Starting phenix.real_space_refine on Sat Jul 4 19:21:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mim_23856/07_2026/7mim_23856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mim_23856/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mim_23856/07_2026/7mim_23856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mim_23856/07_2026/7mim_23856.map" model { file = "/net/cci-nas-00/data/ceres_data/7mim_23856/07_2026/7mim_23856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mim_23856/07_2026/7mim_23856.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mim_23856/07_2026/7mim_23856.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mim_23856/07_2026/7mim_23856.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 7.61, per 1000 atoms: 0.33 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=17, 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 131 " - pdb=" SG CYS C 131 " distance=0.00 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 146 " distance=0.00 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 171 " distance=0.00 Simple disulfide: pdb=" SG CYS C 271 " - pdb=" SG CYS C 271 " distance=0.00 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 446 " distance=0.00 Simple disulfide: pdb=" SG CYS C 496 " - pdb=" SG CYS C 496 " distance=0.00 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 550 " distance=0.00 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 612 " distance=0.00 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 612 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 619 " distance=0.00 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 721 " distance=0.00 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 731 " distance=0.00 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 746.0 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: 0.52 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: 3.04 Time building geometry restraints manager: 2.54 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: 13238 29.61 - 59.22: 681 59.22 - 88.83: 132 88.83 - 118.45: 32 118.45 - 148.06: 20 Dihedral angle restraints: 14103 sinusoidal: 6547 harmonic: 7556 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.85 65.85 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.85 65.85 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.82 65.82 1 1.00e+01 1.00e-02 5.67e+01 ... (remaining 14100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2606 0.058 - 0.116: 597 0.116 - 0.173: 93 0.173 - 0.231: 21 0.231 - 0.289: 11 Chirality restraints: 3328 Sorted by residual: chirality pdb=" CG LEU D 469 " pdb=" CB LEU D 469 " pdb=" CD1 LEU D 469 " pdb=" CD2 LEU D 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU C 469 " pdb=" CB LEU C 469 " pdb=" CD1 LEU C 469 " pdb=" CD2 LEU C 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU B 469 " pdb=" CB LEU B 469 " pdb=" CD1 LEU B 469 " pdb=" CD2 LEU B 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3325 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 383 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 384 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 384 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 384 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 383 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 384 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 383 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 384 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " 0.030 5.00e-02 4.00e+02 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 129 2.60 - 3.18: 16828 3.18 - 3.75: 30071 3.75 - 4.33: 44197 4.33 - 4.90: 73303 Nonbonded interactions: 164528 Sorted by model distance: nonbonded pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " model vdw 2.031 3.760 nonbonded pdb=" O LEU C 469 " pdb=" OH TYR C 540 " model vdw 2.327 3.040 nonbonded pdb=" O LEU D 469 " pdb=" OH TYR D 540 " model vdw 2.328 3.040 nonbonded pdb=" O LEU B 469 " pdb=" OH TYR B 540 " model vdw 2.328 3.040 nonbonded pdb=" O LEU A 469 " pdb=" OH TYR A 540 " model vdw 2.328 3.040 ... (remaining 164523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 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: 1.360 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.030 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- 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 23147 