Starting phenix.real_space_refine on Sun Sep 29 16:46:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/09_2024/7mim_23856.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/09_2024/7mim_23856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/09_2024/7mim_23856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/09_2024/7mim_23856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/09_2024/7mim_23856.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/09_2024/7mim_23856.cif" } resolution = 3.42 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 124 5.16 5 Na 4 4.78 5 C 15064 2.51 5 N 3476 2.21 5 O 4024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22728 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 471 Unusual residues: {' NA': 3, 'POV': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 469 Unusual residues: {' NA': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Restraints were copied for chains: C Time building chain proxies: 18.50, per 1000 atoms: 0.81 Number of scatterers: 22728 At special positions: 0 Unit cell: (129.285, 129.285, 132.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 36 15.00 Na 4 11.00 O 4024 8.00 N 3476 7.00 C 15064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 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: 4.89 Conformation dependent library (CDL) restraints added in 2.7 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 62.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.873A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.514A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.516A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.519A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.829A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.568A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.522A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.798A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.763A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.502A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.537A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.558A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.529A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.709A pdb=" N ARG A 371 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.568A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.242A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.615A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 508 removed outlier: 3.655A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.699A pdb=" N ILE A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 517' Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.946A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 4.295A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 570 through 586 removed outlier: 3.626A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.561A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 4.071A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.686A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 685 removed outlier: 4.269A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.513A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.570A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 removed outlier: 3.514A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 removed outlier: 3.517A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.519A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.829A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.569A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.522A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.798A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.763A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.502A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.537A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.559A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.528A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.708A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.568A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.242A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.615A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 508 removed outlier: 3.655A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 517 removed outlier: 3.698A pdb=" N ILE B 516 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 512 through 517' Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.946A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 removed outlier: 4.295A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 564 No H-bonds generated for 'chain 'B' and resid 562 through 564' Processing helix chain 'B' and resid 570 through 586 removed outlier: 3.626A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 576 " --> pdb=" O MET B 572 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.562A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 4.071A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 removed outlier: 3.685A pdb=" N LEU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 