Starting phenix.real_space_refine on Sat Jul 4 18:28:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mik_23854/07_2026/7mik_23854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mik_23854/07_2026/7mik_23854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mik_23854/07_2026/7mik_23854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mik_23854/07_2026/7mik_23854.map" model { file = "/net/cci-nas-00/data/ceres_data/7mik_23854/07_2026/7mik_23854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mik_23854/07_2026/7mik_23854.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mik_23854/07_2026/7mik_23854.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mik_23854/07_2026/7mik_23854.cif" } resolution = 3.12 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 124 5.16 5 Na 4 4.78 5 C 15064 2.51 5 N 3476 2.21 5 O 4024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22728 Number of models: 1 Model: "" Number of chains: 8 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: "C" 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: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 524 Unusual residues: {' NA': 4, 'POV': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} 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: "C" 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: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 5.25, per 1000 atoms: 0.23 Number of scatterers: 22728 At special positions: 0 Unit cell: (127.842, 127.842, 130.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 36 15.00 Na 4 11.00 O 4024 8.00 N 3476 7.00 C 15064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.02 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.02 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.02 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.02 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: 1.38 Conformation dependent library (CDL) restraints added in 915.9 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: 128 helices and 8 sheets defined 63.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.535A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.542A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.558A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.602A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.669A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.627A pdb=" N THR A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.636A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.518A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.703A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.676A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.574A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.610A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.520A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.810A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.532A pdb=" N PHE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 507 removed outlier: 3.694A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 Processing helix chain 'A' and resid 520 through 543 removed outlier: 3.746A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.632A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.732A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 568' Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.687A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.589A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.588A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.510A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.975A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.774A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.637A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.534A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.541A pdb=" N GLN B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.559A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.602A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.669A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.627A pdb=" N THR B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.636A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.517A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.703A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.676A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.574A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.610A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.520A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.810A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.531A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 507 removed outlier: 3.694A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 Processing helix chain 'B' and resid 520 through 543 removed outlier: 3.746A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.631A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.733A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 568' Processing helix chain 'B' and resid 569 through 574 Processing helix chain 'B' and resid 574 through 586 removed outlier: 3.687A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.590A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.588A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 removed outlier: 3.509A pdb=" N LEU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.975A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.774A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.637A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.534A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.542A pdb=" N GLN C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.559A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.603A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.669A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.627A