Z= 0.486 Angle : 1.366 12.463 30985 Z= 0.572 Chirality : 0.054 0.289 3328 Planarity : 0.006 0.054 3712 Dihedral : 18.848 148.058 9168 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 ( 3) SS BOND : angle 0.35645 / 0.19 ( 17) 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 : 0.710 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: 0.1790 time to fit residues: 108.0016 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 : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: 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 A 735 ASN B 220 ASN B 227 GLN B 394 ASN B 452 ASN B 477 HIS B 735 ASN C 220 ASN C 227 GLN C 394 ASN C 452 ASN C 477 HIS C 735 ASN D 220 ASN D 227 GLN D 394 ASN D 452 ASN D 477 HIS D 735 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.136579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.097616 restraints weight = 30501.740| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.57 r_work: 0.2829 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 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 = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23147 Z= 0.110 Angle : 0.547 8.236 30985 Z= 0.283 Chirality : 0.040 0.154 3328 Planarity : 0.005 0.061 3712 Dihedral : 20.382 121.080 4120 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.31 % Allowed : 7.53 % Favored : 91.16 % 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: -3.86 (0.13), residues: 2552 helix: -2.65 (0.10), residues: 1528 sheet: 1.00 (0.64), residues: 76 loop : -2.44 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 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 D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (23144) covalent geometry : angle 0.54685 / 0.28 (30968) SS BOND : bond 0.00105 / 0.05 ( 3) SS BOND : angle 0.06049 / 0.03 ( 17) hydrogen bonds : bond 0.04806 / 3.13 ( 804) hydrogen bonds : angle 3.81086 / 2.65 ( 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 363 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 333 time to evaluate : 0.846 Fit side-chains REVERT: A 121 LYS cc_start: 0.8478 (mttm) cc_final: 0.8016 (mtpp) REVERT: A 173 MET cc_start: 0.8332 (mtt) cc_final: 0.8129 (mtt) REVERT: A 323 MET cc_start: 0.8846 (ttm) cc_final: 0.8524 (ttp) REVERT: A 447 PHE cc_start: 0.8718 (m-10) cc_final: 0.8502 (m-80) REVERT: A 488 MET cc_start: 0.7579 (tpp) cc_final: 0.7182 (mtp) REVERT: A 509 ARG cc_start: 0.5841 (ptp-170) cc_final: 0.5609 (mtm110) REVERT: A 546 GLU cc_start: 0.8351 (tp30) cc_final: 0.7899 (mm-30) REVERT: A 618 ASP cc_start: 0.7209 (m-30) cc_final: 0.6963 (p0) REVERT: A 707 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8320 (pp) REVERT: A 743 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8683 (ptmm) REVERT: B 121 LYS cc_start: 0.8476 (mttm) cc_final: 0.8013 (mtpp) REVERT: B 173 MET cc_start: 0.8348 (mtt) cc_final: 0.8143 (mtt) REVERT: B 323 MET cc_start: 0.8848 (ttm) cc_final: 0.8513 (ttp) REVERT: B 447 PHE cc_start: 0.8709 (m-10) cc_final: 0.8499 (m-80) REVERT: B 488 MET cc_start: 0.7591 (tpp) cc_final: 0.7204 (mtp) REVERT: B 509 ARG cc_start: 0.5839 (ptp-170) cc_final: 0.5605 (mtm110) REVERT: B 546 GLU cc_start: 0.8362 (tp30) cc_final: 0.7897 (mm-30) REVERT: B 618 ASP cc_start: 0.7215 (m-30) cc_final: 0.6973 (p0) REVERT: B 707 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8317 (pp) REVERT: B 743 LYS cc_start: 0.8912 (ptpt) cc_final: 0.8682 (ptmm) REVERT: C 121 LYS cc_start: 0.8481 (mttm) cc_final: 0.8018 (mtpp) REVERT: C 173 MET cc_start: 0.8326 (mtt) cc_final: 0.8125 (mtt) REVERT: C 323 MET cc_start: 0.8844 (ttm) cc_final: 0.8510 (ttp) REVERT: C 488 MET cc_start: 0.7573 (tpp) cc_final: 0.7182 (mtp) REVERT: C 546 GLU cc_start: 0.8349 (tp30) cc_final: 0.7892 (mm-30) REVERT: C 618 ASP cc_start: 0.7217 (m-30) cc_final: 0.6975 (p0) REVERT: C 707 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8316 (pp) REVERT: C 743 LYS cc_start: 0.8910 (ptpt) cc_final: 0.8680 (ptmm) REVERT: D 121 LYS cc_start: 0.8489 (mttm) cc_final: 0.8032 (mtpp) REVERT: D 323 MET cc_start: 0.8840 (ttm) cc_final: 0.8517 (ttp) REVERT: D 488 MET cc_start: 0.7614 (tpp) cc_final: 0.7142 (mtp) REVERT: D 509 ARG cc_start: 0.5851 (ptp-170) cc_final: 0.5604 (mtm110) REVERT: D 546 GLU cc_start: 0.8338 (tp30) cc_final: 0.7895 (mm-30) REVERT: D 743 LYS cc_start: 0.8907 (ptpt) cc_final: 0.8675 (ptmm) outliers start: 30 outliers final: 7 residues processed: 