4.269A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.513A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.570A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.514A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 removed outlier: 3.517A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.519A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.829A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.569A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.523A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.797A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.763A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.502A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.537A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.559A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.528A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.709A pdb=" N ARG C 371 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.569A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.242A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.616A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 508 removed outlier: 3.655A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 517 removed outlier: 3.698A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 512 through 517' Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.946A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 561 removed outlier: 4.294A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 564 No H-bonds generated for 'chain 'C' and resid 562 through 564' Processing helix chain 'C' and resid 570 through 586 removed outlier: 3.626A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 576 " --> pdb=" O MET C 572 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.562A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 4.071A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 removed outlier: 3.686A pdb=" N LEU C 655 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 685 removed outlier: 4.269A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 705 removed outlier: 3.513A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.570A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 148 removed outlier: 3.514A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.516A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.518A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.829A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.569A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.523A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.798A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.764A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.502A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.537A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.559A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.528A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 removed outlier: 3.708A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER D 372 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.568A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.242A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.615A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 508 removed outlier: 3.657A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 517 removed outlier: 3.699A pdb=" N ILE D 516 " --> pdb=" O ASP D 512 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 512 through 517' Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.945A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 561 removed outlier: 4.295A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 564 No H-bonds generated for 'chain 'D' and resid 562 through 564' Processing helix chain 'D' and resid 570 through 586 removed outlier: 3.626A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.562A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 4.071A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 removed outlier: 3.686A pdb=" N LEU D 655 " --> pdb=" O PRO D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 685 removed outlier: 4.270A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 705 removed outlier: 3.513A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 7.341A pdb=" N LYS A 376 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP A 391 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 722 through 724 removed outlier: 7.200A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 382 removed outlier: 7.341A pdb=" N LYS B 376 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP B 391 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 385 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 722 through 724 removed outlier: 7.200A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 376 through 382 removed outlier: 7.341A pdb=" N LYS C 376 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP C 391 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 385 " --> pdb=" O TYR C 382 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 722 through 724 removed outlier: 7.200A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 382 removed outlier: 7.341A pdb=" N LYS D 376 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP D 391 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 385 " --> pdb=" O TYR D 382 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 722 through 724 removed outlier: 7.200A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 804 hydrogen bonds defined for protein. 