pdb=" N THR C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 271 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.636A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.518A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.703A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.676A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.574A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.610A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.520A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.811A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.532A pdb=" N PHE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 507 removed outlier: 3.694A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 497 " --> pdb=" O TRP C 493 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 520 Processing helix chain 'C' and resid 520 through 543 removed outlier: 3.746A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 3.631A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 removed outlier: 3.733A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 563 through 568' Processing helix chain 'C' and resid 569 through 574 Processing helix chain 'C' and resid 574 through 586 removed outlier: 3.688A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.590A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.587A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 removed outlier: 3.510A pdb=" N LEU C 655 " --> pdb=" O PRO C 651 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.975A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 705 removed outlier: 3.774A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.638A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.535A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.541A pdb=" N GLN D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 158 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.558A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.603A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.669A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.627A pdb=" N THR D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 271 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.636A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.518A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.703A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.675A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.575A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.610A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.520A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.811A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.532A pdb=" N PHE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 457 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 507 removed outlier: 3.694A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 520 Processing helix chain 'D' and resid 520 through 543 removed outlier: 3.746A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 560 removed outlier: 3.631A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.734A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 563 through 568' Processing helix chain 'D' and resid 569 through 574 Processing helix chain 'D' and resid 574 through 586 removed outlier: 3.687A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.589A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.588A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 removed outlier: 3.510A pdb=" N LEU D 655 " --> pdb=" O PRO D 651 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.975A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 705 removed outlier: 3.774A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.638A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.777A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 722 through 724 removed outlier: 6.970A 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: 6.777A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 722 through 724 removed outlier: 6.970A 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: 6.777A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 722 through 724 removed outlier: 6.970A 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: 6.778A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 722 through 724 removed outlier: 6.970A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.99 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: 6000 1.44 - 1.56: 13436 1.56 - 1.69: 72 1.69 - 1.82: 204 Bond restraints: 23144 Sorted by residual: bond pdb=" C21 POV A 909 " pdb=" O21 POV A 909 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C21 POV D 903 " pdb=" O21 POV D 903 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C21 POV C 902 " pdb=" O21 POV C 902 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C21 POV D 906 " pdb=" O21 POV D 906 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 23139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 29516 2.70 - 5.40: 956 5.40 - 8.09: 274 8.09 - 10.79: 122 10.79 - 13.49: 100 Bond angle restraints: 30968 Sorted by residual: angle pdb=" C12 POV A 905 " pdb=" N POV A 905 " pdb=" C14 POV A 905 " ideal model delta sigma weight residual 107.13 120.62 -13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C12 POV B 907 " pdb=" N POV B 907 " pdb=" C14 POV B 907 " ideal model delta sigma weight residual 107.13 120.59 -13.46 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C GLY D 262 " pdb=" N GLU D 263 " pdb=" CA GLU D 263 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C GLY A 262 " pdb=" N GLU A 263 " pdb=" CA GLU A 263 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C12 POV C 907 " pdb=" N POV C 907 " pdb=" C14 POV C 907 " ideal model delta sigma weight residual 107.13 120.53 -13.40 