352 average time/residue: 0.1711 time to fit residues: 90.6612 Evaluate side-chains 279 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 269 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 255 GLN 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: chunk 241 optimal weight: 0.0000 chunk 189 optimal weight: 5.9990 chunk 173 optimal weight: 0.1980 chunk 124 optimal weight: 0.0030 chunk 40 optimal weight: 0.1980 chunk 204 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 233 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS A 561 ASN B 244 HIS B 561 ASN C 244 HIS C 561 ASN D 244 HIS D 561 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101729 restraints weight = 30210.978| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.56 r_work: 0.2901 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23147 Z= 0.080 Angle : 0.469 8.756 30985 Z= 0.236 Chirality : 0.037 0.143 3328 Planarity : 0.004 0.060 3712 Dihedral : 17.767 100.034 4120 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.44 % Allowed : 8.63 % Favored : 89.93 % 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: -2.22 (0.15), residues: 2552 helix: -1.01 (0.13), residues: 1520 sheet: 0.97 (0.63), residues: 76 loop : -2.33 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 509 TYR 0.016 0.001 TYR A 540 PHE 0.016 0.001 PHE C 193 TRP 0.016 0.001 TRP D 493 HIS 0.001 0.000 HIS D 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00167 / 0.08 (23144) covalent geometry : angle 0.46875 / 0.24 (30968) SS BOND : bond 0.00057 / 0.03 ( 3) SS BOND : angle 0.13836 / 0.08 ( 17) hydrogen bonds : bond 0.03245 / 2.11 ( 804) hydrogen bonds : angle 3.16863 / 2.18 ( 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 348 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 315 time to evaluate : 0.766 Fit side-chains REVERT: A 121 LYS cc_start: 0.8473 (mttm) cc_final: 0.8027 (mtpp) REVERT: A 138 LEU cc_start: 0.8160 (mt) cc_final: 0.7835 (mp) REVERT: A 253 LYS cc_start: 0.7677 (ttpt) cc_final: 0.7359 (ttpp) REVERT: A 488 MET cc_start: 0.7474 (tpp) cc_final: 0.7191 (mtp) REVERT: A 509 ARG cc_start: 0.5848 (ptp-170) cc_final: 0.5440 (mtm110) REVERT: A 546 GLU cc_start: 0.8227 (tp30) cc_final: 0.7809 (mm-30) REVERT: A 618 ASP cc_start: 0.7197 (m-30) cc_final: 0.6988 (p0) REVERT: A 743 LYS cc_start: 0.8964 (ptpt) cc_final: 0.8675 (ptmm) REVERT: B 121 LYS cc_start: 0.8461 (mttm) cc_final: 0.8018 (mtpp) REVERT: B 253 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7384 (ttpp) REVERT: B 488 MET cc_start: 0.7465 (tpp) cc_final: 0.7190 (mtp) REVERT: B 509 ARG cc_start: 0.5839 (ptp-170) cc_final: 0.5436 (mtm110) REVERT: B 546 GLU cc_start: 0.8228 (tp30) cc_final: 0.7871 (mm-30) REVERT: B 618 ASP cc_start: 0.7204 (m-30) cc_final: 0.6997 (p0) REVERT: B 743 LYS cc_start: 0.8970 (ptpt) cc_final: 0.8685 (ptmm) REVERT: C 121 LYS cc_start: 0.8462 (mttm) cc_final: 0.8021 (mtpp) REVERT: C 488 MET cc_start: 0.7498 (tpp) cc_final: 0.7159 (mtp) REVERT: C 546 GLU cc_start: 0.8232 (tp30) cc_final: 0.7824 (mm-30) REVERT: C 618 ASP cc_start: 0.7200 (m-30) cc_final: 0.6995 (p0) REVERT: C 743 LYS cc_start: 0.8960 (ptpt) cc_final: 0.8671 (ptmm) REVERT: D 121 LYS cc_start: 0.8477 (mttm) cc_final: 0.8060 (mtpp) REVERT: D 253 LYS cc_start: 0.7744 (ttpt) cc_final: 0.7429 (ttpp) REVERT: D 488 MET cc_start: 0.7547 (tpp) cc_final: 0.7148 (mtp) REVERT: D 509 ARG cc_start: 0.5852 (ptp-170) cc_final: 0.5445 (mtm110) REVERT: D 546 GLU cc_start: 0.8211 (tp30) cc_final: 0.7821 (mm-30) REVERT: D 743 LYS cc_start: 0.8956 (ptpt) cc_final: 0.8667 (ptmm) outliers start: 33 outliers final: 15 residues processed: 334 average time/residue: 0.1516 time to fit residues: 77.7321 Evaluate side-chains 277 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 262 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 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: chunk 109 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 452 ASN C 452 ASN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.091061 restraints weight = 30825.862| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.60 r_work: 0.2738 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23147 Z= 0.172 Angle : 0.566 8.713 30985 Z= 0.287 Chirality : 0.042 0.150 3328 Planarity : 0.004 0.055 3712 Dihedral : 18.132 107.060 4120 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.36 % Allowed : 11.03 % Favored : 87.61 % 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: -1.67 (0.16), residues: 2552 helix: -0.55 (0.13), residues: 1536 sheet: 1.18 (0.64), residues: 76 loop : -2.14 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 509 TYR 0.017 0.002 TYR A 540 PHE 0.013 0.001 PHE B 316 TRP 0.011 0.001 TRP C 493 HIS 0.005 0.001 HIS C 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (23144) covalent geometry : angle 0.56652 / 0.29 (30968) SS BOND : bond 0.00153 / 0.08 ( 3) SS BOND : angle 0.19772 / 0.10 ( 17) hydrogen bonds : bond 0.05379 / 3.51 ( 804) hydrogen bonds : angle 3.65038 / 2.51 ( 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 282 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.784 Fit side-chains REVERT: A 253 LYS cc_start: 0.7658 (ttpt) cc_final: 0.7384 (ttpp) REVERT: A 320 MET cc_start: 0.8695 (mtp) cc_final: 0.8449 (mtp) REVERT: A 546 GLU cc_start: 0.8403 (tp30) cc_final: 0.7887 (mm-30) REVERT: A 555 MET cc_start: 0.8780 (mtm) cc_final: 0.8260 (mtp) REVERT: A 743 LYS cc_start: 0.8968 (ptpt) cc_final: 0.8585 (ptmm) REVERT: B 253 LYS cc_start: 0.7653 (ttpt) cc_final: 0.7378 (ttpp) REVERT: B 320 MET cc_start: 0.8695 (mtp) cc_final: 0.8444 (mtp) REVERT: B 546 GLU cc_start: 0.8444 (tp30) cc_final: 0.7911 (mm-30) REVERT: B 743 LYS cc_start: 0.8942 (ptpt) cc_final: 0.8570 (ptmm) REVERT: C 320 MET cc_start: 0.8694 (mtp) cc_final: 0.8443 (mtp) REVERT: C 546 GLU cc_start: 0.8451 (tp30) cc_final: 0.7913 (mm-30) REVERT: C 743 LYS cc_start: 0.8963 (ptpt) cc_final: 0.8578 (ptmm) REVERT: D 253 LYS cc_start: 0.7696 (ttpt) cc_final: 0.7413 (ttpp) REVERT: D 320 MET cc_start: 0.8698 (mtp) cc_final: 0.8449 (mtp) REVERT: D 546 GLU cc_start: 0.8440 (tp30) cc_final: 0.7912 (mm-30) REVERT: D 555 MET cc_start: 0.8791 (mtm) cc_final: 0.8284 (mtp) REVERT: D 743 LYS cc_start: 0.8966 (ptpt) cc_final: 0.8581 (ptmm) outliers start: 31 outliers final: 24 residues processed: 277 average time/residue: 0.1693 time to fit residues: 70.2433 Evaluate side-chains 248 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 452 ASN C 452 ASN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.092782 restraints weight = 30329.826| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.60 r_work: 0.2763 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23147 Z= 0.127 Angle : 0.505 9.335 30985 Z= 0.257 Chirality : 0.040 0.130 3328 Planarity : 0.004 0.055 3712 Dihedral : 17.435 102.655 4120 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.10 % Allowed : 11.16 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.15 (0.16), residues: 2552 helix: -0.05 (0.13), residues: 1540 sheet: 1.13 (0.65), residues: 76 loop : -2.09 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 509 TYR 0.015 0.001 TYR B 540 PHE 0.013 0.001 PHE C 316 TRP 0.010 0.001 TRP D 493 HIS 0.003 0.001 HIS D 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (23144) covalent geometry : angle 0.50534 / 0.26 (30968) SS BOND : bond 0.00109 / 0.05 ( 3) SS BOND : angle 0.05943 / 0.03 ( 17) hydrogen bonds : bond 0.04280 / 2.79 ( 804) hydrogen bonds : angle 3.33336 / 2.29 ( 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 284 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.697 Fit side-chains REVERT: A 253 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7424 (ttpp) REVERT: A 452 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8538 (m110) REVERT: A 509 ARG cc_start: 0.5730 (ptp-110) cc_final: 0.5257 (mtm-85) REVERT: A 546 GLU cc_start: 0.8439 (tp30) cc_final: 0.7944 (mm-30) REVERT: A 743 LYS cc_start: 0.8937 (ptpt) cc_final: 0.8568 (ptmm) REVERT: B 253 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7413 (ttpp) REVERT: B 452 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8534 (m110) REVERT: B 509 ARG cc_start: 0.5724 (ptp-110) cc_final: 0.5251 (mtm-85) REVERT: B 546 GLU cc_start: 0.8439 (tp30) cc_final: 0.7960 (mm-30) REVERT: B 743 LYS cc_start: 0.8897 (ptpt) cc_final: 0.8562 (ptmm) REVERT: C 452 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8542 (m110) REVERT: C 546 GLU cc_start: 0.8448 (tp30) cc_final: 0.7965 (mm-30) REVERT: C 743 LYS cc_start: 0.8942 (ptpt) cc_final: 0.8573 (ptmm) REVERT: D 253 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7462 (ttpp) REVERT: D 452 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8555 (m110) REVERT: D 509 ARG cc_start: 0.5723 (ptp-110) cc_final: 0.5247 (mtm-85) REVERT: D 546 GLU cc_start: 0.8442 (tp30) cc_final: 0.7966 (mm-30) REVERT: D 743 LYS cc_start: 0.8941 (ptpt) cc_final: 0.8570 (ptmm) outliers start: 48 outliers final: 26 residues processed: 273 average time/residue: 0.1663 time to fit residues: 68.4769 Evaluate side-chains 244 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 272 THR 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 452 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 337 ARG 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 452 ASN Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 140 optimal weight: 0.0060 chunk 167 optimal weight: 9.9990 chunk 164 optimal weight: 0.0370 chunk 201 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 chunk 85 optimal weight: 0.0170 chunk 132 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 452 ASN C 452 ASN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.140326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.100595 restraints weight = 28840.015| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.45 r_work: 0.2763 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 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: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23147 Z= 0.078 Angle : 0.449 9.300 30985 Z= 0.230 Chirality : 0.037 0.124 3328 Planarity : 0.003 0.055 3712 Dihedral : 16.297 96.523 4120 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.40 % Allowed : 11.47 % Favored : 87.13 % 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: -0.20 (0.17), residues: 2552 helix: 0.80 (0.14), residues: 1508 sheet: 1.06 (0.65), residues: 76 loop : -1.76 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 509 TYR 0.017 0.001 TYR A 540 PHE 0.011 0.001 PHE B 316 TRP 0.015 0.001 TRP D 710 HIS 0.001 0.000 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00165 / 0.08 (23144) covalent geometry : angle 0.44900 / 0.23 (30968) SS BOND : bond 0.00007 / 0.00 ( 3) SS BOND : angle 0.01808 / 0.01 ( 17) hydrogen bonds : bond 0.02810 / 1.82 ( 804) hydrogen bonds : angle 3.02350 / 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 257 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.784 Fit side-chains REVERT: A 138 LEU cc_start: 0.8044 (mt) cc_final: 0.7797 (mp) REVERT: A 253 LYS cc_start: 0.7624 (ttpt) cc_final: 0.7342 (ttpp) REVERT: A 509 ARG cc_start: 0.5631 (ptp-110) cc_final: 0.5171 (mtm-85) REVERT: A 546 GLU cc_start: 0.8276 (tp30) cc_final: 0.7738 (mm-30) REVERT: A 712 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.6578 (mmm160) REVERT: A 743 LYS cc_start: 0.8898 (ptpt) cc_final: 0.8410 (ptmm) REVERT: B 253 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7352 (ttpp) REVERT: B 509 ARG cc_start: 0.5627 (ptp-110) cc_final: 0.5167 (mtm-85) REVERT: B 546 GLU cc_start: 0.8248 (tp30) cc_final: 0.7732 (mm-30) REVERT: B 712 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.6544 (mmm160) REVERT: B 743 LYS cc_start: 0.8868 (ptpt) cc_final: 0.8454 (ptmm) REVERT: C 138 LEU cc_start: 0.8026 (mt) cc_final: 0.7789 (mp) REVERT: C 475 LEU cc_start: 0.1164 (OUTLIER) cc_final: 0.0948 (tm) REVERT: C 488 MET cc_start: 0.7280 (mmt) cc_final: 0.6464 (mtp) REVERT: C 546 GLU cc_start: 0.8251 (tp30) cc_final: 0.7683 (mm-30) REVERT: C 712 ARG cc_start: 0.7234 (mmm-85) cc_final: 0.6534 (mmm160) REVERT: C 743 LYS cc_start: 0.8896 (ptpt) cc_final: 0.8406 (ptmm) REVERT: D 138 LEU cc_start: 0.8023 (mt) cc_final: 0.7783 (mp) REVERT: D 253 LYS cc_start: 0.7630 (ttpt) cc_final: 0.7330 (ttpp) REVERT: D 509 ARG cc_start: 0.5625 (ptp-110) cc_final: 0.5163 (mtm-85) REVERT: D 546 GLU cc_start: 0.8250 (tp30) cc_final: 0.7686 (mm-30) REVERT: D 743 LYS cc_start: 0.8895 (ptpt) cc_final: 0.8404 (ptmm) outliers start: 32 outliers final: 14 residues processed: 255 average time/residue: 0.1588 time to fit residues: 62.7177 Evaluate side-chains 221 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 703 PHE 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 C residue 703 PHE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 254 optimal weight: 0.0170 chunk 225 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 214 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 452 ASN C 452 ASN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.101451 restraints weight = 28573.719| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.36 r_work: 0.2764 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 