2400 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: 5.66 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3432 1.31 - 1.44: 6004 1.44 - 1.56: 13432 1.56 - 1.69: 72 1.69 - 1.82: 204 Bond restraints: 23144 Sorted by residual: bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.336 1.397 -0.061 1.20e-02 6.94e+03 2.60e+01 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.336 1.396 -0.060 1.20e-02 6.94e+03 2.52e+01 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.336 1.396 -0.060 1.20e-02 6.94e+03 2.51e+01 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.336 1.396 -0.060 1.20e-02 6.94e+03 2.50e+01 bond pdb=" C21 POV D 905 " pdb=" O21 POV D 905 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 23139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 29584 2.49 - 4.99: 858 4.99 - 7.48: 298 7.48 - 9.97: 120 9.97 - 12.46: 108 Bond angle restraints: 30968 Sorted by residual: angle pdb=" C ASP B 468 " pdb=" N LEU B 469 " pdb=" CA LEU B 469 " ideal model delta sigma weight residual 120.09 127.05 -6.96 1.25e+00 6.40e-01 3.10e+01 angle pdb=" C ASP A 468 " pdb=" N LEU A 469 " pdb=" CA LEU A 469 " ideal model delta sigma weight residual 120.09 127.01 -6.92 1.25e+00 6.40e-01 3.07e+01 angle pdb=" C ASP C 468 " pdb=" N LEU C 469 " pdb=" CA LEU C 469 " ideal model delta sigma weight residual 120.09 127.00 -6.91 1.25e+00 6.40e-01 3.05e+01 angle pdb=" C ASP D 468 " pdb=" N LEU D 469 " pdb=" CA LEU D 469 " ideal model delta sigma weight residual 120.09 127.00 -6.91 1.25e+00 6.40e-01 3.05e+01 angle pdb=" C GLU D 367 " pdb=" N LYS D 368 " pdb=" CA LYS D 368 " ideal model delta sigma weight residual 120.09 126.02 -5.93 1.25e+00 6.40e-01 2.25e+01 ... (remaining 30963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.61: 13296 29.61 - 59.22: 807 59.22 - 88.83: 142 88.83 - 118.45: 32 118.45 - 148.06: 20 Dihedral angle restraints: 14297 sinusoidal: 6741 harmonic: 7556 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.85 65.85 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.85 65.85 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.82 65.82 1 1.00e+01 1.00e-02 5.67e+01 ... (remaining 14294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2606 0.058 - 0.116: 597 0.116 - 0.173: 93 0.173 - 0.231: 21 0.231 - 0.289: 11 Chirality restraints: 3328 Sorted by residual: chirality pdb=" CG LEU D 469 " pdb=" CB LEU D 469 " pdb=" CD1 LEU D 469 " pdb=" CD2 LEU D 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU C 469 " pdb=" CB LEU C 469 " pdb=" CD1 LEU C 469 " pdb=" CD2 LEU C 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU B 469 " pdb=" CB LEU B 469 " pdb=" CD1 LEU B 469 " pdb=" CD2 LEU B 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3325 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 383 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 384 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 384 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 384 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 383 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 384 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 383 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 384 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " 0.030 5.00e-02 4.00e+02 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 129 2.60 - 3.18: 16828 3.18 - 3.75: 30071 3.75 - 4.33: 44197 4.33 - 4.90: 73303 Nonbonded interactions: 164528 Sorted by model distance: nonbonded pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " model vdw 2.031 3.760 nonbonded pdb=" O LEU C 469 " pdb=" OH TYR C 540 " model vdw 2.327 3.040 nonbonded pdb=" O LEU D 469 " pdb=" OH TYR D 540 " model vdw 2.328 3.040 nonbonded pdb=" O LEU B 469 " pdb=" OH TYR B 540 " model vdw 2.328 3.040 nonbonded pdb=" O LEU A 469 " pdb=" OH TYR A 540 " model vdw 2.328 3.040 ... (remaining 164523 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 118 through 757 or resid 901 through 909)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 118 through 757 or resid 901 through 909)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 51.830 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 : 0.010 0.093 23144 Z= 0.605 Angle : 1.366 12.463 30968 Z= 0.572 Chirality : 0.054 0.289 3328 Planarity : 0.006 0.054 3712 Dihedral : 19.541 148.058 9384 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.95 (0.10), residues: 2552 helix: -4.76 (0.04), residues: 1456 sheet: 0.62 (0.60), residues: 76 loop : -2.75 (0.15), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 433 HIS 0.005 0.001 HIS A 301 PHE 0.020 0.002 PHE A 436 TYR 0.014 0.002 TYR D 451 ARG 0.009 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 2.546 Fit side-chains REVERT: A 121 LYS cc_start: 0.8366 (mttm) cc_final: 0.7949 (mtmt) REVERT: A 129 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8072 (mm-30) REVERT: A 323 MET cc_start: 0.8469 (ttm) cc_final: 0.8120 (ttp) REVERT: A 509 ARG cc_start: 0.6111 (ptp-170) cc_final: 0.5896 (mtm110) REVERT: