Starting phenix.real_space_refine on Thu Mar 5 14:10:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mim_23856/03_2026/7mim_23856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mim_23856/03_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_23856/03_2026/7mim_23856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mim_23856/03_2026/7mim_23856.map" model { file = "/net/cci-nas-00/data/ceres_data/7mim_23856/03_2026/7mim_23856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mim_23856/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 7.27, per 1000 atoms: 0.32 Number of scatterers: 22728 At special positions: 0 Unit cell: (129.285, 129.285, 132.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 36 15.00 Na 4 11.00 O 4024 8.00 N 3476 7.00 C 15064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=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: 1.99 Conformation dependent library (CDL) restraints added in 955.4 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: 0.63 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: 3.38 Time building geometry restraints manager: 2.64 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: 13318 29.61 - 59.22: 807 59.22 - 88.83: 142 88.83 - 118.45: 32 118.45 - 148.06: 20 Dihedral angle restraints: 14319 sinusoidal: 6763 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 14316 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: 1.220 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 22.070 Find NCS groups from input model: 0.520 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 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 : 19.541 148.058 9384 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.01013 (23144) covalent geometry : angle 1.36620 (30968) SS BOND : bond 0.00022 ( 3) SS BOND : angle 0.35645 ( 17) hydrogen bonds : bond 0.37044 ( 804) hydrogen bonds : angle 8.95720 ( 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 : 0.610 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: 0.1772 time to fit residues: 106.1042 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 : 0.844 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 227 GLN A 394 ASN A 452 ASN A 477 HIS B 220 ASN B 227 GLN B 394 ASN B 452 ASN B 477 HIS C 220 ASN C 227 GLN C 394 ASN C 452 ASN C 477 HIS D 220 ASN D 227 GLN D 394 ASN D 452 ASN D 477 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.136609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.097500 restraints weight = 30530.880| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.57 r_work: 0.2829 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 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 = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2515 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= 0.111 Angle : 0.547 8.212 30985 Z= 0.283 Chirality : 0.040 0.155 3328 Planarity : 0.005 0.061 3712 Dihedral : 21.167 120.654 4336 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.23 % Allowed : 7.62 % 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: -3.87 (0.13), residues: 2552 helix: -2.66 (0.10), residues: 1528 sheet: 1.01 (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 0.013 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 covalent geometry : bond 0.00244 (23144) covalent geometry : angle 0.54721 (30968) SS BOND : bond 0.00079 ( 3) SS BOND : angle 0.04145 ( 17) hydrogen bonds : bond 0.04795 ( 804) hydrogen bonds : angle 3.80928 ( 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 364 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 336 time to evaluate : 0.606 Fit side-chains REVERT: A 121 LYS cc_start: 0.8479 (mttm) cc_final: 0.8022 (mtpp) REVERT: A 323 MET cc_start: 0.8847 (ttm) cc_final: 0.8528 (ttp) REVERT: A 488 MET cc_start: 0.7606 (tpp) cc_final: 0.7208 (mtp) REVERT: A 509 ARG cc_start: 0.5837 (ptp-170) cc_final: 0.5610 (mtm110) REVERT: A 546 GLU cc_start: 0.8341 (tp30) cc_final: 0.7889 (mm-30) REVERT: A 618 ASP cc_start: 0.7205 (m-30) cc_final: 0.6961 (p0) REVERT: A 743 LYS cc_start: 0.8912 (ptpt) cc_final: 0.8683 (ptmm) REVERT: B 121 LYS cc_start: 0.8478 (mttm) cc_final: 0.8017 (mtpp) REVERT: B 323 MET cc_start: 0.8846 (ttm) cc_final: 0.8526 (ttp) REVERT: B 447 PHE cc_start: 0.8709 (m-10) cc_final: 0.8498 (m-80) REVERT: B 488 MET cc_start: 0.7601 (tpp) cc_final: 0.7213 (mtp) REVERT: B 509 ARG cc_start: 0.5840 (ptp-170) cc_final: 0.5610 (mtm110) REVERT: B 546 GLU cc_start: 0.8361 (tp30) cc_final: 0.7899 (mm-30) REVERT: B 618 ASP cc_start: 0.7210 (m-30) cc_final: 0.6971 (p0) REVERT: B 743 LYS cc_start: 0.8913 (ptpt) cc_final: 0.8685 (ptmm) REVERT: C 121 LYS cc_start: 0.8484 (mttm) cc_final: 0.8025 (mtpp) REVERT: C 323 MET cc_start: 0.8846 (ttm) cc_final: 0.8525 (ttp) REVERT: C 488 MET cc_start: 0.7592 (tpp) cc_final: 0.7202 (mtp) REVERT: C 546 GLU cc_start: 0.8332 (tp30) cc_final: 0.7878 (mm-30) REVERT: C 618 ASP cc_start: 0.7211 (m-30) cc_final: 0.6972 (p0) REVERT: C 707 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8319 (pp) REVERT: C 743 LYS cc_start: 0.8910 (ptpt) cc_final: 0.8680 (ptmm) REVERT: D 121 LYS cc_start: 0.8488 (mttm) cc_final: 0.8031 (mtpp) REVERT: D 323 MET cc_start: 0.8843 (ttm) cc_final: 0.8522 (ttp) REVERT: D 488 MET cc_start: 0.7624 (tpp) cc_final: 0.7150 (mtp) REVERT: D 509 ARG cc_start: 0.5847 (ptp-170) cc_final: 0.5605 (mtm110) REVERT: D 546 GLU cc_start: 0.8331 (tp30) cc_final: 0.7891 (mm-30) REVERT: D 743 LYS cc_start: 0.8906 (ptpt) cc_final: 0.8676 (ptmm) outliers start: 28 outliers final: 5 residues processed: 355 average time/residue: 0.1724 time to fit residues: 91.4163 Evaluate side-chains 275 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 269 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain B residue 519 ASP 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: 0.0870 chunk 189 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 124 optimal weight: 0.0040 chunk 40 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.8176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 561 ASN A 735 ASN B 244 HIS B 561 ASN B 735 ASN C 244 HIS C 561 ASN C 735 ASN D 244 HIS D 561 ASN D 735 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.091893 restraints weight = 30788.507| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.60 r_work: 0.2750 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23147 Z= 0.165 Angle : 0.568 8.287 30985 Z= 0.287 Chirality : 0.042 0.142 3328 Planarity : 0.004 0.060 3712 Dihedral : 19.948 110.673 4336 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.84 % Allowed : 8.89 % Favored : 89.27 % 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: -2.50 (0.15), residues: 2552 helix: -1.29 (0.12), residues: 1532 sheet: 1.18 (0.65), residues: 76 loop : -2.36 (0.17), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 509 TYR 0.017 0.002 TYR D 575 PHE 0.015 0.001 PHE C 193 TRP 0.013 0.001 TRP D 493 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00402 (23144) covalent geometry : angle 0.56853 (30968) SS BOND : bond 0.00147 ( 3) SS BOND : angle 0.16965 ( 17) hydrogen bonds : bond 0.05503 ( 804) hydrogen bonds : angle 3.63221 ( 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 310 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 0.610 Fit side-chains REVERT: A 509 ARG cc_start: 0.5953 (ptp-170) cc_final: 