3060 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= 0.371 Angle : 0.630 7.567 48868 Z= 0.342 Chirality : 0.041 0.161 5367 Planarity : 0.005 0.070 6282 Dihedral : 4.391 54.598 4839 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.63 % Favored : 94.30 % 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: 1.18 (0.12), residues: 1947 sheet: -1.04 (0.24), residues: 494 loop : -1.16 (0.14), residues: 1998 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 766 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 681 time to evaluate : 4.643 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: 0.9206 (m110) cc_final: 0.8678 (t0) REVERT: A 383 ASP cc_start: 0.7791 (t70) cc_final: 0.6781 (p0) REVERT: A 568 LYS cc_start: 0.8705 (tttm) cc_final: 0.8484 (tttt) REVERT: B 109 ASN cc_start: 0.9021 (m-40) cc_final: 0.8803 (m-40) REVERT: B 502 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7435 (m) REVERT: B 691 CYS cc_start: 0.8506 (m) cc_final: 0.8158 (m) REVERT: B 723 MET cc_start: 0.8385 (tpt) cc_final: 0.8086 (tpt) REVERT: C 521 GLU cc_start: 0.6564 (mm-30) cc_final: 0.5904 (pm20) REVERT: C 604 MET cc_start: 0.7728 (tpp) cc_final: 0.7213 (tpp) REVERT: C 637 PHE cc_start: 0.5978 (m-10) cc_final: 0.5705 (m-10) REVERT: D 21 MET cc_start: 0.6186 (tmm) cc_final: 0.5613 (tpp) REVERT: D 427 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: E 415 MET cc_start: 0.8301 (mmp) cc_final: 0.8052 (mmm) REVERT: E 575 ILE cc_start: 0.9356 (mm) cc_final: 0.9086 (mm) REVERT: F 253 LEU cc_start: 0.6953 (mt) cc_final: 0.6459 (tp) REVERT: F 320 LYS cc_start: 0.7505 (mmmm) cc_final: 0.7035 (mmtm) REVERT: F 448 PHE cc_start: 0.7380 (m-10) cc_final: 0.7004 (m-10) REVERT: F 481 VAL cc_start: 0.9070 (t) cc_final: 0.8790 (m) REVERT: F 614 GLN cc_start: 0.8381 (mm110) cc_final: 0.6840 (pp30) REVERT: G 101 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7771 (tppt) REVERT: G 152 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.3724 (p0) outliers start: 85 outliers final: 45 residues processed: 745 average time/residue: 1.0380 time to fit residues: 1215.8216 Evaluate side-chains 635 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 587 time to evaluate : 4.526 ------------------------------------------------------------------------------- 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 D residue 427 ASP 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 428 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 392 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 354 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.131838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103726 restraints weight = 279794.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.107482 restraints weight = 109702.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.109732 restraints weight = 63114.621| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36297 Z= 0.235 Angle : 0.546 7.606 48868 Z= 0.289 Chirality : 0.038 0.145 5367 Planarity : 0.004 0.059 6282 Dihedral : 4.267 55.020 4836 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 2.04 % Allowed : 22.55 % Favored : 75.41 % 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: -0.08 (0.13), residues: 4439 helix: 1.29 (0.12), residues: 1949 sheet: -1.05 (0.23), residues: 494 loop : -1.14 (0.14), residues: 1996 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 0.021 0.001 PHE B 504 TYR 0.017 0.001 TYR F 635 ARG 0.011 0.000 ARG B 733 *********************** 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 699 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 619 time to evaluate : 4.532 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: A 185 ASN cc_start: 0.9169 (m110) cc_final: 0.8644 (t0) REVERT: A 386 MET cc_start: 0.7681 (mtp) cc_final: 0.7176 (mtp) REVERT: A 579 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7117 (mt0) REVERT: B 109 ASN cc_start: 0.9012 (m-40) cc_final: 0.8757 (m-40) REVERT: B 459 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7582 (ppp) REVERT: B 691 CYS cc_start: 0.8523 (m) cc_final: 0.8117 (m) REVERT: C 34 ARG cc_start: 0.8110 (tpt170) cc_final: 0.7897 (tpt170) REVERT: C 51 TRP cc_start: 0.8096 (m-10) cc_final: 0.7594 (m-10) REVERT: C 229 GLU cc_start: 0.8443 (mp0) cc_final: 0.8190 (mm-30) REVERT: C 521 GLU cc_start: 0.6596 (mm-30) cc_final: 0.5889 (pm20) REVERT: C 548 GLN cc_start: 0.8935 (tt0) cc_final: 0.8473 (tp-100) REVERT: C 624 SER cc_start: 0.7629 (OUTLIER) cc_final: 0.7193 (t) REVERT: D 21 MET cc_start: 0.6195 (tmm) cc_final: 0.5640 (tpp) REVERT: D 358 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8184 (tptt) REVERT: D 515 THR cc_start: 0.9052 (m) cc_final: 0.8770 (t) REVERT: E 130 ASP cc_start: 0.7702 (t0) cc_final: 0.7498 (t0) REVERT: E 227 MET cc_start: 0.6827 (pmm) cc_final: 0.5023 (mmm) REVERT: E 415 MET cc_start: 0.8235 (mmp) cc_final: 0.8006 (mmm) REVERT: E 575 ILE cc_start: 0.9344 (mm) cc_final: 0.9054 (mm) REVERT: F 266 ARG cc_start: 0.8732 (mtt180) cc_final: 0.8430 (mtt-85) REVERT: F 320 LYS cc_start: 0.7532 (mmmm) cc_final: 0.7046 (mmtm) REVERT: F 448 PHE cc_start: 0.7455 (m-10) cc_final: 0.7099 (m-10) REVERT: F 521 GLU cc_start: 0.7572 (mp0) cc_final: 0.7353 (mp0) REVERT: F 610 MET cc_start: 0.8228 (tpt) cc_final: 0.7993 (tpt) REVERT: F 614 GLN cc_start: 0.8466 (mm110) cc_final: 0.6704 (pp30) REVERT: G 101 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7778 (tppt) REVERT: G 152 ASP cc_start: 0.6430 (OUTLIER) cc_final: 0.3615 (p0) outliers start: 80 outliers final: 54 residues processed: 676 average time/residue: 0.9734 time to fit residues: 1040.6916 Evaluate side-chains 639 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 581 time to evaluate : 4.574 ------------------------------------------------------------------------------- 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 579 GLN Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 459 MET 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 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 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 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 272 optimal weight: 1.9990 chunk 314 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 44 optimal weight: 0.0670 chunk 7 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 305 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 271 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- 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** C 692 ASN F 277 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.131678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.103576 restraints weight = 280519.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.107389 restraints weight = 109019.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.109641 restraints weight = 62652.707| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36297 Z= 0.180 Angle : 0.523 8.887 48868 Z= 0.273 Chirality : 0.038 0.148 5367 Planarity : 0.004 0.051 6282 Dihedral : 4.181 57.000 4836 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 1.96 % Allowed : 22.58 % Favored : 75.46 % 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: 0.04 (0.13), residues: 4439 helix: 1.43 (0.12), residues: 1941 sheet: -1.04 (0.24), residues: 474 loop : -1.10 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 553 HIS 0.011 0.001 HIS E 745 PHE 0.022 0.001 PHE C 596 TYR 0.024 0.001 TYR F 635 ARG 0.003 0.000 ARG C 178 *********************** 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 691 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 614 time to evaluate : 5.073 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: A 185 ASN cc_start: 0.9107 (m110) cc_final: 0.8648 (t0) REVERT: A 386 MET cc_start: 0.7761 (mtp) cc_final: 0.7168 (mtp) REVERT: A 579 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7032 (mt0) REVERT: B 109 ASN cc_start: 0.9022 (m-40) cc_final: 0.8759 (m-40) REVERT: B 256 GLU cc_start: 0.8484 (tp30) cc_final: 0.8163 (mm-30) REVERT: B 459 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7550 (ppp) REVERT: B 538 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7640 (ttm) REVERT: B 630 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: B 691 CYS cc_start: 0.8516 (m) cc_final: 0.8070 (m) REVERT: C 51 TRP cc_start: 0.8045 (m-10) cc_final: 0.7567 (m-10) REVERT: C 521 GLU cc_start: 0.6569 (mm-30) cc_final: 0.5881 (pm20) REVERT: C 548 GLN cc_start: 0.8836 (tt0) cc_final: 0.8268 (tp-100) REVERT: C 624 SER cc_start: 0.7545 (OUTLIER) cc_final: 0.7126 (t) REVERT: D 21 MET cc_start: 0.6192 (tmm) cc_final: 0.5584 (tpp) REVERT: D 98 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6239 (mt-10) REVERT: D 358 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8200 (tptt) REVERT: D 415 SER cc_start: 0.8928 (OUTLIER) cc_final: 0.8519 (t) REVERT: D 515 THR cc_start: 0.9035 (m) cc_final: 0.8731 (t) REVERT: D 592 SER cc_start: 0.8647 (m) cc_final: 0.8281 (t) REVERT: E 130 ASP cc_start: 0.7788 (t0) cc_final: 0.7547 (t0) REVERT: E 575 ILE cc_start: 0.9320 (mm) cc_final: 0.9032 (mm) REVERT: F 22 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8482 (mt) REVERT: F 329 ARG cc_start: 0.7128 (ttt180) cc_final: 0.6914 (ttt180) REVERT: F 404 MET cc_start: 0.7345 (mmt) cc_final: 0.7139 (mmt) REVERT: F 448 PHE cc_start: 0.7520 (m-10) cc_final: 0.7153 (m-10) REVERT: F 521 GLU cc_start: 0.7607 (mp0) cc_final: 0.7314 (mp0) REVERT: F 610 MET cc_start: 0.8289 (tpt) cc_final: 0.7824 (tpt) REVERT: F 614 