A 561 ASN cc_start: 0.9119 (m-40) cc_final: 0.8832 (m-40) REVERT: A 743 LYS cc_start: 0.8867 (ptpt) cc_final: 0.8564 (ptmm) REVERT: B 121 LYS cc_start: 0.8366 (mttm) cc_final: 0.7948 (mtmt) REVERT: B 129 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 141 ASP cc_start: 0.7769 (m-30) cc_final: 0.7511 (m-30) REVERT: B 323 MET cc_start: 0.8447 (ttm) cc_final: 0.8099 (ttp) REVERT: B 509 ARG cc_start: 0.6097 (ptp-170) cc_final: 0.5890 (mtm110) REVERT: B 561 ASN cc_start: 0.9075 (m-40) cc_final: 0.8789 (m-40) REVERT: B 743 LYS cc_start: 0.8864 (ptpt) cc_final: 0.8554 (ptmm) REVERT: C 121 LYS cc_start: 0.8396 (mttm) cc_final: 0.7972 (mtmt) REVERT: C 129 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8079 (mm-30) REVERT: C 141 ASP cc_start: 0.7769 (m-30) cc_final: 0.7512 (m-30) REVERT: C 323 MET cc_start: 0.8463 (ttm) cc_final: 0.8112 (ttp) REVERT: C 561 ASN cc_start: 0.9101 (m-40) cc_final: 0.8808 (m-40) REVERT: C 743 LYS cc_start: 0.8858 (ptpt) cc_final: 0.8555 (ptmm) REVERT: D 121 LYS cc_start: 0.8404 (mttm) cc_final: 0.7980 (mtmt) REVERT: D 129 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8079 (mm-30) REVERT: D 141 ASP cc_start: 0.7780 (m-30) cc_final: 0.7422 (m-30) REVERT: D 323 MET cc_start: 0.8499 (ttm) cc_final: 0.8156 (ttp) REVERT: D 509 ARG cc_start: 0.6144 (ptp-170) cc_final: 0.5933 (mtm110) REVERT: D 561 ASN cc_start: 0.9136 (m-40) cc_final: 0.8804 (m-40) REVERT: D 743 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8565 (ptmm) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.3981 time to fit residues: 236.9533 Evaluate side-chains 255 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.0370 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 227 GLN A 394 ASN A 452 ASN A 477 HIS A 735 ASN B 220 ASN B 227 GLN B 394 ASN B 452 ASN B 477 HIS B 735 ASN C 220 ASN C 227 GLN C 394 ASN C 452 ASN C 477 HIS C 735 ASN D 220 ASN D 227 GLN D 394 ASN D 452 ASN D 477 HIS D 735 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23144 Z= 0.154 Angle : 0.546 8.154 30968 Z= 0.283 Chirality : 0.040 0.155 3328 Planarity : 0.005 0.063 3712 Dihedral : 21.260 120.903 4336 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.36 % Allowed : 7.66 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.13), residues: 2552 helix: -2.62 (0.10), residues: 1528 sheet: 0.99 (0.64), residues: 76 loop : -2.45 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 710 HIS 0.002 0.001 HIS D 301 PHE 0.023 0.001 PHE C 193 TYR 0.014 0.001 TYR B 575 ARG 0.004 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 334 time to evaluate : 2.408 Fit side-chains REVERT: A 121 LYS cc_start: 0.8142 (mttm) cc_final: 0.7727 (mtpp) REVERT: A 173 MET cc_start: 0.7815 (mtt) cc_final: 0.7608 (mtt) REVERT: A 323 MET cc_start: 0.8229 (ttm) cc_final: 0.7873 (ttp) REVERT: A 447 PHE cc_start: 0.8469 (m-10) cc_final: 0.8166 (m-80) REVERT: A 488 MET cc_start: 0.7225 (tpp) cc_final: 0.6834 (mtp) REVERT: A 509 ARG cc_start: 0.5807 (ptp-170) cc_final: 0.5507 (mtm110) REVERT: A 546 GLU cc_start: 0.8061 (tp30) cc_final: 0.7496 (mm-30) REVERT: A 707 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7823 (pp) REVERT: A 743 LYS cc_start: 0.8876 (ptpt) cc_final: 0.8565 (ptmm) REVERT: B 121 LYS cc_start: 0.8141 (mttm) cc_final: 0.7727 (mtpp) REVERT: B 173 MET cc_start: 0.7792 (mtt) cc_final: 0.7583 (mtt) REVERT: B 323 MET cc_start: 0.8187 (ttm) cc_final: 0.7834 (ttp) REVERT: B 447 PHE cc_start: 0.8451 (m-10) cc_final: 0.8153 (m-80) REVERT: B 488 MET cc_start: 0.7236 (tpp) cc_final: 0.6850 (mtp) REVERT: B 509 ARG cc_start: 0.5796 (ptp-170) cc_final: 0.5495 (mtm110) REVERT: B 546 GLU cc_start: 0.8041 (tp30) cc_final: 0.7422 (mm-30) REVERT: B 618 ASP cc_start: 0.7062 (m-30) cc_final: 0.6805 (p0) REVERT: B 707 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7788 (pp) REVERT: B 743 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8557 (ptmm) REVERT: C 121 LYS cc_start: 0.8158 (mttm) cc_final: 0.7742 (mtpp) REVERT: C 173 MET cc_start: 0.7816 (mtt) cc_final: 0.7611 (mtt) REVERT: C 323 MET cc_start: 0.8221 (ttm) cc_final: 0.7856 (ttp) REVERT: C 447 PHE cc_start: 0.8491 (m-10) cc_final: 0.8180 (m-80) REVERT: C 488 MET cc_start: 0.7240 (tpp) cc_final: 0.6855 (mtp) REVERT: C 546 GLU cc_start: 0.8050 (tp30) cc_final: 0.7431 (mm-30) REVERT: C 618 ASP cc_start: 0.7054 (m-30) cc_final: 0.6800 (p0) REVERT: C 707 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7808 (pp) REVERT: C 743 LYS cc_start: 0.8870 (ptpt) cc_final: 0.8555 (ptmm) REVERT: D 121 LYS cc_start: 0.8184 (mttm) cc_final: 0.7769 (mtpp) REVERT: D 323 MET cc_start: 0.8266 (ttm) cc_final: 0.7919 (ttp) REVERT: D 447 PHE cc_start: 0.8476 (m-10) cc_final: 0.8190 (m-80) REVERT: D 488 MET cc_start: 0.7387 (tpp) cc_final: 0.6894 (mtp) REVERT: D 509 ARG cc_start: 0.5818 (ptp-170) cc_final: 0.5528 (mtm110) REVERT: D 546 GLU cc_start: 0.8070 (tp30) cc_final: 0.7519 (mm-30) REVERT: D 743 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8565 (ptmm) outliers start: 31 outliers final: 4 residues processed: 353 average time/residue: 0.3825 time to fit residues: 199.9363 Evaluate side-chains 276 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 269 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 