Starting phenix.real_space_refine on Tue Oct 27 00:14:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mim_23856/10_2026/7mim_23856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mim_23856/10_2026/7mim_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mim_23856/10_2026/7mim_23856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mim_23856/10_2026/7mim_23856.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mim_23856/10_2026/7mim_23856.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mim_23856/10_2026/7mim_23856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mim_23856/10_2026/7mim_23856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mim_23856/10_2026/7mim_23856.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/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: 7.37, per 1000 atoms: 0.32 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=4, 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 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 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: 1.82 Conformation dependent library (CDL) restraints added in 915.1 milliseconds 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: 0.60 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: 2.92 Time building geometry restraints manager: 2.48 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: 13218 29.61 - 59.22: 681 59.22 - 88.83: 133 88.83 - 118.45: 32 118.45 - 148.06: 20 Dihedral angle restraints: 14084 sinusoidal: 6528 harmonic: 7556 Sorted by residual: dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.86 65.86 1 1.00e+01 1.00e-02 5.67e+01 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 ... (remaining 14081 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: 2.33 - 2.84: 6733 2.84 - 3.36: 18359 3.36 - 3.87: 32670 3.87 - 4.39: 38907 4.39 - 4.90: 67856 Nonbonded interactions: 164525 Sorted by model distance: 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 nonbonded pdb=" OD1 ASN C 298 " pdb=" ND1 HIS C 301 " model vdw 2.354 3.120 ... (remaining 164520 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 909) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 118 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: 1.510 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.190 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 23148 Z= 0.486 Angle : 1.366 12.463 30976 Z= 0.572 Chirality : 0.054 0.289 3328 Planarity : 0.006 0.054 3712 Dihedral : 18.848 148.058 9168 Min Nonbonded Distance : 2.327 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG B 149 TYR 0.014 0.002 TYR D 451 PHE 0.020 0.002 PHE A 436 TRP 0.012 0.002 TRP B 433 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.01013 / 0.49 (23144) covalent geometry : angle 1.36620 / 0.57 (30968) SS BOND : bond 0.00022 / 0.01 ( 4) SS BOND : angle 0.60603 / 0.39 ( 8) hydrogen bonds : bond 0.37044 / 24.23 ( 804) hydrogen bonds : angle 8.95720 / 6.28 ( 2400) *********************** 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 to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.905 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: 0.8397 (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: 0.8500 (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: 0.1702 time to fit residues: 103.0093 Evaluate side-chains 255 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 71] chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN A 227 GLN A 394 ASN A 452 ASN A 477 HIS B 220 ASN B 227 GLN B 394 ASN B 452 ASN B 477 HIS C 220 ASN C 227 GLN C 394 ASN C 452 ASN C 477 HIS D 220 ASN D 227 GLN D 394 ASN D 452 ASN D 477 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.097009 restraints weight = 30481.734| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.57 r_work: 0.2821 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23148 Z= 0.115 Angle : 0.549 8.041 30976 Z= 0.285 Chirality : 0.040 0.155 3328 Planarity : 0.005 0.062 3712 Dihedral : 20.531 121.402 4120 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.44 % Allowed : 7.62 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.13), residues: 2552 helix: -2.58 (0.10), residues: 1528 sheet: 1.01 (0.64), residues: 76 loop : -2.45 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 149 TYR 0.014 0.001 TYR A 575 PHE 0.023 0.001 PHE C 193 TRP 0.013 0.001 TRP C 710 HIS 0.002 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (23144) covalent geometry : angle 0.54865 / 0.29 (30968) SS BOND : bond 0.00074 / 0.04 ( 4) SS BOND : angle 0.08656 / 0.06 ( 8) hydrogen bonds : bond 0.05240 / 3.41 ( 804) hydrogen bonds : angle 3.85192 / 2.68 ( 2400) *********************** 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 367 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 334 time to evaluate : 