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 = 0.2762 r_free = 0.2762 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: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23147 Z= 0.081 Angle : 0.464 12.516 30985 Z= 0.231 Chirality : 0.038 0.132 3328 Planarity : 0.003 0.055 3712 Dihedral : 15.552 94.369 4120 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.92 % Allowed : 12.17 % Favored : 86.91 % 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: 0.20 (0.17), residues: 2552 helix: 1.16 (0.14), residues: 1508 sheet: 1.07 (0.66), residues: 76 loop : -1.63 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 509 TYR 0.013 0.001 TYR B 540 PHE 0.012 0.001 PHE C 316 TRP 0.010 0.001 TRP A 710 HIS 0.002 0.000 HIS D 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.08 (23144) covalent geometry : angle 0.46430 / 0.23 (30968) SS BOND : bond 0.00031 / 0.02 ( 3) SS BOND : angle 0.07249 / 0.04 ( 17) hydrogen bonds : bond 0.03038 / 1.97 ( 804) hydrogen bonds : angle 3.01293 / 2.07 ( 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 249 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.781 Fit side-chains REVERT: A 138 LEU cc_start: 0.8064 (mt) cc_final: 0.7801 (mp) REVERT: A 253 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7345 (ttpp) REVERT: A 546 GLU cc_start: 0.8236 (tp30) cc_final: 0.7667 (mm-30) REVERT: A 611 LYS cc_start: 0.7185 (tptm) cc_final: 0.6945 (tppt) REVERT: A 712 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.6636 (mmm160) REVERT: A 743 LYS cc_start: 0.8913 (ptpt) cc_final: 0.8446 (ptmm) REVERT: B 138 LEU cc_start: 0.8071 (mt) cc_final: 0.7823 (mp) REVERT: B 253 LYS cc_start: 0.7632 (ttpt) cc_final: 0.7352 (ttpp) REVERT: B 546 GLU cc_start: 0.8226 (tp30) cc_final: 0.7677 (mm-30) REVERT: B 712 ARG cc_start: 0.7336 (mmm-85) cc_final: 0.6651 (mmm160) REVERT: B 743 LYS cc_start: 0.8838 (ptpt) cc_final: 0.8405 (ptmm) REVERT: C 138 LEU cc_start: 0.8065 (mt) cc_final: 0.7788 (mp) REVERT: C 475 LEU cc_start: 0.1230 (OUTLIER) cc_final: 0.0980 (tm) REVERT: C 546 GLU cc_start: 0.8181 (tp30) cc_final: 0.7647 (mm-30) REVERT: C 712 ARG cc_start: 0.7316 (mmm-85) cc_final: 0.6634 (mmm160) REVERT: C 743 LYS cc_start: 0.8908 (ptpt) cc_final: 0.8439 (ptmm) REVERT: D 138 LEU cc_start: 0.8047 (mt) cc_final: 0.7796 (mp) REVERT: D 253 LYS cc_start: 0.7655 (ttpt) cc_final: 0.7355 (ttpp) REVERT: D 546 GLU cc_start: 0.8213 (tp30) cc_final: 0.7639 (mm-30) REVERT: D 743 LYS cc_start: 0.8910 (ptpt) cc_final: 0.8440 (ptmm) outliers start: 21 outliers final: 13 residues processed: 245 average time/residue: 0.1645 time to fit residues: 61.7790 Evaluate side-chains 226 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 703 PHE 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 C residue 703 PHE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 159 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 252 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN D 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.093221 restraints weight = 28970.509| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.41 r_work: 0.2687 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23147 Z= 0.128 Angle : 0.518 12.131 30985 Z= 0.259 Chirality : 0.040 0.153 3328 Planarity : 0.003 0.054 3712 Dihedral : 15.912 97.547 4120 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.09 % Allowed : 12.74 % 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: 0.13 (0.17), residues: 2552 helix: 1.08 (0.14), residues: 1524 sheet: 1.05 (0.66), residues: 76 loop : -1.66 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 509 TYR 0.030 0.001 TYR B 540 PHE 0.012 0.001 PHE C 316 TRP 0.007 0.001 TRP C 493 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (23144) covalent geometry : angle 0.51796 / 0.26 (30968) SS BOND : bond 0.00153 / 0.08 ( 3) SS BOND : angle 0.10952 / 0.06 ( 17) hydrogen bonds : bond 0.04223 / 2.74 ( 804) hydrogen bonds : angle 3.28725 / 2.25 ( 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 236 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.843 Fit side-chains REVERT: A 153 ASP cc_start: 0.6797 (m-30) cc_final: 0.6480 (p0) REVERT: A 253 LYS cc_start: 0.7577 (ttpt) cc_final: 0.7282 (ttpp) REVERT: A 330 ASN cc_start: 0.7793 (t0) cc_final: 0.7555 (t0) REVERT: A 546 GLU cc_start: 0.8381 (tp30) cc_final: 0.7806 (mm-30) REVERT: A 611 LYS cc_start: 0.7231 (tptm) cc_final: 