519 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 232 optimal weight: 0.8980 chunk 251 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 561 ASN B 244 HIS B 561 ASN C 244 HIS C 561 ASN D 244 HIS D 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23144 Z= 0.165 Angle : 0.513 8.688 30968 Z= 0.258 Chirality : 0.039 0.134 3328 Planarity : 0.004 0.060 3712 Dihedral : 19.246 106.721 4336 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.93 % Allowed : 8.67 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2552 helix: -1.08 (0.13), residues: 1520 sheet: 1.11 (0.65), residues: 76 loop : -2.31 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 710 HIS 0.003 0.001 HIS A 471 PHE 0.015 0.001 PHE C 193 TYR 0.019 0.001 TYR B 540 ARG 0.011 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 296 time to evaluate : 2.493 Fit side-chains REVERT: A 121 LYS cc_start: 0.8157 (mttm) cc_final: 0.7758 (mtpp) REVERT: A 253 LYS cc_start: 0.7490 (ttpt) cc_final: 0.7221 (ttpp) REVERT: A 323 MET cc_start: 0.8116 (ttm) cc_final: 0.7868 (ttp) REVERT: A 447 PHE cc_start: 0.8436 (m-10) cc_final: 0.8169 (m-80) REVERT: A 488 MET cc_start: 0.7212 (tpp) cc_final: 0.6875 (mtp) REVERT: A 509 ARG cc_start: 0.5929 (ptp-170) cc_final: 0.5455 (mtm110) REVERT: A 546 GLU cc_start: 0.8063 (tp30) cc_final: 0.7401 (mm-30) REVERT: A 743 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8499 (ptmm) REVERT: B 121 LYS cc_start: 0.8147 (mttm) cc_final: 0.7753 (mtpp) REVERT: B 253 LYS cc_start: 0.7491 (ttpt) cc_final: 0.7222 (ttpp) REVERT: B 323 MET cc_start: 0.8092 (ttm) cc_final: 0.7845 (ttp) REVERT: B 447 PHE cc_start: 0.8441 (m-10) cc_final: 0.8185 (m-80) REVERT: B 488 MET cc_start: 0.7215 (tpp) cc_final: 0.6888 (mtp) REVERT: B 509 ARG cc_start: 0.5920 (ptp-170) cc_final: 0.5448 (mtm110) REVERT: B 546 GLU cc_start: 0.8026 (tp30) cc_final: 0.7390 (mm-30) REVERT: B 743 LYS cc_start: 0.8908 (ptpt) cc_final: 0.8497 (ptmm) REVERT: C 121 LYS cc_start: 0.8164 (mttm) cc_final: 0.7769 (mtpp) REVERT: C 323 MET cc_start: 0.8112 (ttm) cc_final: 0.7860 (ttp) REVERT: C 447 PHE cc_start: 0.8436 (m-10) cc_final: 0.8168 (m-80) REVERT: C 488 MET cc_start: 0.7190 (tpp) cc_final: 0.6776 (mtp) REVERT: C 546 GLU cc_start: 0.8045 (tp30) cc_final: 0.7409 (mm-30) REVERT: C 743 LYS cc_start: 0.8911 (ptpt) cc_final: 0.8492 (ptmm) REVERT: D 121 LYS cc_start: 0.8189 (mttm) cc_final: 0.7779 (mtpp) REVERT: D 253 LYS cc_start: 0.7552 (ttpt) cc_final: 0.7280 (ttpp) REVERT: D 323 MET cc_start: 0.8158 (ttm) cc_final: 0.7909 (ttp) REVERT: D 447 PHE cc_start: 0.8448 (m-10) cc_final: 0.8207 (m-80) REVERT: D 488 MET cc_start: 0.7276 (tpp) cc_final: 0.6859 (mtp) REVERT: D 509 ARG cc_start: 0.5938 (ptp-170) cc_final: 0.5476 (mtm110) REVERT: D 546 GLU cc_start: 0.8066 (tp30) cc_final: 0.7443 (mm-30) REVERT: D 743 LYS cc_start: 0.8918 (ptpt) cc_final: 0.8505 (ptmm) outliers start: 44 outliers final: 20 residues processed: 321 average time/residue: 0.4093 time to fit residues: 195.5843 Evaluate side-chains 291 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 0.4980 chunk 122 optimal weight: 0.4980 chunk 221 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23144 Z= 0.147 Angle : 0.485 8.703 30968 Z= 0.245 Chirality : 0.039 0.139 3328 Planarity : 0.004 0.059 3712 Dihedral : 18.044 103.582 4336 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.23 % Allowed : 9.37 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.16), residues: 2552 helix: -0.22 (0.13), residues: 1508 sheet: 1.04 (0.64), residues: 76 loop : -2.05 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 710 HIS 0.004 0.001 HIS C 471 PHE 0.012 0.001 PHE D 193 TYR 0.016 0.001 TYR B 540 ARG 0.010 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 285 time to evaluate : 2.441 Fit side-chains REVERT: A 121 LYS cc_start: 0.8162 (mttm) cc_final: 0.7750 (mtpp) REVERT: A 253 LYS cc_start: 0.7480 (ttpt) cc_final: 0.7209 (ttpp) REVERT: A 447 PHE cc_start: 0.8435 (m-10) cc_final: 0.8153 (m-80) REVERT: A 488 MET cc_start: 0.7218 (tpp) cc_final: 0.6840 (mtp) REVERT: A 509 ARG cc_start: 0.5870 (ptp-170) cc_final: 0.5442 (mtm110) REVERT: A 546 GLU cc_start: 0.8050 (tp30) cc_final: 0.7323 (mm-30) REVERT: A 743 LYS cc_start: 0.8848 (ptpt) cc_final: 0.8423 (ptmm) REVERT: B 121 LYS cc_start: 0.8171 (mttm) cc_final: 0.7724 (mtpp) REVERT: B 253 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7206 (ttpp) REVERT: B 320 MET cc_start: 0.8191 (mmm) cc_final: 0.7981 (mtp) REVERT: B 447 PHE cc_start: 0.8416 (m-10) cc_final: 0.8142 (m-80) REVERT: B 488 MET cc_start: 0.7215 (tpp) cc_final: 0.6834 (mtp) REVERT: B 509 ARG cc_start: 0.5862 (ptp-170) cc_final: 0.5435 (mtm110) REVERT: B 546 GLU cc_start: 0.7980 (tp30) cc_final: 0.7296 (mm-30) REVERT: B 743 LYS cc_start: 0.8832 (ptpt) cc_final: 0.8418 (ptmm) REVERT: C 121 LYS cc_start: 0.8220 (mttm) cc_final: 0.7767 (mtpp) REVERT: C 320 MET cc_start: 0.8198 (mmm) cc_final: 0.7994 (mtp) REVERT: C 447 PHE cc_start: 0.8435 (m-10) cc_final: 0.8153 (m-80) REVERT: C 488 MET cc_start: 0.7223 (tpp) cc_final: 0.6831 (mtp) REVERT: C 546 GLU cc_start: 0.8002 (tp30) cc_final: 0.7257 (mm-30) REVERT: C 743 LYS cc_start: 0.8845 (ptpt) cc_final: 0.8419 (ptmm) REVERT: D 121 LYS cc_start: 