0.794 Fit side-chains REVERT: A 121 LYS cc_start: 0.8484 (mttm) cc_final: 0.8022 (mtpp) REVERT: A 320 MET cc_start: 0.9009 (mmp) cc_final: 0.8204 (mmm) REVERT: A 323 MET cc_start: 0.8773 (ttm) cc_final: 0.8425 (ttp) REVERT: A 447 PHE cc_start: 0.8728 (m-10) cc_final: 0.8500 (m-80) REVERT: A 488 MET cc_start: 0.7599 (tpp) cc_final: 0.7196 (mtp) REVERT: A 509 ARG cc_start: 0.5856 (ptp-170) cc_final: 0.5613 (mtm110) REVERT: A 546 GLU cc_start: 0.8351 (tp30) cc_final: 0.7903 (mm-30) REVERT: A 618 ASP cc_start: 0.7206 (m-30) cc_final: 0.6965 (p0) REVERT: A 743 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8681 (ptmm) REVERT: B 121 LYS cc_start: 0.8477 (mttm) cc_final: 0.8015 (mtpp) REVERT: B 320 MET cc_start: 0.9006 (mmp) cc_final: 0.8193 (mmm) REVERT: B 323 MET cc_start: 0.8807 (ttm) cc_final: 0.8451 (ttp) REVERT: B 447 PHE cc_start: 0.8721 (m-10) cc_final: 0.8481 (m-80) REVERT: B 488 MET cc_start: 0.7586 (tpp) cc_final: 0.7192 (mtp) REVERT: B 509 ARG cc_start: 0.5859 (ptp-170) cc_final: 0.5611 (mtm110) REVERT: B 546 GLU cc_start: 0.8374 (tp30) cc_final: 0.7906 (mm-30) REVERT: B 618 ASP cc_start: 0.7327 (m-30) cc_final: 0.7022 (p0) REVERT: B 707 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8305 (pp) REVERT: B 743 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8682 (ptmm) REVERT: C 121 LYS cc_start: 0.8482 (mttm) cc_final: 0.8022 (mtpp) REVERT: C 320 MET cc_start: 0.9007 (mmp) cc_final: 0.8193 (mmm) REVERT: C 323 MET cc_start: 0.8831 (ttm) cc_final: 0.8481 (ttp) REVERT: C 447 PHE cc_start: 0.8752 (m-10) cc_final: 0.8540 (m-80) REVERT: C 488 MET cc_start: 0.7595 (tpp) cc_final: 0.7194 (mtp) REVERT: C 546 GLU cc_start: 0.8374 (tp30) cc_final: 0.7912 (mm-30) REVERT: C 618 ASP cc_start: 0.7331 (m-30) cc_final: 0.7025 (p0) REVERT: C 707 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8289 (pp) REVERT: C 743 LYS cc_start: 0.8907 (ptpt) cc_final: 0.8675 (ptmm) REVERT: D 121 LYS cc_start: 0.8491 (mttm) cc_final: 0.8034 (mtpp) REVERT: D 320 MET cc_start: 0.9008 (mmp) cc_final: 0.8199 (mmm) REVERT: D 323 MET cc_start: 0.8760 (ttm) cc_final: 0.8427 (ttp) REVERT: D 447 PHE cc_start: 0.8708 (m-10) cc_final: 0.8485 (m-80) REVERT: D 488 MET cc_start: 0.7637 (tpp) cc_final: 0.7149 (mtp) REVERT: D 509 ARG cc_start: 0.5865 (ptp-170) cc_final: 0.5609 (mtm110) REVERT: D 546 GLU cc_start: 0.8350 (tp30) cc_final: 0.7904 (mm-30) REVERT: D 743 LYS cc_start: 0.8902 (ptpt) cc_final: 0.8668 (ptmm) outliers start: 33 outliers final: 5 residues processed: 353 average time/residue: 0.1642 time to fit residues: 87.1085 Evaluate side-chains 275 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 268 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 255 GLN 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: [241, 189, 173, 124, 40, 204, 88, 114, 233, 106, 4] chunk 241 optimal weight: 0.0770 chunk 189 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 124 optimal weight: 0.0170 chunk 40 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 233 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS B 244 HIS C 244 HIS D 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.098741 restraints weight = 30426.619| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.61 r_work: 0.2856 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23148 Z= 0.087 Angle : 0.478 7.952 30976 Z= 0.242 Chirality : 0.038 0.150 3328 Planarity : 0.004 0.061 3712 Dihedral : 17.904 101.607 4120 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.49 % Allowed : 9.06 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 2552 helix: -0.95 (0.13), residues: 1516 sheet: 0.97 (0.64), residues: 76 loop : -2.28 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 509 TYR 0.017 0.001 TYR C 540 PHE 0.016 0.001 PHE C 193 TRP 0.012 0.001 TRP A 710 HIS 0.003 0.000 HIS D 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (23144) covalent geometry : angle 0.47841 / 0.24 (30968) SS BOND : bond 0.00078 / 0.04 ( 4) SS BOND : angle 0.14660 / 0.09 ( 8) hydrogen bonds : bond 0.03648 / 2.38 ( 804) hydrogen bonds : angle 3.22417 / 2.22 ( 2400) *********************** 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 330 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 0.787 Fit side-chains REVERT: A 121 LYS cc_start: 0.8456 (mttm) cc_final: 0.8032 (mtpp) REVERT: A 138 LEU cc_start: 0.8170 (mt) cc_final: 0.7873 (mp) REVERT: A 253 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7443 (ttpp) REVERT: A 323 MET cc_start: 0.8716 (ttm) cc_final: 0.8487 (ttp) REVERT: A 488 MET cc_start: 0.7522 (tpp) cc_final: 0.7209 (mtp) REVERT: A 509 ARG cc_start: 0.5860 (ptp-170) cc_final: 0.5446 (mtm110) REVERT: A 546 GLU cc_start: 0.8227 (tp30) cc_final: 0.7804 (mm-30) REVERT: A 618 ASP cc_start: 0.7237 (m-30) cc_final: 0.7019 (p0) REVERT: A 743 LYS