0.5600 (mtm110) REVERT: A 546 GLU cc_start: 0.8492 (tp30) cc_final: 0.8026 (mm-30) REVERT: A 707 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8369 (pp) REVERT: A 743 LYS cc_start: 0.8930 (ptpt) cc_final: 0.8604 (ptmm) REVERT: B 447 PHE cc_start: 0.8789 (m-10) cc_final: 0.8563 (m-80) REVERT: B 488 MET cc_start: 0.7640 (tpp) cc_final: 0.7192 (mtp) REVERT: B 509 ARG cc_start: 0.5946 (ptp-170) cc_final: 0.5594 (mtm110) REVERT: B 546 GLU cc_start: 0.8464 (tp30) cc_final: 0.7883 (mm-30) REVERT: B 707 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8248 (pp) REVERT: B 712 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7462 (mmm-85) REVERT: B 743 LYS cc_start: 0.8935 (ptpt) cc_final: 0.8613 (ptmm) REVERT: C 546 GLU cc_start: 0.8476 (tp30) cc_final: 0.7895 (mm-30) REVERT: C 743 LYS cc_start: 0.8930 (ptpt) cc_final: 0.8604 (ptmm) REVERT: D 509 ARG cc_start: 0.5950 (ptp-170) cc_final: 0.5598 (mtm110) REVERT: D 546 GLU cc_start: 0.8442 (tp30) cc_final: 0.7887 (mm-30) REVERT: D 721 CYS cc_start: 0.8811 (m) cc_final: 0.8606 (p) REVERT: D 743 LYS cc_start: 0.8924 (ptpt) cc_final: 0.8599 (ptmm) outliers start: 42 outliers final: 18 residues processed: 287 average time/residue: 0.1753 time to fit residues: 75.2745 Evaluate side-chains 266 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 517 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: 3.9990 chunk 241 optimal weight: 7.9990 chunk 216 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 242 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.094740 restraints weight = 30602.217| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.61 r_work: 0.2796 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3108 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= 0.105 Angle : 0.490 8.748 30985 Z= 0.247 Chirality : 0.039 0.144 3328 Planarity : 0.004 0.057 3712 Dihedral : 18.551 105.110 4336 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.58 % Allowed : 9.24 % Favored : 89.19 % 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: -1.63 (0.16), residues: 2552 helix: -0.43 (0.13), residues: 1532 sheet: 1.14 (0.65), residues: 76 loop : -2.30 (0.17), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 509 TYR 0.017 0.001 TYR A 540 PHE 0.016 0.001 PHE C 193 TRP 0.011 0.001 TRP D 710 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00244 (23144) covalent geometry : angle 0.49001 (30968) SS BOND : bond 0.00044 ( 3) SS BOND : angle 0.10174 ( 17) hydrogen bonds : bond 0.03936 ( 804) hydrogen bonds : angle 3.25809 ( 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 315 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 0.793 Fit side-chains REVERT: A 253 LYS cc_start: 0.7731 (ttpt) cc_final: 0.7459 (ttpp) REVERT: A 320 MET cc_start: 0.8660 (mmm) cc_final: 0.8340 (mmm) REVERT: A 509 ARG cc_start: 0.5785 (ptp-170) cc_final: 0.5370 (mtm110) REVERT: A 546 GLU cc_start: 0.8368 (tp30) cc_final: 0.7731 (mm-30) REVERT: A 743 LYS cc_start: 0.8932 (ptpt) cc_final: 0.8578 (ptmm) REVERT: B 253 LYS cc_start: 0.7732 (ttpt) cc_final: 0.7460 (ttpp) REVERT: B 320 MET cc_start: 0.8662 (mmm) cc_final: 0.8340 (mmm) REVERT: B 447 PHE cc_start: 0.8762 (m-10) cc_final: 0.8538 (m-80) REVERT: B 488 MET cc_start: 0.7603 (tpp) cc_final: 0.7199 (mtp) REVERT: B 509 ARG cc_start: 0.5777 (ptp-170) cc_final: 0.5368 (mtm110) REVERT: B 546 GLU cc_start: 0.8335 (tp30) cc_final: 0.7798 (mm-30) REVERT: B 743 LYS cc_start: 0.8928 (ptpt) cc_final: 0.8579 (ptmm) REVERT: C 320 MET cc_start: 0.8671 (mmm) cc_final: 0.8354 (mmm) REVERT: C 546 GLU cc_start: 0.8352 (tp30) cc_final: 0.7757 (mm-30) REVERT: C 743 LYS cc_start: 0.8926 (ptpt) cc_final: 0.8573 (ptmm) REVERT: D 253 LYS cc_start: 0.7761 (ttpt) cc_final: 0.7479 (ttpp) REVERT: D 320 MET cc_start: 0.8662 (mmm) cc_final: 0.8343 (mmm) REVERT: D 509 ARG cc_start: 0.5786 (ptp-170) cc_final: 0.5372 (mtm110) REVERT: D 546 GLU cc_start: 0.8342 (tp30) cc_final: 0.7758 (mm-30) REVERT: D 743 LYS cc_start: 0.8926 (ptpt) cc_final: 0.8573 (ptmm) outliers start: 36 outliers final: 22 residues processed: 302 average time/residue: 0.1687 time to fit residues: 78.1029 Evaluate side-chains 276 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain C residue 128 SER 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 458 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 208 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.093139 restraints weight = 29997.540| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.53 r_work: 0.2788 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3224 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= 0.115 Angle : 0.496 9.037 30985 Z= 0.252 Chirality : 0.040 0.143 3328 Planarity : 0.004 0.055 3712 Dihedral : 17.832 105.201 4336 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.23 % Allowed : 10.42 % Favored : 88.35 % 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: -0.94 (0.16), residues: 2552 helix: 0.16 (0.14), residues: 1512 sheet: 1.15 (0.66), residues: 76 loop : -2.00 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 712 TYR 0.016 0.001 TYR A 540 PHE 0.012 0.001 PHE A 316 TRP 0.009 0.001 TRP B 710 HIS 0.003 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00273 (23144) covalent geometry : angle 0.49649 (30968) SS BOND : bond 0.00074 ( 3) SS BOND : angle 0.13157 ( 17) hydrogen bonds : bond 0.04213 ( 804) hydrogen bonds : angle 3.29153 ( 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 275 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.797 Fit side-chains REVERT: A 253 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7438 (ttpp) REVERT: A 546 GLU cc_start: 0.8391 (tp30) cc_final: 0.7847 (mm-30) REVERT: B 253 LYS cc_start: 0.7702 (ttpt) cc_final: 0.7436 (ttpp) REVERT: B 447 PHE cc_start: 0.8755 (m-10) cc_final: 0.8503 (m-80) REVERT: B 488 MET cc_start: 0.7606 (tpp) cc_final: 0.7201 (mtp) REVERT: B 546 GLU cc_start: 0.8400 (tp30) cc_final: 0.7843 (mm-30) REVERT: C 546 GLU cc_start: 0.8390 (tp30) cc_final: 0.7850 (mm-30) REVERT: D 253 LYS cc_start: 0.7720 (ttpt) cc_final: 0.7437 (ttpp) REVERT: D 546 GLU cc_start: 0.8389 (tp30) cc_final: 0.7865 (mm-30) outliers start: 28 outliers final: 21 residues processed: 267 average time/residue: 0.1625 time to fit residues: 66.5017 Evaluate side-chains 251 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 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: 0.7980 chunk 104 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 164 optimal weight: 0.0370 chunk 201 optimal weight: 0.5980 chunk 186 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.092967 restraints weight = 30241.128| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.60 r_work: 0.2766 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 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 = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3364 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= 0.124 Angle : 0.504 9.925 30985 Z= 0.255 Chirality : 0.040 0.147 3328 Planarity : 0.004 0.055 3712 Dihedral : 17.569 104.688 4336 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.23 % Allowed : 10.90 % Favored : 87.87 % 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: -0.67 (0.16), residues: 2552 helix: 0.41 (0.14), residues: 1540 sheet: 1.12 (0.66), residues: 76 loop : -2.02 