0.8203 (mttm) cc_final: 0.7807 (mtpp) REVERT: D 253 LYS cc_start: 0.7489 (ttpt) cc_final: 0.7195 (ttpp) REVERT: D 447 PHE cc_start: 0.8444 (m-10) cc_final: 0.8194 (m-80) REVERT: D 488 MET cc_start: 0.7298 (tpp) cc_final: 0.6897 (mtp) REVERT: D 509 ARG cc_start: 0.5882 (ptp-170) cc_final: 0.5462 (mtm110) REVERT: D 546 GLU cc_start: 0.8031 (tp30) cc_final: 0.7304 (mm-30) REVERT: D 743 LYS cc_start: 0.8857 (ptpt) cc_final: 0.8433 (ptmm) outliers start: 28 outliers final: 14 residues processed: 297 average time/residue: 0.3808 time to fit residues: 168.7709 Evaluate side-chains 269 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 255 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN B 452 ASN C 452 ASN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 23144 Z= 0.312 Angle : 0.580 8.717 30968 Z= 0.293 Chirality : 0.043 0.155 3328 Planarity : 0.004 0.055 3712 Dihedral : 18.476 108.552 4336 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.97 % Allowed : 10.77 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2552 helix: -0.19 (0.13), residues: 1548 sheet: 1.16 (0.65), residues: 76 loop : -2.16 (0.17), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 559 HIS 0.005 0.001 HIS B 471 PHE 0.020 0.001 PHE D 193 TYR 0.016 0.002 TYR B 540 ARG 0.010 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 230 time to evaluate : 2.366 Fit side-chains REVERT: A 364 GLU cc_start: 0.7953 (pt0) cc_final: 0.7559 (pm20) REVERT: A 447 PHE cc_start: 0.8516 (m-10) cc_final: 0.8201 (m-80) REVERT: A 452 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7908 (m110) REVERT: A 546 GLU cc_start: 0.8212 (tp30) cc_final: 0.7468 (mm-30) REVERT: A 679 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7490 (tt0) REVERT: B 320 MET cc_start: 0.8410 (mmm) cc_final: 0.7262 (mmm) REVERT: B 364 GLU cc_start: 0.7999 (pt0) cc_final: 0.7560 (pm20) REVERT: B 447 PHE cc_start: 0.8500 (m-10) cc_final: 0.8191 (m-80) REVERT: B 452 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7886 (m110) REVERT: B 546 GLU cc_start: 0.8184 (tp30) cc_final: 0.7451 (mm-30) REVERT: C 320 MET cc_start: 0.8423 (mmm) cc_final: 0.7202 (mmm) REVERT: C 364 GLU cc_start: 0.7947 (pt0) cc_final: 0.7554 (pm20) REVERT: C 447 PHE cc_start: 0.8515 (m-10) cc_final: 0.8201 (m-80) REVERT: C 452 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7905 (m110) REVERT: C 546 GLU cc_start: 0.8188 (tp30) cc_final: 0.7446 (mm-30) REVERT: C 679 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7491 (tt0) REVERT: D 364 GLU cc_start: 0.7928 (pt0) cc_final: 0.7556 (pm20) REVERT: D 447 PHE cc_start: 0.8532 (m-10) cc_final: 0.8223 (m-80) REVERT: D 546 GLU cc_start: 0.8214 (tp30) cc_final: 0.7483 (mm-30) outliers start: 45 outliers final: 24 residues processed: 264 average time/residue: 0.3852 time to fit residues: 152.5781 Evaluate side-chains 244 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 217 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.0980 chunk 222 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 452 ASN B 178 ASN B 452 ASN C 178 ASN C 452 ASN D 178 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23144 Z= 0.139 Angle : 0.480 10.217 30968 Z= 0.244 Chirality : 0.039 0.150 3328 Planarity : 0.004 0.055 3712 Dihedral : 17.496 103.455 4336 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.44 % Allowed : 10.64 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2552 helix: 0.51 (0.14), residues: 1520 sheet: 1.05 (0.65), residues: 76 loop : -1.88 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 710 HIS 0.002 0.000 HIS D 301 PHE 0.017 0.001 PHE D 193 TYR 0.017 0.001 TYR D 540 ARG 0.004 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 242 time to evaluate : 2.505 Fit side-chains REVERT: A 447 PHE cc_start: 0.8357 (m-10) cc_final: 0.8092 (m-80) REVERT: A 475 LEU cc_start: 0.1393 (OUTLIER) cc_final: 0.1154 (tm) REVERT: A 488 MET cc_start: 0.7205 (mmt) cc_final: 0.6362 (mtp) REVERT: A 509 ARG cc_start: 0.5671 (ptp-110) cc_final: 0.5170 (mtm-85) REVERT: A 546 GLU cc_start: 0.8193 (tp30) cc_final: 0.7470 (mm-30) REVERT: A 712 ARG cc_start: 0.7198 (mmm-85) cc_final: 0.6495 (mmm160) REVERT: B 320 MET cc_start: 0.8137 (mmm) cc_final: 0.7556 (mmm) REVERT: B 447 PHE cc_start: 0.8371 (m-10) cc_final: 0.8077 (m-80) REVERT: B 475 LEU cc_start: 0.1325 (OUTLIER) cc_final: 0.1095 (tm) REVERT: B 488 MET cc_start: 0.7172 (mmt) cc_final: 0.6338 (mtp) REVERT: B 509 ARG cc_start: 0.5666 (ptp-110) cc_final: 0.5164 (mtm-85) REVERT: B 546 GLU cc_start: 0.8179 (tp30) cc_final: 0.7414 (mm-30) REVERT: B 712 ARG cc_start: 0.7177 (mmm-85) cc_final: 0.6478 (mmm160) REVERT: C 320 MET cc_start: 0.8211 (mmm) cc_final: 0.7543 (mmm) REVERT: C 447 PHE cc_start: 0.8386 (m-10) cc_final: 0.8086 (m-80) REVERT: C 475 LEU cc_start: 0.1344 (OUTLIER) cc_final: 0.1117 (tm) REVERT: C 488 MET cc_start: 0.7169 (mmt) cc_final: 0.6338 (mtp) REVERT: C 546 GLU cc_start: 0.8168 (tp30) cc_final: 0.7456 (mm-30) REVERT: C 712 ARG cc_start: 0.7196 (mmm-85) cc_final: 0.6495 (mmm160) REVERT: D 447 PHE cc_start: 0.8416 (m-10) cc_final: 0.8127 (m-80) REVERT: D 475 LEU cc_start: 0.1619 (OUTLIER) cc_final: 0.1391 (tm) REVERT: D 488 MET cc_start: 0.7278 (tpp) cc_final: 0.6912 (mtp) REVERT: D 509 ARG