3.00e+00 1.11e-01 2.00e+01 ... (remaining 30963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.47: 13178 30.47 - 60.94: 731 60.94 - 91.40: 125 91.40 - 121.87: 30 121.87 - 152.34: 20 Dihedral angle restraints: 14084 sinusoidal: 6528 harmonic: 7556 Sorted by residual: dihedral pdb=" CA GLN C 313 " pdb=" C GLN C 313 " pdb=" N ASN C 314 " pdb=" CA ASN C 314 " ideal model delta harmonic sigma weight residual -180.00 -131.17 -48.83 0 5.00e+00 4.00e-02 9.54e+01 dihedral pdb=" CA GLN D 313 " pdb=" C GLN D 313 " pdb=" N ASN D 314 " pdb=" CA ASN D 314 " ideal model delta harmonic sigma weight residual -180.00 -131.20 -48.80 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA GLN B 313 " pdb=" C GLN B 313 " pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta harmonic sigma weight residual 180.00 -131.23 -48.77 0 5.00e+00 4.00e-02 9.51e+01 ... (remaining 14081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2761 0.065 - 0.130: 479 0.130 - 0.195: 76 0.195 - 0.259: 8 0.259 - 0.324: 4 Chirality restraints: 3328 Sorted by residual: 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 -2.27 -0.32 2.00e-01 2.50e+01 2.63e+00 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 -2.27 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CG LEU A 469 " pdb=" CB LEU A 469 " pdb=" CD1 LEU A 469 " pdb=" CD2 LEU A 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 3325 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " 0.038 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO A 344 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 343 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO D 344 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 344 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 344 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 343 " -0.038 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO C 344 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 344 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 344 " -0.032 5.00e-02 4.00e+02 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 994 2.72 - 3.26: 19629 3.26 - 3.81: 32180 3.81 - 4.35: 44455 4.35 - 4.90: 75098 Nonbonded interactions: 172356 Sorted by model distance: nonbonded pdb="NA NA A 911 " pdb="NA NA A 912 " model vdw 2.170 1.900 nonbonded pdb=" OH TYR B 650 " pdb=" O LYS C 545 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR A 650 " pdb=" O LYS B 545 " model vdw 2.333 3.040 nonbonded pdb=" O LYS A 545 " pdb=" OH TYR D 650 " model vdw 2.344 3.040 nonbonded pdb=" OD1 ASN C 298 " pdb=" ND1 HIS C 301 " model vdw 2.355 3.120 ... (remaining 172351 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 908) selection = (chain 'B' and resid 118 through 908) selection = (chain 'C' and resid 118 through 908) selection = chain 'D' } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 17.610 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 23148 Z= 0.491 Angle : 1.473 13.491 30976 Z= 0.651 Chirality : 0.052 0.324 3328 Planarity : 0.006 0.057 3712 Dihedral : 19.737 152.341 9168 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.53 % Allowed : 4.47 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -6.20 (0.10), residues: 2552 helix: -4.84 (0.04), residues: 1540 sheet: -1.74 (0.57), residues: 76 loop : -2.56 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 363 TYR 0.017 0.003 TYR B 461 PHE 0.028 0.003 PHE C 526 TRP 0.014 0.002 TRP D 710 HIS 0.010 0.002 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.01034 / 0.49 (23144) covalent geometry : angle 1.47300 / 0.65 (30968) SS BOND : bond 0.00839 / 0.42 ( 4) SS BOND : angle 0.79124 / 0.47 ( 8) hydrogen bonds : bond 0.37697 / 24.15 ( 868) hydrogen bonds : angle 9.56362 / 6.62 ( 2592) *********************** 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 483 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 471 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7150 (pt0) REVERT: A 229 ASP cc_start: 0.7764 (m-30) cc_final: 0.7552 (m-30) REVERT: A 257 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 322 ASP cc_start: 0.7640 (t70) cc_final: 0.7302 (t0) REVERT: A 337 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7451 (mtt-85) REVERT: A 434 LYS cc_start: 0.8026 (mtpm) cc_final: 0.7652 (mmtt) REVERT: A 647 ASN cc_start: 0.8221 (t160) cc_final: 0.7936 (t0) REVERT: A 683 ASN cc_start: 0.7706 (m110) cc_final: 0.7342 (m-40) REVERT: B 211 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7352 (pt0) REVERT: B 257 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7006 (mt-10) REVERT: B 322 ASP cc_start: 0.7677 (t70) cc_final: 0.7454 (t0) REVERT: C 257 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6954 (mt-10) REVERT: C 322 ASP cc_start: 0.7504 (t70) cc_final: 0.7299 (t0) REVERT: C 337 ARG cc_start: 0.7909 (mtp-110) cc_final: 0.7498 (mtt-85) REVERT: C 434 LYS cc_start: 0.8037 (mtpm) cc_final: 0.7777 (mmtp) REVERT: C 545 LYS cc_start: 0.7267 (mtmm) cc_final: 0.7066 (mptt) REVERT: C 647 ASN cc_start: 0.8247 (t160) cc_final: 0.7971 (t0) REVERT: C 683 ASN cc_start: 0.7739 (m110) cc_final: 0.7480 (m-40) REVERT: C 687 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6959 (pt0) REVERT: C 738 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8331 (tttm) REVERT: C 744 THR cc_start: 0.8667 (t) cc_final: 0.8461 (m) REVERT: D 211 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7203 (pt0) REVERT: D 257 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6868 (mt-10) REVERT: D 322 ASP cc_start: 0.7615 (t70) cc_final: 0.7338 (t0) REVERT: D 337 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7496 (mtt-85) REVERT: D 434 LYS cc_start: 0.8045 (mtpm) cc_final: 0.7735 (mmtt) REVERT: D 647 ASN cc_start: 0.8197 (t160) cc_final: 0.7970 (t0) REVERT: D 683 ASN cc_start: 0.7776 (m110) cc_final: 0.7440 (m-40) REVERT: D 738 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8397 (tttm) outliers start: 12 outliers final: 5 residues processed: 479 average time/residue: 0.1623 time to fit residues: 118.0230 Evaluate side-chains 319 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 314 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 284 ASN A 314 ASN A 471 HIS A 646 GLN A 647 ASN B 178 ASN B 251 ASN B 284 ASN B 314 ASN B 471 HIS B 646 GLN B 647 ASN C 178 ASN C 251 ASN C 314 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN C 647 ASN D 178 ASN D 314 ASN D 471 HIS D 646 GLN D 647 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.166774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117854 restraints weight = 24426.201| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.04 r_work: 0.3031 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23148 Z= 0.115 Angle : 0.547 5.876 30976 Z= 0.283 Chirality : 0.039 0.120 3328 Planarity : 0.004 0.036 3712 Dihedral : 21.304 175.984 4130 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.27 % Allowed : 7.14 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.03 (0.13), residues: 2552 helix: -2.74 (0.10), residues: 1556 sheet: -1.09 (0.54), residues: 76 loop : -2.37 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 136 TYR 0.015 0.001 TYR C 575 PHE 0.015 0.001 PHE A 193 TRP 0.011 0.001 TRP C 559 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (23144) covalent geometry : angle 0.54748 / 0.28 (30968) SS BOND : bond 0.00171 / 0.09 ( 4) SS BOND : angle 0.38831 / 0.23 ( 8) hydrogen bonds : bond 0.05416 / 3.53 ( 868) hydrogen bonds : angle 4.19210 / 2.85 ( 2592) *********************** 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 358 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7491 (tt0) REVERT: A 257 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 337 ARG cc_start: 0.8406 (mtp-110) cc_final: 0.7875 (mtt-85) REVERT: A 434 LYS cc_start: 0.8130 (mtpm) cc_final: 0.7778 (mmtp) REVERT: A 647 ASN cc_start: 0.8158 (t0) cc_final: 0.7929 (t0) REVERT: A 683 ASN cc_start: 0.7929 (m110) cc_final: 0.7519 (m-40) REVERT: B 229 ASP cc_start: 0.7360 (t70) cc_final: 0.7050 (t0) REVERT: B 257 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7320 (mt-10) REVERT: B 283 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6994 (mt-10) REVERT: B 311 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7934 (mtpp) REVERT: C 160 HIS cc_start: 0.6290 (t-90) cc_final: 0.5527 (m170) REVERT: C 161 LYS cc_start: 0.7524 (mmtt) cc_final: 0.7117 (mmmt) REVERT: C 257 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7413 (mt-10) REVERT: C 337 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.7823 (mtt-85) REVERT: C 434 LYS cc_start: 0.8099 (mtpm) cc_final: 0.7757 (mmtp) REVERT: C 496 CYS cc_start: 0.8298 (t) cc_final: 0.7943 (t) REVERT: C 683 ASN cc_start: 0.7984 (m110) cc_final: 0.7580 (m-40) REVERT: D 211 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7500 (tt0) REVERT: D 257 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7348 (mt-10) REVERT: D 337 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.7858 (mtt-85) REVERT: D 434 LYS cc_start: 0.8127 (mtpm) cc_final: 0.7763 (mmtp) REVERT: D 647 ASN cc_start: 0.8228 (t0) cc_final: 0.8020 (t0) REVERT: D 683 ASN cc_start: 0.7910 (m110) cc_final: 0.7532 (m-40) outliers start: 29 outliers final: 9 residues processed: 357 average time/residue: 0.1713 time to fit residues: 91.0965 Evaluate side-chains 291 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 282 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 495 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 241 optimal weight: 0.0270 chunk 189 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 114 optimal weight: 0.0370 chunk 233 optimal weight: 0.0770 chunk 106 optimal weight: 0.0980 chunk 4 optimal weight: 5.9990 overall best weight: 0.8476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 646 GLN B 160 HIS B 646 GLN C 471 HIS C 646 GLN D 160 HIS D 646 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.163257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114087 restraints weight = 24476.858| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.07 r_work: 0.2952 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23148 Z= 0.095 Angle : 0.495 8.370 30976 Z= 0.249 Chirality : 0.038 0.126 3328 Planarity : 0.003 0.028 3712 Dihedral : 18.821 110.776 4120 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.27 % Allowed : 8.23 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.18 (0.15), residues: 2552 helix: -1.02 (0.12), residues: 1552 sheet: -0.70 (0.55), residues: 76 loop : -2.08 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 712 TYR 0.012 0.001 TYR C 575 PHE 0.013 0.001 PHE A 316 TRP 0.008 0.001 TRP D 559 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (23144) covalent geometry : angle 0.49516 / 0.25 (30968) SS BOND : bond 0.00104 / 0.05 ( 4) SS BOND : angle 0.27914 / 0.17 ( 8) hydrogen bonds : bond 0.04516 / 2.95 ( 868) hydrogen bonds : angle 3.68289 / 2.50 ( 2592) *********************** 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 315 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 286 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7270 (mt-10) REVERT: A 337 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.7827 (mtt-85) REVERT: A 434 LYS cc_start: 0.8122 (mtpm) cc_final: 0.7763 (mmtp) REVERT: A 683 ASN cc_start: 0.7909 (m110) cc_final: 0.7513 (m-40) REVERT: A 738 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8519 (ttpt) REVERT: B 257 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7293 (mt-10) REVERT: B 311 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7864 (mtpp) REVERT: C 161 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7278 (mmmt) REVERT: C 257 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7316 (mt-10) REVERT: C 315 ASP cc_start: 0.7336 (p0) cc_final: 0.7036 (t0) REVERT: C 337 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7771 (mtt-85) REVERT: C 434 LYS cc_start: 0.8122 (mtpm) cc_final: 0.7767 (mmtp) REVERT: C 496 CYS cc_start: 0.8300 (t) cc_final: 0.7947 (t) REVERT: C 683 ASN cc_start: 0.7925 (m110) cc_final: 0.7522 (m-40) REVERT: C 738 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8536 (ttpt) REVERT: D 257 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7277 (mt-10) REVERT: D 322 ASP cc_start: 0.7919 (t0) cc_final: 0.7557 (m-30) REVERT: D 337 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.7778 (mtt-85) REVERT: D 434 LYS cc_start: 0.8065 (mtpm) cc_final: 0.7729 (mmtp) REVERT: D 683 ASN cc_start: 0.7955 (m110) cc_final: 0.7515 (m-40) REVERT: D 738 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8504 (ttpt) outliers start: 29 outliers final: 8 residues processed: 313 average time/residue: 0.1582 time to fit residues: 75.8217 Evaluate side-chains 278 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 398 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 109 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 216 optimal weight: 0.0970 chunk 145 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 646 GLN A 647 ASN B 646 GLN C 646 GLN D 646 GLN D 647 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.157879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.112743 restraints weight = 24678.600| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.10 r_work: 0.2940 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23148 Z= 0.109 Angle : 0.546 12.669 30976 Z= 0.263 Chirality : 0.039 0.160 3328 Planarity : 0.003 0.027 3712 Dihedral : 17.972 92.017 4120 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.23 % Allowed : 9.19 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.41 (0.16), residues: 2552 helix: -0.32 (0.13), residues: 1556 sheet: -0.45 (0.56), residues: 76 loop : -1.93 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 567 TYR 0.012 0.001 TYR A 451 PHE 0.015 0.001 PHE D 316 TRP 0.006 0.001 TRP C 692 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (23144) covalent geometry : angle 0.54601 / 0.26 (30968) SS BOND : bond 0.00115 / 0.06 ( 4) SS BOND : angle 0.30236 / 0.18 ( 8) hydrogen bonds : bond 0.04686 / 3.06 ( 868) hydrogen bonds : angle 3.66366 / 2.48 ( 2592) *********************** 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 307 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 0.816 Fit side-chains REVERT: A 141 ASP cc_start: 0.5984 (t70) cc_final: 0.5764 (t70) REVERT: A 214 GLU cc_start: 0.8045 (tt0) cc_final: 0.7328 (pt0) REVERT: A 257 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7328 (mt-10) REVERT: A 286 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7710 (mp10) REVERT: A 337 ARG cc_start: 0.8423 (mtp-110) cc_final: 0.7933 (mtt-85) REVERT: A 350 LYS cc_start: 0.8487 (tppt) cc_final: 0.8116 (tttt) REVERT: A 434 LYS cc_start: 0.8169 (mtpm) cc_final: 0.7865 (mmtp) REVERT: A 683 ASN cc_start: 0.8015 (m110) cc_final: 0.7649 (m-40) REVERT: A 738 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8289 (mtpp) REVERT: A 741 GLU cc_start: 0.7393 (mp0) cc_final: 0.7177 (mp0) REVERT: B 214 GLU cc_start: 0.8065 (tt0) cc_final: 0.7343 (pt0) REVERT: B 257 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 311 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7875 (mtpp) REVERT: B 350 LYS cc_start: 0.8494 (tppt) cc_final: 0.8122 (tttt) REVERT: C 161 LYS cc_start: 0.7826 (mmtt) cc_final: 0.7478 (mmmt) REVERT: C 214 GLU cc_start: 0.8064 (tt0) cc_final: 0.7346 (pt0) REVERT: C 257 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7309 (mt-10) REVERT: C 315 ASP cc_start: 0.7377 (p0) cc_final: 0.7110 (t0) REVERT: C 337 ARG cc_start: 0.8352 (mtp-110) cc_final: 0.7879 (mtt-85) REVERT: C 350 LYS cc_start: 0.8480 (tppt) cc_final: 0.8110 (tttt) REVERT: C 434 LYS cc_start: 0.8174 (mtpm) cc_final: 0.7861 (mmtp) REVERT: C 496 CYS cc_start: 0.8228 (t) cc_final: 0.7856 (t) REVERT: C 683 ASN cc_start: 0.8037 (m110) cc_final: 0.7580 (m-40) REVERT: C 738 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8501 (mtpp) REVERT: D 141 ASP cc_start: 0.6046 (t70) cc_final: 0.5823 (t70) REVERT: D 214 GLU cc_start: 0.8018 (tt0) cc_final: 0.7312 (pt0) REVERT: D 257 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7337 (mt-10) REVERT: D 337 ARG cc_start: 0.8357 (mtp-110) cc_final: 0.7891 (mtt-85) REVERT: D 350 LYS cc_start: 0.8474 (tppt) cc_final: 0.8106 (tttt) REVERT: D 434 LYS cc_start: 0.8168 (mtpm) cc_final: 0.7853 (mmtp) REVERT: D 683 ASN cc_start: 0.8031 (m110) cc_final: 0.7643 (m-40) REVERT: D 738 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8474 (mtpp) outliers start: 28 outliers final: 19 residues processed: 302 average time/residue: 0.1428 time to fit residues: 66.4013 Evaluate side-chains 277 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 97 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 646 GLN B 647 ASN C 646 GLN C 647 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.153252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.104087 restraints weight = 24439.010| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.97 r_work: 0.2900 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23148 Z= 0.210 Angle : 0.653 10.112 30976 Z= 0.321 Chirality : 0.044 0.170 3328 Planarity : 0.004 0.029 3712 Dihedral : 19.069 108.970 4120 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.75 % Allowed : 9.54 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.46 (0.16), residues: 2552 helix: -0.32 (0.13), residues: 1548 sheet: -0.47 (0.57), residues: 76 loop : -2.03 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.016 0.002 TYR A 451 PHE 0.021 0.002 PHE B 526 TRP 0.009 0.001 TRP C 692 HIS 0.008 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.21 (23144) covalent geometry : angle 0.65332 / 0.32 (30968) SS BOND : bond 0.00110 / 0.06 ( 4) SS BOND : angle 0.24491 / 0.15 ( 8) hydrogen bonds : bond 0.06510 / 4.22 ( 868) hydrogen bonds : angle 3.96436 / 2.68 ( 2592) *********************** 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 311 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 0.641 Fit side-chains REVERT: A 257 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 337 ARG cc_start: 0.8442 (mtp-110) cc_final: 0.7978 (mtt-85) REVERT: A 434 LYS cc_start: 0.8307 (mtpm) cc_final: 0.7910 (mmtt) REVERT: A 683 ASN cc_start: 0.8050 (m110) cc_final: 0.7663 (m-40) REVERT: A 738 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8448 (mtpp) REVERT: B 257 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7458 (mt-10) REVERT: B 311 LYS cc_start: 0.8468 (ttpp) cc_final: 0.8037 (mtpp) REVERT: C 257 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7509 (mt-10) REVERT: C 337 ARG cc_start: 0.8391 (mtp-110) cc_final: 0.7952 (mtt-85) REVERT: C 434 LYS cc_start: 0.8335 (mtpm) cc_final: 0.7915 (mmtt) REVERT: C 683 ASN cc_start: 0.8042 (m110) cc_final: 0.7635 (m-40) REVERT: C 738 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8458 (mtpp) REVERT: D 257 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7433 (mt-10) REVERT: D 337 ARG cc_start: 0.8383 (mtp-110) cc_final: 0.7951 (mtt-85) REVERT: D 434 LYS cc_start: 0.8323 (mtpm) cc_final: 0.7923 (mmtt) REVERT: D 683 ASN cc_start: 0.8064 (m110) cc_final: 0.7652 (m-40) REVERT: D 738 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8496 (mtpp) outliers start: 40 outliers final: 30 residues processed: 297 average time/residue: 0.1493 time to fit residues: 68.5570 Evaluate side-chains 276 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 79 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 167 optimal weight: 0.0980 chunk 164 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 646 GLN B 646 GLN C 330 ASN C 646 GLN D 646 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.158739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.113691 restraints weight = 24469.952| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.15 r_work: 0.2931 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23148 Z= 0.096 Angle : 0.507 13.056 30976 Z= 0.250 Chirality : 0.038 0.138 3328 Planarity : 0.003 0.027 3712 Dihedral : 17.366 89.849 4120 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.18 % Allowed : 10.81 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.85 (0.16), residues: 2552 helix: 0.23 (0.13), residues: 1560 sheet: -0.16 (0.59), residues: 76 loop : -1.93 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.010 0.001 TYR A 575 PHE 0.016 0.001 PHE C 316 TRP 0.008 0.001 TRP C 710 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (23144) covalent geometry : angle 0.50739 / 0.25 (30968) SS BOND : bond 0.00116 / 0.06 ( 4) SS BOND : angle 0.23500 / 0.15 ( 8) hydrogen bonds : bond 0.04138 / 2.70 ( 868) hydrogen bonds : angle 3.63167 / 2.46 ( 2592) *********************** 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 286 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 0.907 Fit side-chains REVERT: A 257 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7312 (mt-10) REVERT: A 337 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.7960 (mtt-85) REVERT: A 434 LYS cc_start: 0.8350 (mtpm) cc_final: 0.7888 (mmtp) REVERT: A 683 ASN cc_start: 0.8046 (m110) cc_final: 0.7544 (m-40) REVERT: A 738 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8389 (mtpp) REVERT: A 741 GLU cc_start: 0.7626 (mp0) cc_final: 0.7392 (mp0) REVERT: B 257 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 311 LYS cc_start: 0.8285 (ttpp) cc_final: 0.7906 (mtpp) REVERT: C 161 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7534 (mmmt) REVERT: C 337 ARG cc_start: 0.8552 (mtp-110) cc_final: 0.7891 (mtt-85) REVERT: C 434 LYS cc_start: 0.8344 (mtpm) cc_final: 0.7893 (mmtp) REVERT: C 496 CYS cc_start: 0.8193 (t) cc_final: 0.7860 (t) REVERT: C 683 ASN cc_start: 0.8021 (m110) cc_final: 0.7485 (m-40) REVERT: C 738 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8328 (mtpp) REVERT: C 741 GLU cc_start: 0.7643 (mp0) cc_final: 0.7235 (mp0) REVERT: D 257 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7325 (mt-10) REVERT: D 337 ARG cc_start: 0.8553 (mtp-110) cc_final: 0.7891 (mtt-85) REVERT: D 434 LYS cc_start: 0.8374 (mtpm) cc_final: 0.7896 (mmtp) REVERT: D 469 LEU cc_start: 0.5062 (OUTLIER) cc_final: 0.4725 (mt) REVERT: D 683 ASN cc_start: 0.8022 (m110) cc_final: 0.7484 (m-40) REVERT: D 702 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8234 (mm-30) REVERT: D 738 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8325 (mtpp) REVERT: D 741 GLU cc_start: 0.7528 (mp0) cc_final: 0.7091 (mp0) outliers start: 27 outliers final: 14 residues processed: 282 average time/residue: 0.1677 time to fit residues: 72.7738 Evaluate side-chains 262 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 0.2980 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 214 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 646 GLN B 646 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.158770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.113644 restraints weight = 24395.921| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.12 r_work: 0.2961 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 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 = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23148 Z= 0.090 Angle : 0.487 10.841 30976 Z= 0.240 Chirality : 0.038 0.159 3328 Planarity : 0.003 0.026 3712 Dihedral : 16.574 87.216 4120 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.83 % Allowed : 11.21 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.33 (0.17), residues: 2552 helix: 