0.6988 (tppt) REVERT: A 712 ARG cc_start: 0.7352 (mmm-85) cc_final: 0.6641 (mmm160) REVERT: B 153 ASP cc_start: 0.6798 (m-30) cc_final: 0.6473 (p0) REVERT: B 253 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7281 (ttpp) REVERT: B 330 ASN cc_start: 0.7789 (t0) cc_final: 0.7549 (t0) REVERT: B 546 GLU cc_start: 0.8363 (tp30) cc_final: 0.7725 (mm-30) REVERT: B 611 LYS cc_start: 0.7242 (tptm) cc_final: 0.6994 (tppt) REVERT: B 712 ARG cc_start: 0.7322 (mmm-85) cc_final: 0.6614 (mmm160) REVERT: C 153 ASP cc_start: 0.6798 (m-30) cc_final: 0.6483 (p0) REVERT: C 475 LEU cc_start: 0.1263 (OUTLIER) cc_final: 0.1031 (tm) REVERT: C 546 GLU cc_start: 0.8379 (tp30) cc_final: 0.7765 (mm-30) REVERT: C 611 LYS cc_start: 0.7240 (tptm) cc_final: 0.6990 (tppt) REVERT: C 712 ARG cc_start: 0.7332 (mmm-85) cc_final: 0.6632 (mmm160) REVERT: D 153 ASP cc_start: 0.6794 (m-30) cc_final: 0.6491 (p0) REVERT: D 253 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7366 (ttpp) REVERT: D 330 ASN cc_start: 0.7785 (t0) cc_final: 0.7547 (t0) REVERT: D 546 GLU cc_start: 0.8343 (tp30) cc_final: 0.7772 (mm-30) outliers start: 25 outliers final: 15 residues processed: 233 average time/residue: 0.1799 time to fit residues: 63.3013 Evaluate side-chains 225 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 18 optimal weight: 0.9990 chunk 246 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 251 optimal weight: 0.0040 chunk 141 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 452 ASN C 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.136385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096782 restraints weight = 28914.575| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.38 r_work: 0.2742 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 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 = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23147 Z= 0.087 Angle : 0.471 10.907 30985 Z= 0.235 Chirality : 0.038 0.141 3328 Planarity : 0.003 0.057 3712 Dihedral : 15.237 93.112 4120 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.83 % Allowed : 12.96 % Favored : 86.21 % 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: 0.43 (0.17), residues: 2552 helix: 1.36 (0.14), residues: 1520 sheet: 1.02 (0.66), residues: 76 loop : -1.59 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 509 TYR 0.026 0.001 TYR A 540 PHE 0.012 0.001 PHE C 316 TRP 0.010 0.001 TRP D 710 HIS 0.002 0.000 HIS C 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (23144) covalent geometry : angle 0.47090 / 0.24 (30968) SS BOND : bond 0.00073 / 0.04 ( 3) SS BOND : angle 0.07511 / 0.04 ( 17) hydrogen bonds : bond 0.03151 / 2.05 ( 804) hydrogen bonds : angle 3.05447 / 2.09 ( 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 250 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.820 Fit side-chains REVERT: A 153 ASP cc_start: 0.6777 (m-30) cc_final: 0.6430 (p0) REVERT: A 253 LYS cc_start: 0.7615 (ttpt) cc_final: 0.7327 (ttpp) REVERT: A 546 GLU cc_start: 0.8327 (tp30) cc_final: 0.7747 (mm-30) REVERT: A 611 LYS cc_start: 0.7182 (tptm) cc_final: 0.6982 (tppt) REVERT: A 712 ARG cc_start: 0.7309 (mmm-85) cc_final: 0.6627 (mmm160) REVERT: A 743 LYS cc_start: 0.8841 (ptpt) cc_final: 0.8385 (ptmm) REVERT: B 153 ASP cc_start: 0.6784 (m-30) cc_final: 0.6429 (p0) REVERT: B 253 LYS cc_start: 0.7612 (ttpt) cc_final: 0.7328 (ttpp) REVERT: B 546 GLU cc_start: 0.8303 (tp30) cc_final: 0.7724 (mm-30) REVERT: B 611 LYS cc_start: 0.7198 (tptm) cc_final: 0.6990 (tppt) REVERT: B 712 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6610 (mmm160) REVERT: B 743 LYS cc_start: 0.8832 (ptpt) cc_final: 0.8420 (ptmm) REVERT: C 153 ASP cc_start: 0.6735 (m-30) cc_final: 0.6395 (p0) REVERT: C 475 LEU cc_start: 0.1379 (OUTLIER) cc_final: 0.1124 (tm) REVERT: C 546 GLU cc_start: 0.8298 (tp30) cc_final: 0.7720 (mm-30) REVERT: C 611 LYS cc_start: 0.7195 (tptm) cc_final: 0.6989 (tppt) REVERT: C 712 ARG cc_start: 0.7307 (mmm-85) cc_final: 0.6638 (mmm160) REVERT: C 743 LYS cc_start: 0.8842 (ptpt) cc_final: 0.8389 (ptmm) REVERT: D 153 ASP cc_start: 0.6737 (m-30) cc_final: 0.6399 (p0) REVERT: D 253 LYS cc_start: 0.7621 (ttpt) cc_final: 0.7321 (ttpp) REVERT: D 546 GLU cc_start: 0.8302 (tp30) cc_final: 0.7731 (mm-30) REVERT: D 743 LYS cc_start: 0.8840 (ptpt) cc_final: 0.8384 (ptmm) outliers start: 19 outliers final: 14 residues processed: 247 average time/residue: 