Starting phenix.real_space_refine on Fri Mar 6 07:14:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oa9_0665/03_2026/6oa9_0665_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oa9_0665/03_2026/6oa9_0665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oa9_0665/03_2026/6oa9_0665_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oa9_0665/03_2026/6oa9_0665_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oa9_0665/03_2026/6oa9_0665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oa9_0665/03_2026/6oa9_0665.map" } resolution = 3.9 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= 0.017 sd= 0.111 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 Zn 2 6.06 5 P 29 5.49 5 S 129 5.16 5 C 18142 2.51 5 N 5035 2.21 5 O 5669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29006 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4206 Classifications: {'peptide': 547} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 518} Chain breaks: 1 Chain: "B" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3767 Classifications: {'peptide': 493} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3759 Classifications: {'peptide': 492} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 464} Chain breaks: 1 Chain: "D" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3747 Classifications: {'peptide': 489} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 461} Chain breaks: 1 Chain: "E" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3786 Classifications: {'peptide': 496} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 468} Chain breaks: 1 Chain: "F" Number of atoms: 4093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4093 Classifications: {'peptide': 533} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 505} Chain breaks: 2 Chain: "K" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "J" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "G" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3762 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 447} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'ATP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25196 SG CYS G 145 47.953 81.487 84.359 1.00137.84 S ATOM 25812 SG CYS G 219 71.508 37.375 89.822 1.00142.70 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU H 173 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU H 173 " occ=0.45 residue: pdb=" N ARG H 174 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG H 174 " occ=0.45 residue: pdb=" N GLY H 175 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY H 175 " occ=0.25 residue: pdb=" N GLY H 176 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY H 176 " occ=0.25 residue: pdb=" N LEU J 273 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU J 273 " occ=0.45 residue: pdb=" N ARG J 274 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG J 274 " occ=0.45 residue: pdb=" N GLY J 275 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY J 275 " occ=0.25 residue: pdb=" N GLY J 276 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY J 276 " occ=0.25 Time building chain proxies: 6.62, per 1000 atoms: 0.23 Number of scatterers: 29006 At special positions: 0 Unit cell: (144.45, 140.4, 178.2, 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) Zn 2 29.99 S 129 16.00 P 29 15.00 O 5669 8.00 N 5035 7.00 C 18142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6870 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 18 sheets defined 40.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 219 through 236 removed outlier: 3.663A pdb=" N GLN A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.717A pdb=" N LYS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.562A pdb=" N GLU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.911A pdb=" N MET A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 306 removed outlier: 3.581A pdb=" N SER A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.950A pdb=" N ILE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.806A pdb=" N ARG A 332 " --> pdb=" O GLU A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.507A pdb=" N ARG A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 removed outlier: 3.547A pdb=" N LEU A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 removed outlier: 3.800A pdb=" N ALA A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 436 removed outlier: 3.665A pdb=" N SER A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.973A pdb=" N PHE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.639A pdb=" N VAL A 489 " --> pdb=" O TRP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.662A pdb=" N LEU A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 removed outlier: 4.246A pdb=" N LYS A 539 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.650A pdb=" N ILE A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 610 through 621 removed outlier: 3.845A pdb=" N THR A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.542A pdb=" N LYS A 625 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.868A pdb=" N ILE A 639 " --> pdb=" O PRO A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.824A pdb=" N ALA A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 removed outlier: 4.096A pdb=" N ILE A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 709 removed outlier: 3.733A pdb=" N ALA A 708 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 709 " --> pdb=" O LYS A 706 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 705 through 709' Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.983A pdb=" N THR A 764 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 765 " --> pdb=" O MET A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 765' Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.815A pdb=" N LEU A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 779 " --> pdb=" O ARG A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 4.141A pdb=" N ARG A 788 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 228 removed outlier: 3.822A pdb=" N GLU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.674A pdb=" N ALA B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.529A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 322 through 326 removed outlier: 4.026A pdb=" N THR B 326 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.504A pdb=" N ARG B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.602A pdb=" N LEU B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 368 " --> pdb=" O PRO B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 368' Processing helix chain 'B' and resid 383 through 393 removed outlier: 3.655A pdb=" N ILE B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 413 Processing helix chain 'B' and resid 419 through 436 removed outlier: 3.613A pdb=" N SER B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.580A pdb=" N PHE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.579A pdb=" N LEU B 499 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 500' Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.687A pdb=" N THR B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 516 " --> pdb=" O GLN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 579 removed outlier: 3.851A pdb=" N ASP B 571 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 572 " --> pdb=" O ASN B 568 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 removed outlier: 3.904A pdb=" N ILE B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 620 removed outlier: 3.544A pdb=" N GLU B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N MET B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.990A pdb=" N ILE B 639 " --> pdb=" O PRO B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 659 through 668 removed outlier: 3.959A pdb=" N LEU B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 687 Processing helix chain 'B' and resid 693 through 713 removed outlier: 3.790A pdb=" N ARG B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 removed outlier: 4.133A pdb=" N ILE C 216 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 227 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.902A pdb=" N LEU C 239 " --> pdb=" O HIS C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 271 Processing helix chain 'C' and resid 290 through 305 removed outlier: 3.656A pdb=" N SER C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.719A pdb=" N SER C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.728A pdb=" N ALA C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 418 through 433 removed outlier: 3.537A pdb=" N SER C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.930A pdb=" N PHE C 462 " --> pdb=" O THR C 458 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 467 " --> pdb=" O ARG C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 removed outlier: 3.879A pdb=" N ASP C 488 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 489 " --> pdb=" O TRP C 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 485 through 489' Processing helix chain 'C' and resid 492 through 499 Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 510 through 517 removed outlier: 3.925A pdb=" N THR C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 545 removed outlier: 3.749A pdb=" N VAL C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 543 " --> pdb=" O LYS C 539 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 545 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 558 removed outlier: 3.669A pdb=" N LEU C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 558 " --> pdb=" O GLY C 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 558' Processing helix chain 'C' and resid 562 through 566 removed outlier: 4.238A pdb=" N GLU C 566 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 3.720A pdb=" N ILE C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 592 removed outlier: 3.540A pdb=" N SER C 591 " --> pdb=" O GLN C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 618 removed outlier: 4.241A pdb=" N LEU C 614 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR C 616 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 removed outlier: 3.759A pdb=" N LYS C 625 " --> pdb=" O ASN C 622 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN C 626 " --> pdb=" O ALA C 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 622 through 626' Processing helix chain 'C' and resid 663 through 672 removed outlier: 4.265A pdb=" N LEU C 667 " --> pdb=" O ARG C 663 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 687 removed outlier: 4.252A pdb=" N ILE C 685 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 704 removed outlier: 3.600A pdb=" N VAL C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.927A pdb=" N ASP D 215 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 216 " --> pdb=" O TYR D 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 216' Processing helix chain 'D' and resid 219 through 228 removed outlier: 3.816A pdb=" N GLN D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.922A pdb=" N ALA D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 266 " --> pdb=" O THR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.584A pdb=" N VAL D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 315 through 320 removed outlier: 3.808A pdb=" N ILE D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 343 Processing helix chain 'D' and resid 383 through 394 Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 417 through 435 removed outlier: 3.889A pdb=" N ILE D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA D 422 " --> pdb=" O GLY D 418 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 492 through 501 removed outlier: 3.695A pdb=" N GLU D 497 " --> pdb=" O ASP D 493 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.600A pdb=" N VAL D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 579 Processing helix chain 'D' and resid 609 through 618 removed outlier: 3.846A pdb=" N THR D 616 " --> pdb=" O ASN D 612 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.844A pdb=" N SER D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 669 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 689 Processing helix chain 'D' and resid 693 through 714 removed outlier: 3.601A pdb=" N ILE D 700 " --> pdb=" O ASP D 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 removed outlier: 4.156A pdb=" N ILE E 226 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET E 229 " --> pdb=" O GLN E 225 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix removed outlier: 3.826A pdb=" N HIS E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.767A pdb=" N ARG E 266 " --> pdb=" O THR E 262 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.504A pdb=" N MET E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 305 removed outlier: 3.868A pdb=" N LYS E 305 " --> pdb=" O GLU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 319 Processing helix chain 'E' and resid 331 through 342 removed outlier: 3.737A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN E 337 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 339 " --> pdb=" O VAL E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 387 through 397 removed outlier: 3.537A pdb=" N LYS E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN E 397 " --> pdb=" O ILE E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.089A pdb=" N LEU E 409 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 437 removed outlier: 3.779A pdb=" N CYS E 425 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS E 436 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 456 removed outlier: 3.842A pdb=" N GLY E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 removed outlier: 3.606A pdb=" N PHE E 462 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 463 " --> pdb=" O MET E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 499 removed outlier: 3.542A pdb=" N GLU E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 509 Processing helix chain 'E' and