0.66 (0.14), residues: 1560 sheet: -0.06 (0.59), residues: 76 loop : -1.75 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.009 0.001 TYR A 575 PHE 0.016 0.001 PHE C 316 TRP 0.007 0.001 TRP C 710 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (23144) covalent geometry : angle 0.48685 / 0.24 (30968) SS BOND : bond 0.00106 / 0.05 ( 4) SS BOND : angle 0.23255 / 0.15 ( 8) hydrogen bonds : bond 0.03909 / 2.55 ( 868) hydrogen bonds : angle 3.48975 / 2.36 ( 2592) *********************** 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 266 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.7927 (mtt-85) REVERT: A 434 LYS cc_start: 0.8326 (mtpm) cc_final: 0.7853 (mmtp) REVERT: A 488 MET cc_start: 0.7176 (mtp) cc_final: 0.6966 (mtm) REVERT: A 683 ASN cc_start: 0.8038 (m110) cc_final: 0.7543 (m-40) REVERT: A 738 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8340 (mtpp) REVERT: A 741 GLU cc_start: 0.7543 (mp0) cc_final: 0.7293 (mp0) REVERT: B 162 LEU cc_start: 0.6744 (mt) cc_final: 0.6454 (mt) REVERT: B 311 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7891 (mtpp) REVERT: C 161 LYS cc_start: 0.7802 (mmtt) cc_final: 0.7372 (mmmt) REVERT: C 162 LEU cc_start: 0.6710 (mt) cc_final: 0.6420 (mt) REVERT: C 337 ARG cc_start: 0.8531 (mtp-110) cc_final: 0.7849 (mtt-85) REVERT: C 434 LYS cc_start: 0.8324 (mtpm) cc_final: 0.7840 (mmtp) REVERT: C 469 LEU cc_start: 0.4805 (OUTLIER) cc_final: 0.4445 (mt) REVERT: C 496 CYS cc_start: 0.8139 (t) cc_final: 0.7839 (t) REVERT: C 683 ASN cc_start: 0.8015 (m110) cc_final: 0.7491 (m-40) REVERT: C 738 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8330 (mtpp) REVERT: C 741 GLU cc_start: 0.7568 (mp0) cc_final: 0.7222 (mp0) REVERT: D 337 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.7847 (mtt-85) REVERT: D 434 LYS cc_start: 0.8345 (mtpm) cc_final: 0.7873 (mmtp) REVERT: D 469 LEU cc_start: 0.4869 (OUTLIER) cc_final: 0.4606 (mp) REVERT: D 683 ASN cc_start: 0.8027 (m110) cc_final: 0.7500 (m-40) REVERT: D 702 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8128 (mm-30) REVERT: D 738 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8270 (mtpp) REVERT: D 741 GLU cc_start: 0.7517 (mp0) cc_final: 0.7068 (mp0) outliers start: 19 outliers final: 10 residues processed: 262 average time/residue: 0.1521 time to fit residues: 61.7163 Evaluate side-chains 249 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 159 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 208 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.155275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.106117 restraints weight = 24328.910| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.97 r_work: 0.2926 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23148 Z= 0.147 Angle : 0.571 12.475 30976 Z= 0.280 Chirality : 0.041 0.150 3328 Planarity : 0.003 0.030 3712 Dihedral : 17.053 93.446 4120 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.79 % Allowed : 11.60 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.16), residues: 2552 helix: 0.54 (0.13), residues: 1548 sheet: -0.16 (0.59), residues: 76 loop : -1.81 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.014 0.002 TYR A 451 PHE 0.018 0.001 PHE D 316 TRP 0.007 0.001 TRP B 692 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (23144) covalent geometry : angle 0.57077 / 0.28 (30968) SS BOND : bond 0.00110 / 0.06 ( 4) SS BOND : angle 0.29167 / 0.18 ( 8) hydrogen bonds : bond 0.05268 / 3.42 ( 868) hydrogen bonds : angle 3.73880 / 2.53 ( 2592) *********************** 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 262 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.845 Fit side-chains REVERT: A 337 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.7973 (mtt-85) REVERT: A 434 LYS cc_start: 0.8252 (mtpm) cc_final: 0.7841 (mmtt) REVERT: A 683 ASN cc_start: 0.8095 (m110) cc_final: 0.7669 (m-40) REVERT: A 738 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8297 (mtpp) REVERT: A 741 GLU cc_start: 0.7391 (mp0) cc_final: 0.7135 (mp0) REVERT: B 311 LYS cc_start: 0.8330 (ttpp) cc_final: 0.7978 (mtpp) REVERT: C 337 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.7895 (mtt-85) REVERT: C 434 LYS cc_start: 0.8262 (mtpm) cc_final: 0.7845 (mmtt) REVERT: C 469 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4617 (mt) REVERT: C 683 ASN cc_start: 0.8079 (m110) cc_final: 0.7647 (m-40) REVERT: C 738 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8299 (mtpp) REVERT: C 741 GLU cc_start: 0.7411 (mp0) cc_final: 0.7165 (mp0) REVERT: D 337 ARG cc_start: 0.8339 (mtp-110) cc_final: 0.7895 (mtt-85) REVERT: D 434 LYS cc_start: 0.8261 (mtpm) cc_final: 0.7855 (mmtt) REVERT: D 683 ASN cc_start: 0.8082 (m110) cc_final: 0.7660 (m-40) REVERT: D 738 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8227 (mtpp) REVERT: D 741 GLU cc_start: 0.7427 (mp0) cc_final: 0.7077 (mp0) outliers start: 18 outliers final: 15 residues processed: 258 average time/residue: 0.1723 time to fit residues: 68.4696 Evaluate side-chains 256 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 18 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 205 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 646 GLN C 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.154962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.110095 restraints weight = 24391.947| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.03 r_work: 0.2927 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23148 Z= 0.150 Angle : 0.564 9.548 30976 Z= 0.278 Chirality : 0.041 0.138 3328 Planarity : 0.003 0.032 3712 Dihedral : 17.156 93.975 4120 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.88 % Allowed : 11.69 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.16), residues: 2552 helix: 0.49 (0.13), residues: 1552 sheet: -0.28 (0.58), residues: 76 loop : -1.87 