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 712 TYR 0.017 0.001 TYR A 540 PHE 0.013 0.001 PHE D 316 TRP 0.008 0.001 TRP A 710 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00299 (23144) covalent geometry : angle 0.50394 (30968) SS BOND : bond 0.00110 ( 3) SS BOND : angle 0.10652 ( 17) hydrogen bonds : bond 0.04277 ( 804) hydrogen bonds : angle 3.31281 ( 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 261 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.813 Fit side-chains REVERT: A 320 MET cc_start: 0.8747 (mmm) cc_final: 0.8409 (mmm) REVERT: A 546 GLU cc_start: 0.8476 (tp30) cc_final: 0.7928 (mm-30) REVERT: A 712 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.6930 (mmm160) REVERT: B 320 MET cc_start: 0.8743 (mmm) cc_final: 0.8394 (mmm) REVERT: B 447 PHE cc_start: 0.8757 (m-10) cc_final: 0.8500 (m-80) REVERT: B 475 LEU cc_start: 0.1681 (OUTLIER) cc_final: 0.1417 (tm) REVERT: B 488 MET cc_start: 0.7642 (tpp) cc_final: 0.7226 (mtp) REVERT: B 546 GLU cc_start: 0.8463 (tp30) cc_final: 0.7935 (mm-30) REVERT: C 320 MET cc_start: 0.8736 (mmm) cc_final: 0.8401 (mmm) REVERT: C 546 GLU cc_start: 0.8481 (tp30) cc_final: 0.7943 (mm-30) REVERT: D 320 MET cc_start: 0.8738 (mmm) cc_final: 0.8400 (mmm) REVERT: D 546 GLU cc_start: 0.8473 (tp30) cc_final: 0.7943 (mm-30) outliers start: 28 outliers final: 18 residues processed: 250 average time/residue: 0.1825 time to fit residues: 68.1543 Evaluate side-chains 236 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 703 PHE 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 703 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.095405 restraints weight = 29954.893| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.57 r_work: 0.2786 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23147 Z= 0.096 Angle : 0.492 12.461 30985 Z= 0.244 Chirality : 0.039 0.144 3328 Planarity : 0.004 0.056 3712 Dihedral : 16.898 102.005 4336 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.49 % Allowed : 10.77 % Favored : 87.74 % 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: 0.90 (0.14), residues: 1520 sheet: 1.05 (0.65), residues: 76 loop : -1.84 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 712 TYR 0.018 0.001 TYR A 540 PHE 0.013 0.001 PHE A 316 TRP 0.011 0.001 TRP C 710 HIS 0.002 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00222 (23144) covalent geometry : angle 0.49201 (30968) SS BOND : bond 0.00072 ( 3) SS BOND : angle 0.01864 ( 17) hydrogen bonds : bond 0.03527 ( 804) hydrogen bonds : angle 3.10687 ( 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 281 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.852 Fit side-chains REVERT: A 153 ASP cc_start: 0.6838 (m-30) cc_final: 0.6491 (p0) REVERT: A 253 LYS cc_start: 0.7705 (ttpt) cc_final: 0.7432 (ttpp) REVERT: A 320 MET cc_start: 0.8603 (mmm) cc_final: 0.8230 (mmm) REVERT: A 546 GLU cc_start: 0.8428 (tp30) cc_final: 0.7867 (mm-30) REVERT: A 712 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.6885 (mmm160) REVERT: B 253 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7430 (ttpp) REVERT: B 320 MET cc_start: 0.8596 (mmm) cc_final: 0.8216 (mmm) REVERT: B 447 PHE cc_start: 0.8625 (m-10) cc_final: 0.8336 (m-80) REVERT: B 475 LEU cc_start: 0.1788 (OUTLIER) cc_final: 0.1420 (tm) REVERT: B 488 MET cc_start: 0.7587 (tpp) cc_final: 0.7185 (mtp) REVERT: B 546 GLU cc_start: 0.8429 (tp30) cc_final: 0.7861 (mm-30) REVERT: B 712 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.6849 (mmm160) REVERT: C 320 MET cc_start: 0.8607 (mmm) cc_final: 0.8236 (mmm) REVERT: C 546 GLU cc_start: 0.8431 (tp30) cc_final: 0.7883 (mm-30) REVERT: C 707 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8124 (pp) REVERT: D 153 ASP cc_start: 0.6799 (m-30) cc_final: 0.6461 (p0) REVERT: D 253 LYS cc_start: 0.7736 (ttpt) cc_final: 0.7449 (ttpp) REVERT: D 320 MET cc_start: 0.8598 (mmm) cc_final: 0.8230 (mmm) REVERT: D 546 GLU cc_start: 0.8435 (tp30) cc_final: 0.7887 (mm-30) outliers start: 34 outliers final: 20 residues processed: 274 average time/residue: 0.1642 time to fit residues: 69.1531 Evaluate side-chains 249 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 491 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 159 optimal weight: 0.0020 chunk 158 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 chunk 193 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.093625 restraints weight = 28937.487| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.39 r_work: 0.2792 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 0.030 23147 Z= 0.108 Angle : 0.503 12.072 30985 Z= 0.250 Chirality : 0.040 0.148 3328 Planarity : 0.004 0.055 3712 Dihedral : 16.696 101.889 4336 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.23 % Allowed : 11.56 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.03 (0.17), residues: 2552 helix: 0.98 (0.14), residues: 1544 sheet: 1.05 (0.66), residues: 76 loop : -1.85 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 712 TYR 0.018 0.001 TYR A 540 PHE 0.013 0.001 PHE A 316 TRP 0.009 0.001 TRP C 710 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00255 (23144) covalent geometry : angle 0.50331 (30968) SS BOND : bond 0.00102 ( 3) SS BOND : angle 0.04281 ( 17) hydrogen bonds : bond 0.03924 ( 804) hydrogen bonds : angle 3.19794 ( 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 263 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.749 Fit side-chains REVERT: A 153 ASP cc_start: 0.6806 (m-30) cc_final: 0.6478 (p0) REVERT: A 320 MET cc_start: 0.8642 (mmm) cc_final: 0.8259 (mmm) REVERT: A 546 GLU cc_start: 0.8383 (tp30) cc_final: 0.7766 (mm-30) REVERT: A 555 MET cc_start: 0.8676 (mtm) cc_final: 0.8412 (mtm) REVERT: A 611 LYS cc_start: 0.7208 (tptm) cc_final: 0.6984 (tppt) REVERT: A 712 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.6868 (mmm160) REVERT: B 153 ASP cc_start: 0.6814 (m-30) cc_final: 0.6482 (p0) REVERT: B 320 MET cc_start: 0.8633 (mmm) cc_final: 0.8240 (mmm) REVERT: B 447 PHE cc_start: 0.8630 (m-10) cc_final: 0.8326 (m-80) REVERT: B 475 LEU cc_start: 0.1912 (OUTLIER) cc_final: 0.1492 (tm) REVERT: B 488 MET cc_start: 0.7589 (tpp) cc_final: 0.7173 (mtp) REVERT: B 546 GLU cc_start: 0.8384 (tp30) cc_final: 0.7780 (mm-30) REVERT: B 611 LYS cc_start: 0.7216 (tptm) cc_final: 0.6984 (tppt) REVERT: B 712 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.6856 (mmm160) REVERT: C 153 ASP cc_start: 0.6816 (m-30) cc_final: 0.6490 (p0) REVERT: C 320 MET cc_start: 0.8633 (mmm) cc_final: 0.8240 (mmm) REVERT: C 546 GLU cc_start: 0.8385 (tp30) cc_final: 0.7788 (mm-30) REVERT: C 611 LYS cc_start: 0.7207 (tptm) cc_final: 0.6978 (tppt) REVERT: D 153 ASP cc_start: 0.6759 (m-30) cc_final: 0.6451 (p0) REVERT: D 253 LYS cc_start: 0.7681 (ttpt) cc_final: 0.7404 (ttpp) REVERT: D 320 MET cc_start: 0.8643 (mmm) cc_final: 0.8258 (mmm) REVERT: D 546 GLU cc_start: 0.8387 (tp30) cc_final: 0.7781 (mm-30) REVERT: D 555 MET cc_start: 0.8674 (mtm) cc_final: 0.8409 (mtm) outliers start: 28 outliers final: 19 residues processed: 258 average time/residue: 0.1896 time to fit residues: 72.7941 Evaluate side-chains 242 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 18 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 205 optimal weight: 0.0570 chunk 129 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 251 optimal weight: 0.3980 