0.1782 time to fit residues: 65.3038 Evaluate side-chains 237 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 211 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.096455 restraints weight = 29069.526| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.44 r_work: 0.2722 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 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 = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23147 Z= 0.097 Angle : 0.482 10.773 30985 Z= 0.241 Chirality : 0.039 0.151 3328 Planarity : 0.004 0.055 3712 Dihedral : 15.182 92.995 4120 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.74 % Allowed : 13.44 % 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: 0.53 (0.17), residues: 2552 helix: 1.44 (0.14), residues: 1520 sheet: 1.01 (0.66), residues: 76 loop : -1.54 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 149 TYR 0.026 0.001 TYR C 540 PHE 0.012 0.001 PHE C 316 TRP 0.010 0.001 TRP D 710 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (23144) covalent geometry : angle 0.48181 / 0.24 (30968) SS BOND : bond 0.00104 / 0.05 ( 3) SS BOND : angle 0.02694 / 0.01 ( 17) hydrogen bonds : bond 0.03474 / 2.26 ( 804) hydrogen bonds : angle 3.12258 / 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 242 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.718 Fit side-chains REVERT: A 153 ASP cc_start: 0.6814 (m-30) cc_final: 0.6434 (p0) REVERT: A 253 LYS cc_start: 0.7602 (ttpt) cc_final: 0.7316 (ttpp) REVERT: A 546 GLU cc_start: 0.8354 (tp30) cc_final: 0.7780 (mm-30) REVERT: A 712 ARG cc_start: 0.7322 (mmm-85) cc_final: 0.6628 (mmm160) REVERT: A 743 LYS cc_start: 0.8861 (ptpt) cc_final: 0.8409 (ptmm) REVERT: B 153 ASP cc_start: 0.6813 (m-30) cc_final: 0.6431 (p0) REVERT: B 253 LYS cc_start: 0.7605 (ttpt) cc_final: 0.7318 (ttpp) REVERT: B 546 GLU cc_start: 0.8310 (tp30) cc_final: 0.7652 (mm-30) REVERT: B 611 LYS cc_start: 0.7195 (tptm) cc_final: 0.6991 (tppt) REVERT: B 712 ARG cc_start: 0.7304 (mmm-85) cc_final: 0.6617 (mmm160) REVERT: B 743 LYS cc_start: 0.8839 (ptpt) cc_final: 0.8429 (ptmm) REVERT: C 153 ASP cc_start: 0.6810 (m-30) cc_final: 0.6439 (p0) REVERT: C 475 LEU cc_start: 0.1385 (OUTLIER) cc_final: 0.1130 (tm) REVERT: C 546 GLU cc_start: 0.8307 (tp30) cc_final: 0.7742 (mm-30) REVERT: C 611 LYS cc_start: 0.7194 (tptm) cc_final: 0.6993 (tppt) REVERT: C 712 ARG cc_start: 0.7340 (mmm-85) cc_final: 0.6658 (mmm160) REVERT: C 743 LYS cc_start: 0.8851 (ptpt) cc_final: 0.8398 (ptmm) REVERT: D 153 ASP cc_start: 0.6790 (m-30) cc_final: 0.6450 (p0) REVERT: D 253 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7347 (ttpp) REVERT: D 546 GLU cc_start: 0.8309 (tp30) cc_final: 0.7745 (mm-30) REVERT: D 743 LYS cc_start: 0.8856 (ptpt) cc_final: 0.8398 (ptmm) outliers start: 17 outliers final: 15 residues processed: 241 average time/residue: 0.1764 time to fit residues: 63.8735 Evaluate side-chains 235 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 66 optimal weight: 5.9990 chunk 209 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 217 optimal weight: 0.0370 chunk 212 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.135978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.096263 restraints weight = 28875.443| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.40 r_work: 0.2736 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- 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: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23147 Z= 0.089 Angle : 0.474 10.795 30985 Z= 0.237 Chirality : 0.038 0.154 3328 Planarity : 0.003 0.056 3712 Dihedral : 14.925 91.011 4120 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.70 % Allowed : 13.66 % Favored : 85.64 % 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: 0.66 (0.17), residues: 2552 helix: 1.56 (0.14), residues: 1520 sheet: 1.01 (0.66), residues: 76 loop : -1.52 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 149 TYR 0.026 0.001 TYR A 540 PHE 0.012 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 0.00203 / 0.09 (23144) covalent geometry : angle 0.47405 / 0.24 (30968) SS BOND : bond 0.00100 / 0.05 ( 3) SS BOND : angle 0.07294 / 0.04 ( 17) hydrogen bonds : bond 0.03218 / 2.09 ( 804) hydrogen bonds : angle 3.07437 / 2.11 ( 2400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4566.64 seconds wall clock time: 79 minutes 5.27 seconds (4745.27 seconds total)