cc_start: 0.8946 (ptpt) cc_final: 0.8624 (ptmm) REVERT: B 121 LYS cc_start: 0.8474 (mttm) cc_final: 0.8025 (mtpp) REVERT: B 253 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7456 (ttpp) REVERT: B 323 MET cc_start: 0.8719 (ttm) cc_final: 0.8488 (ttp) REVERT: B 488 MET cc_start: 0.7515 (tpp) cc_final: 0.7211 (mtp) REVERT: B 509 ARG cc_start: 0.5853 (ptp-170) cc_final: 0.5441 (mtm110) REVERT: B 546 GLU cc_start: 0.8240 (tp30) cc_final: 0.7802 (mm-30) REVERT: B 618 ASP cc_start: 0.7234 (m-30) cc_final: 0.7021 (p0) REVERT: B 743 LYS cc_start: 0.8947 (ptpt) cc_final: 0.8629 (ptmm) REVERT: C 121 LYS cc_start: 0.8463 (mttm) cc_final: 0.8038 (mtpp) REVERT: C 138 LEU cc_start: 0.8160 (mt) cc_final: 0.7864 (mp) REVERT: C 323 MET cc_start: 0.8712 (ttm) cc_final: 0.8484 (ttp) REVERT: C 488 MET cc_start: 0.7521 (tpp) cc_final: 0.7174 (mtp) REVERT: C 546 GLU cc_start: 0.8244 (tp30) cc_final: 0.7808 (mm-30) REVERT: C 618 ASP cc_start: 0.7188 (m-30) cc_final: 0.6957 (p0) REVERT: C 743 LYS cc_start: 0.8946 (ptpt) cc_final: 0.8623 (ptmm) REVERT: D 121 LYS cc_start: 0.8472 (mttm) cc_final: 0.8048 (mtpp) REVERT: D 138 LEU cc_start: 0.8201 (mt) cc_final: 0.7917 (mp) REVERT: D 253 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7501 (ttpp) REVERT: D 323 MET cc_start: 0.8709 (ttm) cc_final: 0.8480 (ttp) REVERT: D 488 MET cc_start: 0.7573 (tpp) cc_final: 0.7193 (mtp) REVERT: D 509 ARG cc_start: 0.5867 (ptp-170) cc_final: 0.5446 (mtm110) REVERT: D 546 GLU cc_start: 0.8225 (tp30) cc_final: 0.7846 (mm-30) REVERT: D 743 LYS cc_start: 0.8941 (ptpt) cc_final: 0.8620 (ptmm) outliers start: 34 outliers final: 11 residues processed: 312 average time/residue: 0.1603 time to fit residues: 76.3975 Evaluate side-chains 278 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 267 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain D residue 128 SER 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: [109, 241, 216, 145, 18, 195, 219, 242, 251, 28, 1] chunk 109 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 195 optimal weight: 0.0770 chunk 219 optimal weight: 1.9990 chunk 242 optimal weight: 0.3980 chunk 251 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 452 ASN B 735 ASN C 452 ASN D 452 ASN D 735 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.095673 restraints weight = 30451.176| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.59 r_work: 0.2794 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23148 Z= 0.099 Angle : 0.484 8.536 30976 Z= 0.245 Chirality : 0.039 0.127 3328 Planarity : 0.004 0.057 3712 Dihedral : 17.290 101.798 4120 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.31 % Allowed : 10.16 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2552 helix: -0.22 (0.13), residues: 1528 sheet: 1.04 (0.65), residues: 76 loop : -2.12 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 509 TYR 0.016 0.001 TYR C 540 PHE 0.011 0.001 PHE B 316 TRP 0.012 0.001 TRP B 493 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (23144) covalent geometry : angle 0.48431 / 0.25 (30968) SS BOND : bond 0.00087 / 0.04 ( 4) SS BOND : angle 0.15882 / 0.13 ( 8) hydrogen bonds : bond 0.03926 / 2.56 ( 804) hydrogen bonds : angle 3.23072 / 2.22 ( 2400) *********************** 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 296 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 266 time to evaluate : 0.690 Fit side-chains REVERT: A 121 LYS cc_start: 0.8525 (mttm) cc_final: 0.8034 (mtpp) REVERT: A 253 LYS cc_start: 0.7685 (ttpt) cc_final: 0.7415 (ttpp) REVERT: A 323 MET cc_start: 0.8759 (ttm) cc_final: 0.8547 (ttp) REVERT: A 452 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8540 (m-40) REVERT: A 488 MET cc_start: 0.7591 (tpp) cc_final: 0.7183 (mtp) REVERT: A 509 ARG cc_start: 0.5943 (ptp-170) cc_final: 0.5549 (mtm110) REVERT: A 546 GLU cc_start: 0.8248 (tp30) cc_final: 0.7781 (mm-30) REVERT: A 743 LYS cc_start: 0.8953 (ptpt) cc_final: 0.8665 (ptmm) REVERT: B 121 LYS cc_start: 0.8501 (mttm) cc_final: 0.8011 (mtpp) REVERT: B 253 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7423 (ttpp) REVERT: B 323 MET cc_start: 0.8762 (ttm) cc_final: 0.8550 (ttp) REVERT: B 452 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8539 (m-40) REVERT: B 488 MET cc_start: 0.7594 (tpp) cc_final: 0.7184 (mtp) REVERT: B 509 ARG cc_start: 0.5942 (ptp-170) cc_final: 0.5556 (mtm110) REVERT: B 546 GLU cc_start: 0.8252 (tp30) cc_final: 0.7837 (mm-30) REVERT: B 743 LYS cc_start: 0.8942 (ptpt) cc_final: 0.8670 (ptmm) REVERT: C 121 LYS cc_start: 0.8521 (mttm) cc_final: 0.8026 (mtpp) REVERT: C 323 MET cc_start: 0.8753 (ttm) cc_final: 0.8542 (ttp) REVERT: C 488 MET cc_start: 0.7598 (tpp) cc_final: 0.7184 (mtp) REVERT: C 546 GLU cc_start: 0.8253 (tp30) cc_final: 0.7788 (mm-30) REVERT: C 743 LYS cc_start: 0.8951 (ptpt) cc_final: 0.8661 (ptmm) REVERT: D 121 LYS cc_start: 0.8539 (mttm) cc_final: 0.8044 (mtpp) REVERT: D 253 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7417 (ttpp) REVERT: D 323 MET cc_start: 0.8745 (ttm) cc_final: 0.8535 (ttp) REVERT: D 452 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8552 (m-40) REVERT: D 488 MET cc_start: 0.7654 (tpp) cc_final: 0.7234 (mtp) REVERT: D 509 ARG cc_start: 0.5945 (ptp-170) cc_final: 0.5551 (mtm110) REVERT: D 546 GLU cc_start: 0.8267 (tp30) cc_final: 0.7793 (mm-30) REVERT: D 743 LYS cc_start: 0.8948 (ptpt) cc_final: 0.8657 (ptmm) outliers start: 30 outliers final: 13 residues processed: 287 average time/residue: 0.1659 time to fit residues: 72.0108 Evaluate side-chains 254 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 128 SER 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 684 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 458 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: [97, 80, 7, 218, 43, 64, 208, 60, 193, 230, 27] chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 208 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 193 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN A 735 ASN B 452 ASN C 452 ASN C 735 ASN D 452 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.095158 restraints weight = 29982.246| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.51 r_work: 0.2789 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23148 Z= 0.109 Angle : 0.484 8.963 30976 Z= 0.246 Chirality : 0.039 0.128 3328 Planarity : 0.003 0.055 3712 Dihedral : 17.005 99.927 4120 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.97 % Allowed : 10.73 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.16), residues: 2552 helix: 0.23 (0.13), residues: 1540 sheet: 1.02 (0.65), residues: 76 loop : -1.92 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 509 TYR 0.016 0.001 TYR D 540 PHE 0.012 0.001 PHE C 316 TRP 0.009 0.001 TRP A 493 HIS 0.002 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (23144) covalent geometry : angle 0.48446 / 0.25 (30968) SS BOND : bond 0.00037 / 0.02 ( 4) SS BOND : angle 0.18030 / 0.12 ( 8) hydrogen bonds : bond 0.03988 / 2.60 ( 804) hydrogen bonds : angle 3.20242 / 2.20 ( 2400) *********************** 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 298 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.803 Fit side-chains REVERT: A 121 LYS cc_start: 0.8493 (mttm) cc_final: 0.8030 (mtpp) REVERT: A 253 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7426 (ttpp) REVERT: A 323 MET cc_start: 0.8737 (ttm) cc_final: 0.8523 (ttp) REVERT: A 475 LEU cc_start: 0.1386 (OUTLIER) cc_final: 0.0956 (tp) REVERT: A 488 MET cc_start: 0.7590 (tpp) cc_final: 0.7136 (mtp) REVERT: A 509 ARG cc_start: 0.5711 (ptp-170) cc_final: 0.5273 (mtm110) REVERT: A 546 GLU cc_start: 0.8357 (tp30) cc_final: 0.7931 (mm-30) REVERT: A 743 LYS cc_start: 0.8950 (ptpt) cc_final: 0.8635 (ptmm) REVERT: B 121 LYS cc_start: 0.8493 (mttm) cc_final: 0.8026 (mtpp) REVERT: B 253 LYS cc_start: 0.7702 (ttpt) cc_final: 0.7439 (ttpp) REVERT: B 323 MET cc_start: 0.8742 (ttm) cc_final: 0.8526 (ttp) REVERT: B 475 LEU cc_start: 0.1590 (OUTLIER) cc_final: 0.1153 (tp) REVERT: B 488 MET cc_start: 0.7591 (tpp) cc_final: 0.7137 (mtp) REVERT: B 509 ARG cc_start: 0.5707 (ptp-170) cc_final: 0.5276 (mtm110) REVERT: B 546 GLU cc_start: 0.8377 (tp30) cc_final: 0.7905 (mm-30) REVERT: B 743 LYS cc_start: 0.8931 (ptpt) cc_final: 0.8635 (ptmm) REVERT: C 121 LYS cc_start: 0.8484 (mttm) cc_final: 0.8017 (mtpp) REVERT: C 323 MET cc_start: 0.8739 (ttm) cc_final: 0.8523 (ttp) REVERT: C 475 LEU cc_start: 0.1636 (OUTLIER) cc_final: 0.1168 (tp) REVERT: C 488 MET cc_start: 0.7594 (tpp) cc_final: 0.7122 (mtp) REVERT: C 546 GLU cc_start: 0.8373 (tp30) cc_final: 0.7936 (mm-30) REVERT: C 743 LYS cc_start: 0.8950 (ptpt) cc_final: 0.8636 (ptmm) REVERT: D 121 LYS cc_start: 0.8493 (mttm) cc_final: 0.8030 (mtpp) REVERT: D 253 LYS cc_start: 0.7695 (ttpt) cc_final: 0.7417 (ttpp) REVERT: D 323 MET cc_start: 0.8729 (ttm) cc_final: 0.8512 (ttp) REVERT: D 475 LEU cc_start: 0.1386 (OUTLIER) cc_final: 0.0923 (tp) REVERT: D 488 MET cc_start: 0.7649 (tpp) cc_final: 0.7229 (mtp) REVERT: D 509 ARG cc_start: 0.5684 (ptp-170) cc_final: 0.5294 (mtm110) REVERT: D 546 GLU cc_start: 0.8358 (tp30) cc_final: 0.7932 (mm-30) REVERT: D 743 LYS cc_start: 0.8947 (ptpt) cc_final: 0.8633 (ptmm) outliers start: 45 outliers final: 23 residues processed: 291 average time/residue: 0.1691 time to fit residues: 73.7173 Evaluate side-chains 264 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 315 ASP 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 475 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 315 ASP 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 C residue 128 