chunk 141 optimal weight: 0.0270 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 178 ASN C 178 ASN D 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.086897 restraints weight = 29322.883| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.49 r_work: 0.2786 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 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 = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3656 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= 0.113 Angle : 0.509 10.861 30985 Z= 0.254 Chirality : 0.040 0.141 3328 Planarity : 0.004 0.075 3712 Dihedral : 16.464 101.394 4336 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.75 % Allowed : 11.47 % Favored : 86.78 % 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: 0.18 (0.17), residues: 2552 helix: 1.12 (0.14), residues: 1548 sheet: 1.02 (0.66), residues: 76 loop : -1.71 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 149 TYR 0.019 0.001 TYR D 540 PHE 0.013 0.001 PHE C 316 TRP 0.009 0.001 TRP C 710 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00270 (23144) covalent geometry : angle 0.50885 (30968) SS BOND : bond 0.00099 ( 3) SS BOND : angle 0.03873 ( 17) hydrogen bonds : bond 0.03917 ( 804) hydrogen bonds : angle 3.21401 ( 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 261 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.643 Fit side-chains REVERT: A 153 ASP cc_start: 0.6672 (m-30) cc_final: 0.6209 (p0) REVERT: A 320 MET cc_start: 0.8619 (mmm) cc_final: 0.8197 (mmm) REVERT: A 546 GLU cc_start: 0.8403 (tp30) cc_final: 0.7719 (mm-30) REVERT: A 555 MET cc_start: 0.8639 (mtm) cc_final: 0.8373 (mtm) REVERT: A 611 LYS cc_start: 0.7181 (tptm) cc_final: 0.6948 (tppt) REVERT: A 712 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.6779 (mmm160) REVERT: B 153 ASP cc_start: 0.6676 (m-30) cc_final: 0.6210 (p0) REVERT: B 320 MET cc_start: 0.8634 (mmm) cc_final: 0.8212 (mmm) REVERT: B 447 PHE cc_start: 0.8573 (m-10) cc_final: 0.8265 (m-80) REVERT: B 475 LEU cc_start: 0.2259 (OUTLIER) cc_final: 0.1727 (tm) REVERT: B 488 MET cc_start: 0.7549 (tpp) cc_final: 0.7152 (mtp) REVERT: B 546 GLU cc_start: 0.8406 (tp30) cc_final: 0.7735 (mm-30) REVERT: B 611 LYS cc_start: 0.7181 (tptm) cc_final: 0.6949 (tppt) REVERT: B 712 ARG cc_start: 0.7489 (mmm-85) cc_final: 0.6719 (mmm160) REVERT: C 153 ASP cc_start: 0.6677 (m-30) cc_final: 0.6215 (p0) REVERT: C 320 MET cc_start: 0.8638 (mmm) cc_final: 0.8215 (mmm) REVERT: C 546 GLU cc_start: 0.8404 (tp30) cc_final: 0.7740 (mm-30) REVERT: C 555 MET cc_start: 0.8636 (mtm) cc_final: 0.8373 (mtm) REVERT: C 611 LYS cc_start: 0.7179 (tptm) cc_final: 0.6946 (tppt) REVERT: D 153 ASP cc_start: 0.6740 (m-30) cc_final: 0.6301 (p0) REVERT: D 320 MET cc_start: 0.8621 (mmm) cc_final: 0.8200 (mmm) REVERT: D 546 GLU cc_start: 0.8413 (tp30) cc_final: 0.7742 (mm-30) REVERT: D 555 MET cc_start: 0.8617 (mtm) cc_final: 0.8348 (mtm) outliers start: 40 outliers final: 24 residues processed: 253 average time/residue: 0.1815 time to fit residues: 68.9230 Evaluate side-chains 240 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.095527 restraints weight = 29061.877| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.33 r_work: 0.2722 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3762 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= 0.100 Angle : 0.497 11.069 30985 Z= 0.247 Chirality : 0.039 0.145 3328 Planarity : 0.004 0.064 3712 Dihedral : 16.069 99.497 4336 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.01 % Allowed : 12.13 % Favored : 86.87 % 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: 0.49 (0.17), residues: 2552 helix: 1.38 (0.14), residues: 1524 sheet: 1.02 (0.65), residues: 76 loop : -1.53 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 149 TYR 0.020 0.001 TYR A 540 PHE 0.014 0.001 PHE D 316 TRP 0.010 0.001 TRP B 710 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00233 (23144) covalent geometry : angle 0.49748 (30968) SS BOND : bond 0.00080 ( 3) SS BOND : angle 0.01411 ( 17) hydrogen bonds : bond 0.03593 ( 804) hydrogen bonds : angle 3.13551 ( 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 249 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.696 Fit side-chains REVERT: A 153 ASP cc_start: 0.6765 (m-30) cc_final: 0.6318 (p0) REVERT: A 320 MET cc_start: 0.8584 (mmm) cc_final: 0.8135 (mmm) REVERT: A 546 GLU cc_start: 0.8373 (tp30) cc_final: 0.7694 (mm-30) REVERT: A 555 MET cc_start: 0.8576 (mtm) cc_final: 0.8321 (mtm) REVERT: A 712 ARG cc_start: 0.7444 (mmm-85) cc_final: 0.6709 (mmm160) REVERT: B 153 ASP cc_start: 0.6769 (m-30) cc_final: 0.6319 (p0) REVERT: B 282 MET cc_start: 0.8459 (ttp) cc_final: 0.8244 (ttm) REVERT: B 320 MET cc_start: 0.8555 (mmm) cc_final: 0.8107 (mmm) REVERT: B 447 PHE cc_start: 0.8467 (m-10) cc_final: 0.8168 (m-80) REVERT: B 475 LEU cc_start: 0.2509 (OUTLIER) cc_final: 0.1886 (tm) REVERT: B 488 MET cc_start: 0.7481 (tpp) cc_final: 0.7090 (mtp) REVERT: B 546 GLU cc_start: 0.8370 (tp30) cc_final: 0.7698 (mm-30) REVERT: B 712 ARG cc_start: 0.7406 (mmm-85) cc_final: 0.6633 (mmm160) REVERT: C 153 ASP cc_start: 0.6771 (m-30) cc_final: 0.6323 (p0) REVERT: C 282 MET cc_start: 0.8452 (ttp) cc_final: 0.8244 (ttm) REVERT: C 320 MET cc_start: 0.8566 (mmm) cc_final: 0.8120 (mmm) REVERT: C 546 GLU cc_start: 0.8362 (tp30) cc_final: 0.7712 (mm-30) REVERT: C 555 MET cc_start: 0.8567 (mtm) cc_final: 0.8313 (mtm) REVERT: D 153 ASP cc_start: 0.6833 (m-30) cc_final: 0.6396 (p0) REVERT: D 320 MET cc_start: 0.8581 (mmm) cc_final: 0.8138 (mmm) REVERT: D 546 GLU cc_start: 0.8363 (tp30) cc_final: 0.7702 (mm-30) REVERT: D 555 MET cc_start: 0.8565 (mtm) cc_final: 0.8300 (mtm) outliers start: 23 outliers final: 19 residues processed: 246 average time/residue: 0.1980 time to fit residues: 71.5808 Evaluate side-chains 240 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 491 LEU 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: 3.9990 chunk 209 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 163 optimal weight: 0.0050 chunk 0 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094385 restraints weight = 28957.710| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.39 r_work: 0.2830 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 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 = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3783 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= 0.102 Angle : 0.498 10.385 30985 Z= 0.249 Chirality : 0.039 0.140 3328 Planarity : 0.004 0.057 3712 Dihedral : 15.957 98.596 4336 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.18 % Allowed : 11.78 % Favored : 87.04 % 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: 0.58 (0.17), residues: 2552 helix: 1.45 (0.14), residues: 1524 sheet: 1.04 (0.65), residues: 76 loop : -1.47 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 149 TYR 0.020 0.001 TYR C 540 PHE 0.013 0.001 PHE D 316 TRP 0.010 0.001 TRP A 710 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00240 (23144) covalent geometry : angle 0.49855 (30968) SS BOND : bond 0.00092 ( 3) SS BOND : angle 0.16073 ( 17) hydrogen bonds : bond 0.03668 ( 804) hydrogen bonds : angle 3.16263 ( 2400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4751.65 seconds wall clock time: 81 minutes 56.88 seconds (4916.88 seconds total)