GLN cc_start: 0.8445 (mm110) cc_final: 0.6671 (pp30) REVERT: G 101 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7778 (tppt) REVERT: G 152 ASP cc_start: 0.6274 (OUTLIER) cc_final: 0.3590 (p0) outliers start: 77 outliers final: 50 residues processed: 667 average time/residue: 1.0247 time to fit residues: 1096.1368 Evaluate side-chains 631 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 572 time to evaluate : 4.610 ------------------------------------------------------------------------------- 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 343 CYS Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 579 GLN 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 459 MET 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 712 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 46 SER 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 524 SER Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 624 SER 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 472 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER 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 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 22 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 495 GLU 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 152 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 309 optimal weight: 0.6980 chunk 384 optimal weight: 0.8980 chunk 392 optimal weight: 3.9990 chunk 265 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN F 277 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.130394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.102409 restraints weight = 284610.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.106260 restraints weight = 109475.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.108575 restraints weight = 62363.364| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36297 Z= 0.155 Angle : 0.509 7.922 48868 Z= 0.262 Chirality : 0.038 0.148 5367 Planarity : 0.004 0.064 6282 Dihedral : 4.085 59.704 4836 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 1.84 % Allowed : 22.73 % Favored : 75.43 % 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: 0.19 (0.13), residues: 4439 helix: 1.57 (0.12), residues: 1949 sheet: -1.00 (0.24), residues: 470 loop : -1.03 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS G 8 PHE 0.019 0.001 PHE D 132 TYR 0.016 0.001 TYR A 644 ARG 0.009 0.000 ARG F 266 *********************** 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 690 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 618 time to evaluate : 4.626 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: A 185 ASN cc_start: 0.9099 (m110) cc_final: 0.8638 (t0) REVERT: A 386 MET cc_start: 0.7544 (mtp) cc_final: 0.7171 (mtp) REVERT: A 495 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7355 (mtp) REVERT: A 579 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7014 (mt0) REVERT: A 642 MET cc_start: 0.9065 (mmp) cc_final: 0.8821 (mmm) REVERT: B 109 ASN cc_start: 0.9018 (m-40) cc_final: 0.8750 (m-40) REVERT: B 256 GLU cc_start: 0.8510 (tp30) cc_final: 0.8020 (mm-30) REVERT: B 364 LEU cc_start: 0.8201 (mt) cc_final: 0.7971 (mt) REVERT: B 459 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7531 (ppp) REVERT: B 538 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7436 (ttm) REVERT: B 630 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: B 691 CYS cc_start: 0.8522 (m) cc_final: 0.8075 (m) REVERT: C 229 GLU cc_start: 0.8371 (mp0) cc_final: 0.8168 (mm-30) REVERT: C 521 GLU cc_start: 0.6636 (mm-30) cc_final: 0.5914 (pm20) REVERT: C 548 GLN cc_start: 0.8834 (tt0) cc_final: 0.8239 (tp-100) REVERT: C 624 SER cc_start: 0.7464 (OUTLIER) cc_final: 0.6894 (t) REVERT: D 21 MET cc_start: 0.6154 (tmm) cc_final: 0.5565 (tpp) REVERT: D 98 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6151 (mt-10) REVERT: D 415 SER cc_start: 0.8926 (p) cc_final: 0.8511 (t) REVERT: D 441 TYR cc_start: 0.8167 (m-80) cc_final: 0.7962 (m-80) REVERT: D 515 THR cc_start: 0.9072 (m) cc_final: 0.8771 (t) REVERT: D 592 SER cc_start: 0.8633 (m) cc_final: 0.8276 (t) REVERT: E 130 ASP cc_start: 0.7805 (t0) cc_final: 0.7549 (t0) REVERT: E 575 ILE cc_start: 0.9305 (mm) cc_final: 0.9011 (mm) REVERT: F 329 ARG cc_start: 0.7100 (ttt180) cc_final: 0.6890 (ttt180) REVERT: F 448 PHE cc_start: 0.7528 (m-10) cc_final: 0.7151 (m-10) REVERT: F 610 MET cc_start: 0.8277 (tpt) cc_final: 0.7634 (tpt) REVERT: F 614 GLN cc_start: 0.8409 (mm110) cc_final: 0.6566 (pp30) REVERT: F 633 GLU cc_start: 0.7496 (mp0) cc_final: 0.6762 (mm-30) REVERT: G 21 GLU cc_start: 0.8678 (pt0) cc_final: 0.8029 (tm-30) REVERT: G 101 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7758 (tppt) REVERT: G 152 