SER Chi-restraints excluded: chain C residue 315 ASP 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 475 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 315 ASP 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 475 LEU 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: [79, 104, 140, 167, 164, 201, 186, 85, 132, 99, 127] chunk 79 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 140 optimal weight: 0.0020 chunk 167 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 127 optimal weight: 0.0070 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 452 ASN D 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.100632 restraints weight = 28670.725| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.40 r_work: 0.2752 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23148 Z= 0.083 Angle : 0.453 9.897 30976 Z= 0.230 Chirality : 0.038 0.122 3328 Planarity : 0.003 0.054 3712 Dihedral : 16.021 95.639 4120 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.09 % Allowed : 11.43 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.17), residues: 2552 helix: 0.89 (0.14), residues: 1508 sheet: 1.04 (0.66), residues: 76 loop : -1.76 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 509 TYR 0.017 0.001 TYR D 540 PHE 0.012 0.001 PHE A 316 TRP 0.011 0.001 TRP C 710 HIS 0.002 0.000 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.08 (23144) covalent geometry : angle 0.45291 / 0.23 (30968) SS BOND : bond 0.00014 / 0.01 ( 4) SS BOND : angle 0.06663 / 0.04 ( 8) hydrogen bonds : bond 0.03179 / 2.07 ( 804) hydrogen bonds : angle 3.01035 / 2.07 ( 2400) *********************** 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 277 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.746 Fit side-chains REVERT: A 121 LYS cc_start: 0.8382 (mttm) cc_final: 0.7942 (mtpp) REVERT: A 138 LEU cc_start: 0.8060 (mt) cc_final: 0.7833 (mp) REVERT: A 253 LYS cc_start: 0.7615 (ttpt) cc_final: 0.7339 (ttpp) REVERT: A 488 MET cc_start: 0.7428 (tpp) cc_final: 0.6995 (mtp) REVERT: A 509 ARG cc_start: 0.5623 (ptp-170) cc_final: 0.5236 (mtm110) REVERT: A 546 GLU cc_start: 0.8222 (tp30) cc_final: 0.7711 (mm-30) REVERT: A 555 MET cc_start: 0.8526 (mtm) cc_final: 0.8277 (ttm) REVERT: A 712 ARG cc_start: 0.7355 (mmm-85) cc_final: 0.6613 (mmm160) REVERT: A 743 LYS cc_start: 0.8885 (ptpt) cc_final: 0.8559 (ptmm) REVERT: B 121 LYS cc_start: 0.8387 (mttm) cc_final: 0.7948 (mtpp) REVERT: B 138 LEU cc_start: 0.8067 (mt) cc_final: 0.7831 (mp) REVERT: B 253 LYS cc_start: 0.7624 (ttpt) cc_final: 0.7348 (ttpp) REVERT: B 488 MET cc_start: 0.7424 (tpp) cc_final: 0.6967 (mtp) REVERT: B 509 ARG cc_start: 0.5585 (ptp-170) cc_final: 0.5182 (mtm110) REVERT: B 546 GLU cc_start: 0.8243 (tp30) cc_final: 0.7736 (mm-30) REVERT: B 555 MET cc_start: 0.8523 (mtm) cc_final: 0.8276 (ttm) REVERT: B 712 ARG cc_start: 0.7365 (mmm-85) cc_final: 0.6620 (mmm160) REVERT: B 743 LYS cc_start: 0.8873 (ptpt) cc_final: 0.8564 (ptmm) REVERT: C 121 LYS cc_start: 0.8377 (mttm) cc_final: 0.7935 (mtpp) REVERT: C 138 LEU cc_start: 0.8060 (mt) cc_final: 0.7818 (mp) REVERT: C 488 MET cc_start: 0.7435 (tpp) cc_final: 0.6973 (mtp) REVERT: C 546 GLU cc_start: 0.8228 (tp30) cc_final: 0.7720 (mm-30) REVERT: C 555 MET cc_start: 0.8554 (mtm) cc_final: 0.8298 (ttm) REVERT: C 712 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6596 (mmm160) REVERT: C 743 LYS cc_start: 0.8889 (ptpt) cc_final: 0.8560 (ptmm) REVERT: D 121 LYS cc_start: 0.8399 (mttm) cc_final: 0.7957 (mtpp) REVERT: D 138 LEU cc_start: 0.8034 (mt) cc_final: 0.7797 (mp) REVERT: D 253 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7345 (ttpp) REVERT: D 475 LEU cc_start: 0.1312 (OUTLIER) cc_final: 0.1102 (tm) REVERT: D 488 MET cc_start: 0.7554 (tpp) cc_final: 0.7147 (mtp) REVERT: D 509 ARG cc_start: 0.5625 (ptp-170) cc_final: 0.5234 (mtm110) REVERT: D 546 GLU cc_start: 0.8254 (tp30) cc_final: 0.7742 (mm-30) REVERT: D 555 MET cc_start: 0.8528 (mtm) cc_final: 0.8280 (ttm) REVERT: D 743 LYS cc_start: 0.8885 (ptpt) cc_final: 0.8558 (ptmm) outliers start: 25 outliers final: 15 residues processed: 271 average time/residue: 0.1599 time to fit residues: 65.8188 Evaluate side-chains 237 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 545 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 545 LYS 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: [9, 72, 58, 254, 225, 52, 79, 80, 118, 214, 87] chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.086619 restraints weight = 29275.678| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.41 r_work: 0.2800 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23148 Z= 0.132 Angle : 0.519 12.097 30976 Z= 0.259 Chirality : 0.041 0.136 3328 Planarity : 0.004 0.053 3712 Dihedral : 16.337 98.277 4120 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.62 % Allowed : 11.73 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2552 helix: 0.87 (0.14), residues: 1536 sheet: 1.05 (0.66), residues: 76 loop : -1.88 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 509 TYR 0.018 0.001 TYR B 540 PHE 0.013 0.001 PHE C 316 TRP 0.006 0.001 TRP A 493 HIS 0.003 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (23144) covalent geometry : angle 0.51894 / 0.26 (30968) SS BOND : bond 0.00139 / 0.07 ( 4) SS BOND : angle 0.28453 / 0.18 ( 8) hydrogen bonds : bond 0.04422 / 2.88 ( 804) hydrogen bonds : angle 3.30293 / 2.27 ( 2400) *********************** 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 256 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.633 Fit side-chains REVERT: A 253 LYS cc_start: 0.7614 (ttpt) cc_final: 0.7332 (ttpp) REVERT: A 488 MET cc_start: 0.7559 (tpp) cc_final: 0.7105 (mtp) REVERT: A 546 GLU cc_start: 0.8438 (tp30) cc_final: 0.7853 (mm-30) REVERT: A 712 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.6790 (mmm160) REVERT: A 743 LYS cc_start: 0.8904 (ptpt) cc_final: 0.8538 (ptmm) REVERT: B 253 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7369 (ttpp) REVERT: B 488 MET cc_start: 0.7561 (tpp) cc_final: 0.7108 (mtp) REVERT: B 546 GLU cc_start: 0.8454 (tp30) cc_final: 0.7854 (mm-30) REVERT: B 712 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.6779 (mmm160) REVERT: B 743 LYS cc_start: 0.8897 (ptpt) cc_final: 0.8536 (ptmm) REVERT: C 488 MET cc_start: 0.7565 (tpp) cc_final: 0.7107 (mtp) REVERT: C 546 GLU cc_start: 0.8448 (tp30) cc_final: 0.7855 (mm-30) REVERT: C 712 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.6790 (mmm160) REVERT: C 743 LYS cc_start: 0.8911 (ptpt) cc_final: 0.8541 (ptmm) REVERT: D 253 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7372 (ttpp) REVERT: D 488 MET cc_start: 0.7603 (tpp) cc_final: 0.7194 (mtp) REVERT: D 546 GLU cc_start: 0.8399 (tp30) cc_final: 0.7849 (mm-30) REVERT: D 743 LYS cc_start: 0.8905 (ptpt) cc_final: 0.8539 (ptmm) outliers start: 37 outliers final: 28 residues processed: 248 average time/residue: 0.1683 time to fit residues: 62.5229 Evaluate side-chains 238 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 278 VAL 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 684 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 128 SER 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 418 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 278 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 491 LEU Chi-restraints excluded: chain D residue 545 LYS 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: [159, 158, 86, 133, 193, 252, 27, 208, 2, 210, 171] chunk 159 optimal weight: 0.7980 chunk 158 optimal weight: 0.0000 chunk 86 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 ASN C 178 ASN D 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.086341 restraints weight = 29263.694| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.52 r_work: 0.2786 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23148 Z= 0.112 Angle : 0.501 11.651 30976 Z= 0.249 Chirality : 0.040 0.138 3328 Planarity : 0.004 0.056 3712 Dihedral : 15.917 96.599 4120 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.36 % Allowed : 12.61 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2552 helix: 1.12 (0.14), residues: 1520 sheet: 1.02 (0.66), residues: 76 loop : -1.74 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 509 TYR 0.015 0.001 TYR D 540 PHE 0.013 0.001 PHE D 316 TRP 0.008 0.001 TRP A 710 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (23144) covalent geometry : angle 0.50069 / 0.25 (30968) SS BOND : bond 0.00109 / 0.05 ( 4) SS BOND : angle 0.06349 / 0.04 ( 8) hydrogen bonds : bond 0.03910 / 2.55 ( 804) hydrogen bonds : angle 3.17301 / 2.18 ( 2400) *********************** 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 245 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.802 Fit side-chains REVERT: A 153 ASP cc_start: 0.6813 (m-30) cc_final: 0.6503 (p0) REVERT: A 253 LYS cc_start: 0.7662 (ttpt) cc_final: 0.7380 (ttpp) REVERT: A 488 MET cc_start: 0.7516 (tpp) cc_final: 0.7081 (mtp) REVERT: A 546 GLU cc_start: 0.8411 (tp30) cc_final: 0.7822 (mm-30) REVERT: A 712 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.6756 (mmm160) REVERT: A 743 LYS cc_start: 0.8894 (ptpt) cc_final: 0.8506 (ptmm) REVERT: B 253 LYS cc_start: 0.7646 (ttpt) cc_final: 0.7372 (ttpp) REVERT: B 488 MET cc_start: 0.7514 (tpp) cc_final: 0.7080 (mtp) REVERT: B 546 GLU cc_start: 0.8374 (tp30) cc_final: 0.7822 (mm-30) REVERT: B 712 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6746 (mmm160) REVERT: B 743 LYS cc_start: 0.8865 (ptpt) cc_final: 0.8464 (ptmm) REVERT: C 488 MET cc_start: 0.7518 (tpp) cc_final: 0.7081 (mtp) REVERT: C 546 GLU