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.013 0.002 TYR A 451 PHE 0.018 0.001 PHE C 316 TRP 0.007 0.001 TRP C 710 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (23144) covalent geometry : angle 0.56362 / 0.28 (30968) SS BOND : bond 0.00127 / 0.06 ( 4) SS BOND : angle 0.26376 / 0.17 ( 8) hydrogen bonds : bond 0.05264 / 3.42 ( 868) hydrogen bonds : angle 3.75267 / 2.54 ( 2592) *********************** 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 260 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.8583 (mtp-110) cc_final: 0.7919 (mtt-85) REVERT: A 434 LYS cc_start: 0.8395 (mtpm) cc_final: 0.7833 (mmtt) REVERT: A 683 ASN cc_start: 0.8105 (m110) cc_final: 0.7608 (m-40) REVERT: A 738 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8357 (mtpp) REVERT: A 741 GLU cc_start: 0.7626 (mp0) cc_final: 0.7224 (mp0) REVERT: B 141 ASP cc_start: 0.6136 (t70) cc_final: 0.5760 (t0) REVERT: B 311 LYS cc_start: 0.8342 (ttpp) cc_final: 0.7954 (mtpp) REVERT: C 141 ASP cc_start: 0.6135 (t70) cc_final: 0.5758 (t0) REVERT: C 337 ARG cc_start: 0.8527 (mtp-110) cc_final: 0.7877 (mtt-85) REVERT: C 434 LYS cc_start: 0.8406 (mtpm) cc_final: 0.7852 (mmtt) REVERT: C 469 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4894 (mt) REVERT: C 683 ASN cc_start: 0.8069 (m110) cc_final: 0.7518 (m-40) REVERT: C 738 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8330 (mtpp) REVERT: C 741 GLU cc_start: 0.7621 (mp0) cc_final: 0.7278 (mp0) REVERT: D 337 ARG cc_start: 0.8521 (mtp-110) cc_final: 0.7867 (mtt-85) REVERT: D 434 LYS cc_start: 0.8387 (mtpm) cc_final: 0.7834 (mmtt) REVERT: D 683 ASN cc_start: 0.8049 (m110) cc_final: 0.7532 (m-40) REVERT: D 738 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8274 (mtpp) REVERT: D 741 GLU cc_start: 0.7565 (mp0) cc_final: 0.7076 (mp0) outliers start: 20 outliers final: 15 residues processed: 256 average time/residue: 0.1721 time to fit residues: 67.3709 Evaluate side-chains 250 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 646 GLN C 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.158904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.113495 restraints weight = 24385.994| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.97 r_work: 0.2967 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23148 Z= 0.092 Angle : 0.493 13.997 30976 Z= 0.242 Chirality : 0.038 0.132 3328 Planarity : 0.003 0.029 3712 Dihedral : 16.314 89.123 4120 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.61 % Allowed : 11.87 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.86 (0.14), residues: 1560 sheet: -0.13 (0.58), residues: 76 loop : -1.74 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 188 TYR 0.008 0.001 TYR C 575 PHE 0.016 0.001 PHE C 316 TRP 0.007 0.001 TRP C 710 HIS 0.003 0.000 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (23144) covalent geometry : angle 0.49319 / 0.24 (30968) SS BOND : bond 0.00082 / 0.04 ( 4) SS BOND : angle 0.22267 / 0.14 ( 8) hydrogen bonds : bond 0.03832 / 2.50 ( 868) hydrogen bonds : angle 3.53541 / 2.39 ( 2592) ********************** 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 252 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.8559 (mtp-110) cc_final: 0.7856 (mtt-85) REVERT: A 434 LYS cc_start: 0.8312 (mtpm) cc_final: 0.7779 (mmtp) REVERT: A 683 ASN cc_start: 0.8008 (m110) cc_final: 0.7483 (m-40) REVERT: A 738 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8290 (mtpp) REVERT: A 741 GLU cc_start: 0.7496 (mp0) cc_final: 0.7197 (mp0) REVERT: B 311 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7877 (mtpp) REVERT: C 337 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.7812 (mtt-85) REVERT: C 434 LYS cc_start: 0.8310 (mtpm) cc_final: 0.7796 (mmtp) REVERT: C 469 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4977 (mt) REVERT: C 496 CYS cc_start: 0.8047 (t) cc_final: 0.7760 (t) REVERT: C 683 ASN cc_start: 0.7976 (m110) cc_final: 0.7422 (m-40) REVERT: C 738 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8259 (mtpp) REVERT: C 741 GLU cc_start: 0.7513 (mp0) cc_final: 0.7140 (mp0) REVERT: D 337 ARG cc_start: 0.8495 (mtp-110) cc_final: 0.7807 (mtt-85) REVERT: D 434 LYS cc_start: 0.8328 (mtpm) cc_final: 0.7796 (mmtp) REVERT: D 683 ASN cc_start: 0.7914 (m110) cc_final: 0.7346 (m-40) REVERT: D 738 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8200 (mtpp) REVERT: D 741 GLU cc_start: 0.7477 (mp0) cc_final: 0.7009 (mp0) outliers start: 14 outliers final: 12 residues processed: 246 average time/residue: 0.1747 time to fit residues: 65.7020 Evaluate side-chains 249 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 66 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 163 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.158167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.108780 restraints weight = 24293.793| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.99 r_work: 0.2948 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23148 Z= 0.102 Angle : 0.502 9.560 30976 Z= 0.248 Chirality : 0.038 0.142 3328 Planarity : 0.003 0.029 3712 Dihedral : 16.172 89.715 4120 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.66 % Allowed : 11.65 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.94 (0.14), residues: 1560 sheet: -0.14 (0.58), residues: 76 loop : -1.71 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 188 TYR 0.011 0.001 TYR A 451 PHE 0.017 0.001 PHE D 316 TRP 0.008 0.001 TRP D 710 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (23144) covalent geometry : angle 0.50218 / 0.25 (30968) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.27155 / 0.17 ( 8) hydrogen bonds : bond 0.04227 / 2.75 ( 868) hydrogen bonds : angle 3.55004 / 2.40 ( 2592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5288.14 seconds wall clock time: 91 minutes 15.49 seconds (5475.49 seconds total)