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.3738 (p0) outliers start: 72 outliers final: 45 residues processed: 665 average time/residue: 0.9813 time to fit residues: 1038.7547 Evaluate side-chains 637 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 584 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 459 MET 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 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 624 SER 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 472 SER Chi-restraints excluded: chain D residue 512 ASP 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 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 532 ASN 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 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 574 GLN Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain F residue 589 MET Chi-restraints excluded: chain F residue 713 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 152 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 248 optimal weight: 3.9990 chunk 339 optimal weight: 5.9990 chunk 437 optimal weight: 3.9990 chunk 386 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 342 optimal weight: 6.9990 chunk 169 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 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** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN F 323 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098084 restraints weight = 285770.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.101723 restraints weight = 110695.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.103881 restraints weight = 63716.995| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36297 Z= 0.286 Angle : 0.552 8.801 48868 Z= 0.294 Chirality : 0.038 0.145 5367 Planarity : 0.004 0.048 6282 Dihedral : 4.276 57.066 4836 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 2.35 % Allowed : 22.63 % Favored : 75.03 % 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: -0.08 (0.13), residues: 4439 helix: 1.34 (0.12), residues: 1951 sheet: -1.10 (0.24), residues: 493 loop : -1.18 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 51 HIS 0.006 0.001 HIS G 8 PHE 0.035 0.001 PHE C 581 TYR 0.020 0.001 TYR F 635 ARG 0.007 0.000 ARG D 85 *********************** 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 679 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 587 time to evaluate : 4.620 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: A 131 TYR cc_start: 0.5878 (t80) cc_final: 0.4339 (t80) REVERT: A 185 ASN cc_start: 0.9132 (m110) cc_final: 0.8667 (t0) REVERT: A 226 MET cc_start: 0.9068 (tmm) cc_final: 0.8726 (tmm) REVERT: A 386 MET cc_start: 0.7764 (mtp) cc_final: 0.7349 (mtp) REVERT: B 364 LEU cc_start: 0.8200 (mt) cc_final: 0.7980 (mt) REVERT: B 459 MET cc_start: 0.8067 (ptm) cc_final: 0.7565 (ppp) REVERT: B 630 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: B 691 CYS cc_start: 0.8563 (m) cc_final: 0.8143 (m) REVERT: C 34 ARG cc_start: 0.8139 (tpt170) cc_final: 0.7855 (tpt170) REVERT: C 521 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6162 (pm20) REVERT: C 624 SER cc_start: 0.7730 (OUTLIER) cc_final: 0.7261 (t) REVERT: D 21 MET cc_start: 0.6164 (tmm) cc_final: 0.5595 (tpp) REVERT: D 98 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6226 (mt-10) REVERT: D 358 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8313 (tptt) REVERT: D 368 ASP cc_start: 0.7164 (m-30) cc_final: 0.6246 (t0) REVERT: D 415 SER cc_start: 0.9048 (p) cc_final: 0.8638 (t) REVERT: D 515 THR cc_start: 0.9068 (m) cc_final: 0.8744 (t) REVERT: E 130 ASP cc_start: 0.7736 (t0) cc_final: 0.7488 (t0) REVERT: E 256 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8135 (mm-30) REVERT: E 575 ILE cc_start: 0.9321 (mm) cc_final: 0.9045 (mm) REVERT: E 713 MET cc_start: 0.3200 (ptm) cc_final: 0.2801 (ptm) REVERT: F 329 ARG cc_start: 0.7279 (ttt180) cc_final: 0.7054 (ttt180) REVERT: F 448 PHE cc_start: 0.7507 (m-10) cc_final: 0.6698 (m-10) REVERT: F 610 MET cc_start: 0.8335 (tpt) cc_final: 0.7794 (tpt) REVERT: G 21 GLU cc_start: 0.8682 (pt0) cc_final: 0.8036 (tm-30) REVERT: G 101 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7792 (tppt) outliers start: 92 outliers final: 70 residues processed: 654 average time/residue: 1.0304 time to fit residues: 1076.9757 Evaluate side-chains 643 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 570 time to evaluate : 4.580 ------------------------------------------------------------------------------- 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 257 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 387 CYS 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 A residue 676 VAL 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 