cc_start: 0.8413 (tp30) cc_final: 0.7814 (mm-30) REVERT: C 712 ARG cc_start: 0.7458 (mmm-85) cc_final: 0.6709 (mmm160) REVERT: C 743 LYS cc_start: 0.8897 (ptpt) cc_final: 0.8504 (ptmm) REVERT: D 153 ASP cc_start: 0.6807 (m-30) cc_final: 0.6518 (p0) REVERT: D 253 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7409 (ttpp) REVERT: D 475 LEU cc_start: 0.1949 (OUTLIER) cc_final: 0.1661 (tm) REVERT: D 488 MET cc_start: 0.7563 (tpp) cc_final: 0.7154 (mtp) REVERT: D 546 GLU cc_start: 0.8420 (tp30) cc_final: 0.7852 (mm-30) REVERT: D 743 LYS cc_start: 0.8897 (ptpt) cc_final: 0.8508 (ptmm) outliers start: 31 outliers final: 25 residues processed: 239 average time/residue: 0.1633 time to fit residues: 59.4202 Evaluate side-chains 233 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 278 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 684 VAL Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 278 VAL 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 517 LEU Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [18, 246, 194, 58, 70, 10, 205, 129, 97, 251, 141] chunk 18 optimal weight: 0.9990 chunk 246 optimal weight: 0.4980 chunk 194 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 0.0470 chunk 10 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 251 optimal weight: 0.0970 chunk 141 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.091292 restraints weight = 29304.598| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.44 r_work: 0.2824 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23148 Z= 0.080 Angle : 0.460 10.672 30976 Z= 0.230 Chirality : 0.038 0.135 3328 Planarity : 0.003 0.058 3712 Dihedral : 14.992 90.631 4120 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.18 % Allowed : 12.70 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2552 helix: 1.50 (0.14), residues: 1512 sheet: 1.00 (0.66), residues: 76 loop : -1.64 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 509 TYR 0.014 0.001 TYR D 540 PHE 0.013 0.001 PHE A 316 TRP 0.013 0.001 TRP D 710 HIS 0.002 0.000 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.08 (23144) covalent geometry : angle 0.46035 / 0.23 (30968) SS BOND : bond 0.00069 / 0.03 ( 4) SS BOND : angle 0.21773 / 0.14 ( 8) hydrogen bonds : bond 0.02811 / 1.83 ( 804) hydrogen bonds : angle 2.93347 / 2.01 ( 2400) *********************** 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 266 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.830 Fit side-chains REVERT: A 138 LEU cc_start: 0.8148 (mt) cc_final: 0.7911 (mp) REVERT: A 153 ASP cc_start: 0.6731 (m-30) cc_final: 0.6374 (p0) REVERT: A 253 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7374 (ttpp) REVERT: A 488 MET cc_start: 0.7461 (tpp) cc_final: 0.7057 (mtp) REVERT: A 546 GLU cc_start: 0.8233 (tp30) cc_final: 0.7696 (mm-30) REVERT: A 712 ARG cc_start: 0.7437 (mmm-85) cc_final: 0.6707 (mmm160) REVERT: A 721 CYS cc_start: 0.8593 (m) cc_final: 0.8379 (p) REVERT: A 731 CYS cc_start: 0.8872 (m) cc_final: 0.8541 (m) REVERT: A 743 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8456 (ptmm) REVERT: B 138 LEU cc_start: 0.8153 (mt) cc_final: 0.7933 (mp) REVERT: B 253 LYS cc_start: 0.7661 (ttpt) cc_final: 0.7381 (ttpp) REVERT: B 488 MET cc_start: 0.7467 (tpp) cc_final: 0.7050 (mtp) REVERT: B 546 GLU cc_start: 0.8259 (tp30) cc_final: 0.7715 (mm-30) REVERT: B 712 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.6714 (mmm160) REVERT: B 731 CYS cc_start: 0.8875 (m) cc_final: 0.8550 (m) REVERT: B 743 LYS cc_start: 0.8834 (ptpt) cc_final: 0.8464 (ptmm) REVERT: C 138 LEU cc_start: 0.8161 (mt) cc_final: 0.7943 (mp) REVERT: C 488 MET cc_start: 0.7473 (tpp) cc_final: 0.7063 (mtp) REVERT: C 546 GLU cc_start: 0.8240 (tp30) cc_final: 0.7705 (mm-30) REVERT: C 712 ARG cc_start: 0.7448 (mmm-85) cc_final: 0.6717 (mmm160) REVERT: C 731 CYS cc_start: 0.8871 (m) cc_final: 0.8543 (m) REVERT: C 743 LYS cc_start: 0.8834 (ptpt) cc_final: 0.8453 (ptmm) REVERT: D 138 LEU cc_start: 0.8074 (mt) cc_final: 0.7846 (mp) REVERT: D 153 ASP cc_start: 0.6781 (m-30) cc_final: 0.6446 (p0) REVERT: D 253 LYS cc_start: 0.7687 (ttpt) cc_final: 0.7381 (ttpp) REVERT: D 475 LEU cc_start: 0.2163 (OUTLIER) cc_final: 0.1775 (tm) REVERT: D 488 MET cc_start: 0.7600 (tpp) cc_final: 0.7207 (mtp) REVERT: D 546 GLU cc_start: 0.8287 (tp30) cc_final: 0.7728 (mm-30) REVERT: D 721 CYS cc_start: 0.8587 (m) cc_final: 0.8375 (p) REVERT: D 731 CYS cc_start: 0.8865 (m) cc_final: 0.8544 (m) REVERT: D 743 LYS cc_start: 0.8831 (ptpt) cc_final: 0.8455 (ptmm) outliers start: 27 outliers final: 21 residues processed: 263 average time/residue: 0.1583 time to fit residues: 64.3139 Evaluate side-chains 252 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 272 THR 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 272 THR