cc_start: 0.5689 (ptp-110) cc_final: 0.5192 (mtm-85) REVERT: D 546 GLU cc_start: 0.8209 (tp30) cc_final: 0.7493 (mm-30) outliers start: 33 outliers final: 16 residues processed: 269 average time/residue: 0.3928 time to fit residues: 157.4563 Evaluate side-chains 236 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 140 optimal weight: 0.4980 chunk 208 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 chunk 246 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 113 optimal weight: 0.0870 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN B 452 ASN C 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23144 Z= 0.187 Angle : 0.502 9.528 30968 Z= 0.255 Chirality : 0.040 0.143 3328 Planarity : 0.003 0.055 3712 Dihedral : 17.398 104.233 4336 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.58 % Allowed : 11.21 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2552 helix: 0.80 (0.14), residues: 1512 sheet: 1.06 (0.65), residues: 76 loop : -1.81 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 710 HIS 0.003 0.001 HIS A 471 PHE 0.015 0.001 PHE D 193 TYR 0.017 0.001 TYR A 540 ARG 0.005 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 2.641 Fit side-chains REVERT: A 447 PHE cc_start: 0.8447 (m-10) cc_final: 0.8143 (m-80) REVERT: A 475 LEU cc_start: 0.1389 (OUTLIER) cc_final: 0.1164 (tm) REVERT: A 509 ARG cc_start: 0.5667 (ptp-110) cc_final: 0.5454 (ptp90) REVERT: A 546 GLU cc_start: 0.8155 (tp30) cc_final: 0.7442 (mm-30) REVERT: B 320 MET cc_start: 0.8320 (mmm) cc_final: 0.7676 (mmm) REVERT: B 447 PHE cc_start: 0.8395 (m-10) cc_final: 0.8089 (m-80) REVERT: B 475 LEU cc_start: 0.1367 (OUTLIER) cc_final: 0.1140 (tm) REVERT: B 509 ARG cc_start: 0.5630 (ptp-110) cc_final: 0.5412 (ptp90) REVERT: B 546 GLU cc_start: 0.8177 (tp30) cc_final: 0.7430 (mm-30) REVERT: C 447 PHE cc_start: 0.8265 (m-10) cc_final: 0.7939 (m-80) REVERT: C 475 LEU cc_start: 0.1376 (OUTLIER) cc_final: 0.1157 (tm) REVERT: C 546 GLU cc_start: 0.8119 (tp30) cc_final: 0.7418 (mm-30) REVERT: D 447 PHE cc_start: 0.8479 (m-10) cc_final: 0.8176 (m-80) REVERT: D 475 LEU cc_start: 0.1916 (OUTLIER) cc_final: 0.1533 (tm) REVERT: D 488 MET cc_start: 0.7305 (tpp) cc_final: 0.6931 (mtp) REVERT: D 509 ARG cc_start: 0.5653 (ptp-110) cc_final: 0.5438 (ptp90) REVERT: D 546 GLU cc_start: 0.8151 (tp30) cc_final: 0.7464 (mm-30) outliers start: 36 outliers final: 18 residues processed: 242 average time/residue: 0.4004 time to fit residues: 142.6847 Evaluate side-chains 231 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 209 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN C 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23144 Z= 0.251 Angle : 0.542 10.614 30968 Z= 0.274 Chirality : 0.042 0.145 3328 Planarity : 0.004 0.053 3712 Dihedral : 17.666 106.158 4336 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.44 % Allowed : 11.82 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2552 helix: 0.69 (0.14), residues: 1552 sheet: 1.04 (0.65), residues: 76 loop : -1.94 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 710 HIS 0.003 0.001 HIS A 301 PHE 0.013 0.001 PHE C 316 TYR 0.014 0.001 TYR A 540 ARG 0.006 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 2.637 Fit side-chains REVERT: A 153 ASP cc_start: 0.6767 (m-30) cc_final: 0.6362 (p0) REVERT: A 364 GLU cc_start: 0.7935 (pt0) cc_final: 0.7545 (pm20) REVERT: A 447 PHE cc_start: 0.8335 (m-10) cc_final: 0.7999 (m-80) REVERT: A 475 LEU cc_start: 0.1378 (OUTLIER) cc_final: 0.1149 (tm) REVERT: A 509 ARG cc_start: 0.5581 (ptp-110) cc_final: 0.5365 (ptp90) REVERT: A 546 GLU cc_start: 0.8238 (tp30) cc_final: 0.7485 (mm-30) REVERT: A 707 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7834 (pp) REVERT: B 153 ASP cc_start: 0.6769 (m-30) cc_final: 0.6360 (p0) REVERT: B 320 MET cc_start: 0.8372 (mmm) cc_final: 0.7199 (mmm) REVERT: B 364 GLU cc_start: 0.7946 (pt0) cc_final: 0.7542 (pm20) REVERT: B 447 PHE cc_start: 0.8278 (m-10) cc_final: 0.7936 (m-80) REVERT: B 475 LEU cc_start: 0.1319 (OUTLIER) cc_final: 0.1089 (tm) REVERT: B 509 ARG cc_start: 0.5573 (ptp-110) cc_final: 0.5358 (ptp90) REVERT: B 546 GLU cc_start: 0.8199 (tp30) cc_final: 0.7458 (mm-30) REVERT: B 707 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7785 (pp) REVERT: C 153 ASP cc_start: 0.6762 (m-30) cc_final: 0.6364 (p0) REVERT: C 320 MET cc_start: 0.8296 (mmm) cc_final: 0.7756 (mmm) REVERT: C 364 GLU cc_start: 0.7937 (pt0) cc_final: 0.7543 (pm20) REVERT: C 447 PHE cc_start: 0.8294 (m-10) cc_final: 0.7946 (m-80) REVERT: C 475 LEU cc_start: 0.1329 (OUTLIER) cc_final: 0.1097 (tm) REVERT: C 546 GLU cc_start: 0.8209 (tp30) cc_final: 0.7465 (mm-30) REVERT: C 707 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7795 (pp) REVERT: D 153 ASP cc_start: 0.6756 (m-30) cc_final: 0.6391 (p0) REVERT: D 364 GLU cc_start: 0.7894 (pt0) cc_final: 0.7539 (pm20) REVERT: D 447 PHE cc_start: 0.8376 (m-10) cc_final: 0.8032 (m-80) REVERT: D 475 LEU cc_start: 0.2465 (OUTLIER) cc_final: 0.1916 (tm) REVERT: D 509 ARG cc_start: 0.5594 (ptp-110) cc_final: 0.5382 (ptp90) REVERT: D 546 GLU cc_start: 0.8241 (tp30) cc_final: 0.7519 (mm-30) outliers start: 33 outliers final: 18 residues processed: 246 average time/residue: 0.4194 time to fit