408 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 504 PHE 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 624 SER 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 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 563 ASN 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 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 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 574 GLN 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 74 ASN Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 94 ASN 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 125 optimal weight: 5.9990 chunk 321 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 330 optimal weight: 3.9990 chunk 368 optimal weight: 0.9980 chunk 294 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 392 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 692 ASN F 323 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.128523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.100711 restraints weight = 283619.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104470 restraints weight = 109206.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.106719 restraints weight = 62344.854| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36297 Z= 0.175 Angle : 0.519 7.691 48868 Z= 0.269 Chirality : 0.038 0.152 5367 Planarity : 0.004 0.058 6282 Dihedral : 4.087 53.764 4834 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.51 % Favored : 95.43 % Rotamer: Outliers : 1.71 % Allowed : 23.27 % Favored : 75.03 % 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: 0.11 (0.13), residues: 4439 helix: 1.55 (0.12), residues: 1942 sheet: -1.01 (0.24), residues: 470 loop : -1.13 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 553 HIS 0.005 0.001 HIS G 8 PHE 0.025 0.001 PHE C 581 TYR 0.015 0.001 TYR A 644 ARG 0.007 0.000 ARG F 397 *********************** 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 655 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 588 time to evaluate : 4.595 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: A 131 TYR cc_start: 0.5827 (t80) cc_final: 0.4189 (t80) REVERT: A 185 ASN cc_start: 0.9128 (m110) cc_final: 0.8591 (t0) REVERT: A 226 MET cc_start: 0.9104 (tmm) cc_final: 0.8777 (tmm) REVERT: A 386 MET cc_start: 0.7786 (mtp) cc_final: 0.7380 (mtp) REVERT: A 579 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7094 (mt0) REVERT: A 642 MET cc_start: 0.9124 (mmp) cc_final: 0.8904 (mmm) REVERT: B 364 LEU cc_start: 0.8289 (mt) cc_final: 0.8084 (mt) REVERT: B 459 MET cc_start: 0.8045 (ptm) cc_final: 0.7543 (ppp) REVERT: B 630 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6378 (m-80) REVERT: B 691 CYS cc_start: 0.8513 (m) cc_final: 0.8078 (m) REVERT: C 521 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6111 (pm20) REVERT: C 624 SER cc_start: 0.7577 (OUTLIER) cc_final: 0.7086 (t) REVERT: D 21 MET cc_start: 0.6197 (tmm) cc_final: 0.5610 (tpp) REVERT: D 98 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6197 (mt-10) REVERT: D 143 MET cc_start: 0.3301 (mpp) cc_final: 0.3047 (mpp) REVERT: D 368 ASP cc_start: 0.7056 (m-30) cc_final: 0.6339 (t0) REVERT: D 415 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8524 (t) REVERT: D 441 TYR cc_start: 0.8185 (m-80) cc_final: 0.7962 (m-80) REVERT: D 515 THR cc_start: 0.9057 (m) cc_final: 0.8751 (t) REVERT: D 592 SER cc_start: 0.8564 (m) cc_final: 0.8257 (t) REVERT: E 130 ASP cc_start: 0.7798 (t0) cc_final: 0.7531 (t0) REVERT: E 227 MET cc_start: 0.6775 (pmm) cc_final: 0.4837 (tpt) REVERT: E 575 ILE cc_start: 0.9315 (mm) cc_final: 0.9029 (mm) REVERT: F 329 ARG cc_start: 0.7240 (ttt180) cc_final: 0.7014 (ttt180) REVERT: F 448 PHE cc_start: 0.7356 (m-10) cc_final: 0.6948 (m-10) REVERT: F 610 MET cc_start: 0.8368 (tpt) cc_final: 0.8161 (tpt) REVERT: F 614 GLN cc_start: 0.8485 (mm110) cc_final: 0.6651 (pp30) REVERT: F 633 GLU cc_start: 0.7427 (mp0) cc_final: 0.6723 (mm-30) REVERT: G 21 GLU cc_start: 0.8658 (pt0) cc_final: 0.8008 (tm-30) REVERT: G 101 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7818 (tppt) outliers start: 67 outliers final: 55 residues processed: 636 average time/residue: 0.9729 time to fit residues: 972.5165 Evaluate side-chains 625 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 565 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 432 GLU 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 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 408 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 504 PHE 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 624 SER 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 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 635 VAL Chi-restraints excluded: chain E residue 