Chi-restraints excluded: chain D residue 278 VAL 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 545 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [82, 34, 174, 175, 123, 32, 55, 230, 75, 211, 101] chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.094620 restraints weight = 28784.858| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.38 r_work: 0.2732 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 0.031 23148 Z= 0.105 Angle : 0.491 10.876 30976 Z= 0.246 Chirality : 0.039 0.134 3328 Planarity : 0.004 0.063 3712 Dihedral : 15.122 92.201 4120 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.05 % Allowed : 12.78 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2552 helix: 1.54 (0.14), residues: 1516 sheet: 1.02 (0.66), residues: 76 loop : -1.57 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 509 TYR 0.013 0.001 TYR B 540 PHE 0.013 0.001 PHE A 316 TRP 0.008 0.001 TRP D 710 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 (23144) covalent geometry : angle 0.49139 / 0.25 (30968) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 0.22845 / 0.13 ( 8) hydrogen bonds : bond 0.03754 / 2.44 ( 804) hydrogen bonds : angle 3.12792 / 2.14 ( 2400) ********************** 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 247 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.710 Fit side-chains REVERT: A 153 ASP cc_start: 0.6802 (m-30) cc_final: 0.6477 (p0) REVERT: A 253 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7367 (ttpp) REVERT: A 488 MET cc_start: 0.7515 (tpp) cc_final: 0.7106 (mtp) REVERT: A 546 GLU cc_start: 0.8354 (tp30) cc_final: 0.7751 (mm-30) REVERT: A 555 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8165 (mtp) REVERT: A 712 ARG cc_start: 0.7511 (mmm-85) cc_final: 0.6775 (mmm160) REVERT: A 743 LYS cc_start: 0.8878 (ptpt) cc_final: 0.8522 (ptmm) REVERT: B 253 LYS cc_start: 0.7652 (ttpt) cc_final: 0.7375 (ttpp) REVERT: B 488 MET cc_start: 0.7523 (tpp) cc_final: 0.7103 (mtp) REVERT: B 546 GLU cc_start: 0.8358 (tp30) cc_final: 0.7839 (mm-30) REVERT: B 555 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8153 (mtp) REVERT: B 712 ARG cc_start: 0.7504 (mmm-85) cc_final: 0.6767 (mmm160) REVERT: B 743 LYS cc_start: 0.8884 (ptpt) cc_final: 0.8524 (ptmm) REVERT: C 488 MET cc_start: 0.7531 (tpp) cc_final: 0.7104 (mtp) REVERT: C 546 GLU cc_start: 0.8344 (tp30) cc_final: 0.7749 (mm-30) REVERT: C 555 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8161 (mtp) REVERT: C 712 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.6774 (mmm160) REVERT: C 743 LYS cc_start: 0.8887 (ptpt) cc_final: 0.8524 (ptmm) REVERT: D 153 ASP cc_start: 0.6799 (m-30) cc_final: 0.6487 (p0) REVERT: D 253 LYS cc_start: 0.7677 (ttpt) cc_final: 0.7389 (ttpp) REVERT: D 475 LEU cc_start: 0.2302 (OUTLIER) cc_final: 0.1885 (tm) REVERT: D 488 MET cc_start: 0.7559 (tpp) cc_final: 0.7021 (mtp) REVERT: D 546 GLU cc_start: 0.8345 (tp30) cc_final: 0.7733 (mm-30) REVERT: D 555 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8150 (mtp) REVERT: D 743 LYS cc_start: 0.8883 (ptpt) cc_final: 0.8525 (ptmm) outliers start: 24 outliers final: 16 residues processed: 243 average time/residue: 0.1639 time to fit residues: 60.2881 Evaluate side-chains 237 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain D residue 272 THR 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 555 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [66, 209, 22, 152, 163, 0, 162, 250, 234, 217, 212] chunk 66 optimal weight: 9.9990 chunk 209 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 152 optimal weight: 0.0870 chunk 163 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 chunk 217 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.090250 restraints weight = 29230.795| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.44 r_work: 0.2748 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23148 Z= 0.085 Angle : 0.468 10.839 30976 Z= 0.234 Chirality : 0.038 0.132 3328 Planarity : 0.004 0.062 3712 Dihedral : 14.723 88.971 4120 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.09 % Allowed : 13.09 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2552 helix: 1.70 (0.14), residues: 1516 sheet: 1.01 (0.67), residues: 76 loop : -1.49 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 509 TYR 0.013 0.001 TYR A 540 PHE 0.013 0.001 PHE C 316 TRP 0.011 0.001 TRP D 710 HIS 0.002 0.000 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.08 (23144) covalent geometry : angle 0.46807 / 0.23 (30968) SS BOND : bond 0.00127 / 0.06 ( 4) SS BOND : angle 0.12600 / 0.10 ( 8) hydrogen bonds : bond 0.03095 / 2.01 ( 804) hydrogen bonds : angle 2.98852 / 2.05 ( 2400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4643.49 seconds wall clock time: 80 minutes 10.25 seconds (4810.25 seconds total)