residues: 152.2853 Evaluate side-chains 235 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 210 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 229 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 150 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23144 Z= 0.135 Angle : 0.481 10.315 30968 Z= 0.245 Chirality : 0.039 0.147 3328 Planarity : 0.004 0.063 3712 Dihedral : 16.691 101.747 4336 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.05 % Allowed : 12.22 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2552 helix: 1.24 (0.14), residues: 1520 sheet: 0.95 (0.65), residues: 76 loop : -1.63 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 710 HIS 0.002 0.000 HIS B 301 PHE 0.013 0.001 PHE D 193 TYR 0.019 0.001 TYR B 540 ARG 0.014 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 227 time to evaluate : 2.437 Fit side-chains REVERT: A 153 ASP cc_start: 0.6617 (m-30) cc_final: 0.6156 (p0) REVERT: A 447 PHE cc_start: 0.8271 (m-10) cc_final: 0.7972 (m-80) REVERT: A 475 LEU cc_start: 0.1306 (OUTLIER) cc_final: 0.1098 (tm) REVERT: A 546 GLU cc_start: 0.8107 (tp30) cc_final: 0.7444 (mm-30) REVERT: B 320 MET cc_start: 0.8220 (mmm) cc_final: 0.7578 (mmm) REVERT: B 447 PHE cc_start: 0.8224 (m-10) cc_final: 0.7917 (m-80) REVERT: B 475 LEU cc_start: 0.1293 (OUTLIER) cc_final: 0.1086 (tm) REVERT: B 546 GLU cc_start: 0.8068 (tp30) cc_final: 0.7412 (mm-30) REVERT: C 153 ASP cc_start: 0.6613 (m-30) cc_final: 0.6156 (p0) REVERT: C 320 MET cc_start: 0.8018 (mmm) cc_final: 0.7401 (mmm) REVERT: C 447 PHE cc_start: 0.8237 (m-10) cc_final: 0.7925 (m-80) REVERT: C 475 LEU cc_start: 0.1426 (OUTLIER) cc_final: 0.1223 (tm) REVERT: C 546 GLU cc_start: 0.8076 (tp30) cc_final: 0.7347 (mm-30) REVERT: D 153 ASP cc_start: 0.6613 (m-30) cc_final: 0.6152 (p0) REVERT: D 447 PHE cc_start: 0.8309 (m-10) cc_final: 0.8003 (m-80) REVERT: D 475 LEU cc_start: 0.2623 (OUTLIER) cc_final: 0.2037 (tm) REVERT: D 488 MET cc_start: 0.7270 (tpp) cc_final: 0.6911 (mtp) REVERT: D 546 GLU cc_start: 0.8109 (tp30) cc_final: 0.7396 (mm-30) outliers start: 24 outliers final: 16 residues processed: 249 average time/residue: 0.3999 time to fit residues: 147.6774 Evaluate side-chains 241 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23144 Z= 0.159 Angle : 0.494 10.467 30968 Z= 0.250 Chirality : 0.039 0.139 3328 Planarity : 0.004 0.065 3712 Dihedral : 16.518 101.615 4336 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.83 % Allowed : 12.48 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2552 helix: 1.34 (0.14), residues: 1520 sheet: 1.00 (0.66), residues: 76 loop : -1.56 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 710 HIS 0.003 0.001 HIS A 301 PHE 0.013 0.001 PHE D 193 TYR 0.019 0.001 TYR D 540 ARG 0.015 0.001 ARG D 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 211 time to evaluate : 2.528 Fit side-chains REVERT: A 447 PHE cc_start: 0.8286 (m-10) cc_final: 0.7970 (m-80) REVERT: A 546 GLU cc_start: 0.8097 (tp30) cc_final: 0.7376 (mm-30) REVERT: A 611 LYS cc_start: 0.7186 (tptm) cc_final: 0.6922 (tppt) REVERT: B 320 MET cc_start: 0.8291 (mmm) cc_final: 0.7662 (mmm) REVERT: B 447 PHE cc_start: 0.8288 (m-10) cc_final: 0.7970 (m-80) REVERT: B 546 GLU cc_start: 0.8046 (tp30) cc_final: 0.7339 (mm-30) REVERT: B 611 LYS cc_start: 0.7194 (tptm) cc_final: 0.6919 (tppt) REVERT: C 320 MET cc_start: 0.8088 (mmm) cc_final: 0.7532 (mmm) REVERT: C 447 PHE cc_start: 0.8289 (m-10) cc_final: 0.7955 (m-80) REVERT: C 546 GLU cc_start: 0.8056 (tp30) cc_final: 0.7355 (mm-30) REVERT: C 555 MET cc_start: 0.8074 (mtm) cc_final: 0.7801 (mtm) REVERT: C 611 LYS cc_start: 0.7248 (tptm) cc_final: 0.6980 (tppt) REVERT: D 153 ASP cc_start: 0.6743 (m-30) cc_final: 0.6335 (p0) REVERT: D 447 PHE cc_start: 0.8309 (m-10) cc_final: 0.7976 (m-80) REVERT: D 475 LEU cc_start: 0.2657 (OUTLIER) cc_final: 0.2039 (tm) REVERT: D 488 MET cc_start: 0.7298 (tpp) cc_final: 0.6927 (mtp) REVERT: D 546 GLU cc_start: 0.8091 (tp30) cc_final: 0.7404 (mm-30) REVERT: D 555 MET cc_start: 0.8149 (mtm) cc_final: 0.7872 (mtm) outliers start: 19 outliers final: 15 residues processed: 229 average time/residue: 0.4003 time to fit residues: 135.2928 Evaluate side-chains 217 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 62 optimal weight: 0.0000 chunk 187 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 203 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101468 restraints weight = 28639.647| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.36 r_work: 0.2772 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23144 Z= 0.119 Angle : 0.481 10.742 30968 Z= 0.240 Chirality : 0.038 0.157 3328 Planarity : 0.004 0.060 3712 Dihedral : 15.753 97.028 4336 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.79 % Allowed : 12.61 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.17), residues: 2552 helix: 1.64 (0.14), residues: 1516 sheet: 0.99 (0.66), residues: 76 loop : -1.45 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 710 HIS 0.002 0.000 HIS C 471 PHE 0.014 0.001 PHE D 193 TYR 0.019 0.001 TYR A 540 ARG 0.014 0.001 ARG D 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4536.44 seconds wall clock time: 81 minutes 54.62 seconds (4914.62 seconds total)