3 ILE 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 532 ASN 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 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE 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 131 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 66 optimal weight: 3.9990 chunk 442 optimal weight: 7.9990 chunk 386 optimal weight: 8.9990 chunk 350 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 407 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 406 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 692 ASN C 727 ASN E 109 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.125130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.097185 restraints weight = 285683.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100765 restraints weight = 110738.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.102912 restraints weight = 63832.039| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36297 Z= 0.301 Angle : 0.560 7.708 48868 Z= 0.299 Chirality : 0.039 0.147 5367 Planarity : 0.004 0.056 6282 Dihedral : 4.256 51.356 4834 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.08 % Favored : 93.85 % Rotamer: Outliers : 2.35 % Allowed : 22.86 % Favored : 74.80 % 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: 1.30 (0.12), residues: 1933 sheet: -1.09 (0.24), residues: 478 loop : -1.26 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 569 HIS 0.005 0.001 HIS C 235 PHE 0.024 0.001 PHE D 132 TYR 0.018 0.001 TYR E 554 ARG 0.006 0.000 ARG F 397 *********************** 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 660 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 568 time to evaluate : 4.610 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: A 131 TYR cc_start: 0.5853 (t80) cc_final: 0.4179 (t80) REVERT: A 185 ASN cc_start: 0.9137 (m110) cc_final: 0.8668 (t0) REVERT: A 386 MET cc_start: 0.7853 (mtp) cc_final: 0.7584 (mtp) REVERT: A 635 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8597 (t) REVERT: B 364 LEU cc_start: 0.8294 (mt) cc_final: 0.8085 (mt) REVERT: B 459 MET cc_start: 0.8065 (ptm) cc_final: 0.7542 (ppp) REVERT: B 630 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.6234 (m-80) REVERT: B 691 CYS cc_start: 0.8582 (m) cc_final: 0.8192 (m) REVERT: C 453 TYR cc_start: 0.7907 (m-80) cc_final: 0.7198 (m-80) REVERT: C 521 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6028 (pm20) REVERT: C 624 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7215 (t) REVERT: X 376 MET cc_start: 0.6648 (mmt) cc_final: 0.5987 (ttt) REVERT: D 21 MET cc_start: 0.6194 (tmm) cc_final: 0.5605 (tpp) REVERT: D 98 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6338 (mt-10) REVERT: D 368 ASP cc_start: 0.7124 (m-30) cc_final: 0.6393 (t0) REVERT: D 515 THR cc_start: 0.9090 (m) cc_final: 0.8774 (t) REVERT: E 117 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8507 (t) REVERT: E 130 ASP cc_start: 0.7823 (t0) cc_final: 0.7549 (t0) REVERT: E 227 MET cc_start: 0.6774 (pmm) cc_final: 0.5155 (tpt) REVERT: E 575 ILE cc_start: 0.9327 (mm) cc_final: 0.9049 (mm) REVERT: F 329 ARG cc_start: 0.7401 (ttt180) cc_final: 0.7078 (ttt180) REVERT: F 448 PHE cc_start: 0.7448 (m-10) cc_final: 0.7083 (m-10) REVERT: G 21 GLU cc_start: 0.8678 (pt0) cc_final: 0.8034 (tm-30) REVERT: G 101 LYS cc_start: 0.8350 (ttmt) cc_final: 0.7871 (tppt) outliers start: 92 outliers final: 73 residues processed: 636 average time/residue: 0.9882 time to fit residues: 999.7833 Evaluate side-chains 628 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 550 time to evaluate : 4.529 ------------------------------------------------------------------------------- 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 343 CYS 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 585 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 635 VAL 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 302 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 504 PHE 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 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 624 SER Chi-restraints excluded: chain C residue 681 ILE 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 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 117 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 527 THR Chi-restraints excluded: chain E residue 532 ASN Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 734 MET 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 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 574 GLN 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 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 96 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 359 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 276 optimal weight: 0.9990 chunk 329 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 650 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN F 442 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.128053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100429 restraints weight = 284392.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.104180 restraints weight = 109358.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.106392 restraints weight = 62261.806| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4892 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 : 0.528 7.911 48868 Z= 0.273 Chirality : 0.038 0.166 5367 Planarity : 0.004 0.073 6282 Dihedral : 4.108 48.345 4834 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 1.71 % Allowed : 23.62 % Favored : 74.67 % 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: 0.08 (0.13), residues: 4439 helix: 1.56 (0.12), residues: 1928 sheet: -1.00 (0.24), residues: 465 loop : -1.17 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 553 HIS 0.007 0.001 HIS G 8 PHE 0.021 0.001 PHE D 132 TYR 0.019 0.001 TYR D 361 ARG 0.007 0.000 ARG F 326 *********************** 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 to be fit. rotamer outliers: 67 poor density : 575 time to evaluate : 4.589 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: A 131 TYR cc_start: 0.5840 (t80) cc_final: 0.4206 (t80) REVERT: A 185 ASN cc_start: 0.9113 (m110) cc_final: 0.8550 (t0) REVERT: A 386 MET cc_start: 0.7924 (mtp) cc_final: 0.7210 (mtp) REVERT: A 579 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: B 364 LEU cc_start: 0.8271 (mt) cc_final: 0.8051 (mt) REVERT: B 459 MET cc_start: 0.8041 (ptm) cc_final: 0.7513 (ppp) REVERT: B 630 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: B 691 CYS cc_start: 0.8549 (m) cc_final: 0.8082 (m) REVERT: C 521 GLU cc_start: 0.6354 (mm-30) cc_final: 0.5969 (pm20) REVERT: C 624 SER cc_start: 0.7540 (OUTLIER) cc_final: 0.6892 (t) REVERT: X 376 MET cc_start: 0.6659 (mmt) cc_final: 0.6031 (ttt) REVERT: D 21 MET cc_start: 0.6207 (tmm) cc_final: 0.5635 (tpp) REVERT: D 98 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6261 (mt-10) REVERT: D 368 ASP cc_start: 0.6958 (m-30) cc_final: 0.6525 (t0) REVERT: D 415 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8532 (t) REVERT: D 515 THR cc_start: 0.9056 (m) cc_final: 0.8748 (t) REVERT: D 592 SER cc_start: 0.8569 (m) cc_final: 0.8242 (t) REVERT: E 130 ASP cc_start: 0.7860 (t0) cc_final: 0.7568 (t0) REVERT: E 227 MET cc_start: 0.6651 (pmm) cc_final: 0.5080 (tpt) REVERT: E 575 ILE cc_start: 0.9306 (mm) cc_final: 0.9032 (mm) REVERT: F 329 ARG cc_start: 0.7268 (ttt180) cc_final: 0.7028 (ttt180) REVERT: F 448 PHE cc_start: 0.7458 (m-10) cc_final: 0.6962 (m-10) REVERT: F 575 TRP cc_start: 0.7777 (m100) cc_final: 0.7318 (m100) REVERT: G 21 GLU cc_start: 0.8651 (pt0) cc_final: 0.7992 (tm-30) REVERT: G 101 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7864 (tppt) outliers start: 67 outliers final: 55 residues processed: 623 average time/residue: 0.9825 time to fit residues: 983.0173 Evaluate side-chains 619 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 559 time to evaluate : 4.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 432 GLU 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 A residue 676 VAL 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 408 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 504 PHE 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 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 624 SER 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 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 635 VAL Chi-restraints excluded: chain D residue 658 SER Chi-restraints excluded: chain E residue 3 ILE 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 532 ASN 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 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain F residue 465 ILE 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 131 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 4 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 401 optimal weight: 0.9980 chunk 379 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN ** E 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.125346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097612 restraints weight = 284182.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.101169 restraints weight = 109803.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.103298 restraints weight = 63174.436| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36297 Z= 0.278 Angle : 0.561 8.263 48868 Z= 0.295 Chirality : 0.039 0.147 5367 Planarity : 0.004 0.047 6282 Dihedral : 4.188 47.404 4834 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.72 % Favored : 94.21 % Rotamer: Outliers : 1.79 % Allowed : 23.60 % Favored : 74.62 % 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: -0.08 (0.13), residues: 4439 helix: 1.41 (0.12), residues: 1931 sheet: -1.08 (0.24), residues: 478 loop : -1.25 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 553 HIS 0.007 0.001 HIS G 8 PHE 0.033 0.001 PHE C 596 TYR 0.016 0.001 TYR E 554 ARG 0.005 0.000 ARG F 324 ********************** 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 621 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 551 time to evaluate : 4.545 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: A 131 TYR cc_start: 0.5836 (t80) cc_final: 0.4182 (t80) REVERT: A 185 ASN cc_start: 0.9127 (m110) cc_final: 0.8635 (t0) REVERT: A 386 MET cc_start: 0.7874 (mtp) cc_final: 0.7510 (mtp) REVERT: B 459 MET cc_start: 0.8052 (ptm) cc_final: 0.7528 (ppp) REVERT: B 630 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.6175 (m-80) REVERT: B 691 CYS cc_start: 0.8660 (m) cc_final: 0.8221 (m) REVERT: C 10 LYS cc_start: 0.8900 (tttt) cc_final: 0.8610 (pttt) REVERT: C 453 TYR cc_start: 0.7885 (m-80) cc_final: 0.7205 (m-80) REVERT: C 521 GLU cc_start: 0.6354 (mm-30) cc_final: 0.6007 (pm20) REVERT: C 624 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7072 (t) REVERT: X 376 MET cc_start: 0.6693 (mmt) cc_final: 0.6046 (ttt) REVERT: D 21 MET cc_start: 0.6202 (tmm) cc_final: 0.5624 (tpp) REVERT: D 98 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6363 (mt-10) REVERT: D 368 ASP cc_start: 0.7060 (m-30) cc_final: 0.6709 (t0) REVERT: D 415 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8625 (t) REVERT: D 515 THR cc_start: 0.9038 (m) cc_final: 0.8742 (t) REVERT: E 130 ASP cc_start: 0.7851 (t0) cc_final: 0.7570 (t0) REVERT: E 227 MET cc_start: 0.6724 (pmm) cc_final: 0.5232 (tpt) REVERT: E 575 ILE cc_start: 0.9307 (mm) cc_final: 0.9041 (mm) REVERT: F 329 ARG cc_start: 0.7413 (ttt180) cc_final: 0.7167 (ttt180) REVERT: F 448 PHE cc_start: 0.7418 (m-10) cc_final: 0.6958 (m-10) REVERT: G 21 GLU cc_start: 0.8648 (pt0) cc_final: 0.7972 (tm-30) REVERT: G 101 LYS cc_start: 0.8385 (ttmt) cc_final: 0.7885 (tppt) outliers start: 70 outliers final: 66 residues processed: 602 average time/residue: 0.9444 time to fit residues: 906.0074 Evaluate side-chains 614 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 544 time to evaluate : 4.580 ------------------------------------------------------------------------------- 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 340 TRP Chi-restraints excluded: chain A residue 343 CYS 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 628 SER 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 302 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 504 PHE 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 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 624 SER 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 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 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 532 ASN 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 369 CYS Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain F residue 465 ILE 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 131 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 161 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 438 optimal weight: 8.9990 chunk 329 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 265 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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** C 527 GLN E 686 GLN F 442 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.127480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099804 restraints weight = 283955.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.103515 restraints weight = 109716.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105728 restraints weight = 62716.440| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36297 Z= 0.183 Angle : 0.538 8.719 48868 Z= 0.278 Chirality : 0.038 0.178 5367 Planarity : 0.004 0.044 6282 Dihedral : 4.120 45.615 4834 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 1.81 % Allowed : 23.67 % Favored : 74.52 % 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: 0.03 (0.13), residues: 4439 helix: 1.53 (0.12), residues: 1926 sheet: -1.04 (0.24), residues: 471 loop : -1.22 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 553 HIS 0.007 0.001 HIS G 8 PHE 0.029 0.001 PHE C 596 TYR 0.018 0.001 TYR A 644 ARG 0.005 0.000 ARG F 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23974.01 seconds wall clock time: 411 minutes 24.45 seconds (24684.45 seconds total)