resid 511 through 517 removed outlier: 3.517A pdb=" N LYS E 515 " --> pdb=" O ASP E 511 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE E 516 " --> pdb=" O GLN E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 543 removed outlier: 3.706A pdb=" N ALA E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 579 removed outlier: 3.761A pdb=" N ARG E 577 " --> pdb=" O PHE E 573 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA E 579 " --> pdb=" O LYS E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 592 removed outlier: 3.512A pdb=" N ILE E 592 " --> pdb=" O LEU E 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 589 through 592' Processing helix chain 'E' and resid 601 through 621 removed outlier: 3.672A pdb=" N ARG E 609 " --> pdb=" O GLY E 605 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN E 613 " --> pdb=" O ARG E 609 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU E 614 " --> pdb=" O VAL E 610 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP E 619 " --> pdb=" O LEU E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 669 removed outlier: 3.654A pdb=" N ILE E 666 " --> pdb=" O ARG E 663 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 667 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN E 668 " --> pdb=" O SER E 665 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA E 669 " --> pdb=" O ILE E 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 663 through 669' Processing helix chain 'E' and resid 681 through 687 Processing helix chain 'E' and resid 703 through 708 Processing helix chain 'E' and resid 709 through 713 removed outlier: 3.734A pdb=" N SER E 712 " --> pdb=" O ILE E 709 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE E 713 " --> pdb=" O LYS E 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 709 through 713' Processing helix chain 'F' and resid 222 through 230 removed outlier: 3.913A pdb=" N GLU F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 230 " --> pdb=" O ILE F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 236 removed outlier: 4.027A pdb=" N HIS F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 removed outlier: 4.089A pdb=" N VAL F 268 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 269 " --> pdb=" O ALA F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 288 through 301 removed outlier: 3.514A pdb=" N GLU F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 332 through 343 removed outlier: 4.341A pdb=" N LEU F 338 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 363 removed outlier: 3.525A pdb=" N SER F 362 " --> pdb=" O ARG F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 395 Processing helix chain 'F' and resid 407 through 413 removed outlier: 3.506A pdb=" N THR F 413 " --> pdb=" O LEU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 435 removed outlier: 3.630A pdb=" N SER F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU F 435 " --> pdb=" O GLN F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 467 removed outlier: 4.133A pdb=" N PHE F 462 " --> pdb=" O THR F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 489 removed outlier: 3.695A pdb=" N VAL F 489 " --> pdb=" O TRP F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 501 removed outlier: 3.614A pdb=" N LYS F 496 " --> pdb=" O LEU F 492 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 497 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 498 " --> pdb=" O GLU F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 515 removed outlier: 3.739A pdb=" N THR F 514 " --> pdb=" O PRO F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 540 removed outlier: 3.636A pdb=" N LEU F 537 " --> pdb=" O GLY F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 545 removed outlier: 4.321A pdb=" N GLU F 544 " --> pdb=" O ALA F 540 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL F 545 " --> pdb=" O VAL F 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 540 through 545' Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 567 through 572 removed outlier: 3.663A pdb=" N ILE F 572 " --> pdb=" O ASN F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 579 Processing helix chain 'F' and resid 610 through 618 removed outlier: 4.379A pdb=" N LEU F 615 " --> pdb=" O VAL F 611 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N THR F 616 " --> pdb=" O ASN F 612 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET F 618 " --> pdb=" O LEU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 671 removed outlier: 3.502A pdb=" N LEU F 664 " --> pdb=" O GLU F 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 687 removed outlier: 3.765A pdb=" N ALA F 686 " --> pdb=" O LEU F 682 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS F 687 " --> pdb=" O THR F 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 682 through 687' Processing helix chain 'F' and resid 699 through 704 Processing helix chain 'F' and resid 705 through 707 No H-bonds generated for 'chain 'F' and resid 705 through 707' Processing helix chain 'F' and resid 709 through 714 removed outlier: 3.593A pdb=" N ILE F 713 " --> pdb=" O ILE F 709 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 31 removed outlier: 3.502A pdb=" N VAL K 26 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER K 28 " --> pdb=" O ASP K 24 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 135 removed outlier: 3.830A pdb=" N VAL H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS H 133 " --> pdb=" O LYS H 129 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 234 Processing helix chain 'J' and resid 255 through 260 removed outlier: 4.442A pdb=" N TYR J 259 " --> pdb=" O THR J 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 125 removed outlier: 3.729A pdb=" N GLU G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU G 125 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 162 removed outlier: 3.645A pdb=" N HIS G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.627A pdb=" N TYR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 256 removed outlier: 3.729A pdb=" N GLU G 247 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.732A pdb=" N VAL G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 310 " --> pdb=" O GLU G 306 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG G 312 " --> pdb=" O LEU G 308 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU G 316 " --> pdb=" O ARG G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 365 removed outlier: 3.762A pdb=" N ILE G 356 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET G 357 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS G 361 " --> pdb=" O MET G 357 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS G 365 " --> pdb=" O HIS G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 3.572A pdb=" N VAL G 409 " --> pdb=" O ALA G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.647A pdb=" N LYS G 505 " --> pdb=" O TYR G 501 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS G 506 " --> pdb=" O GLN G 502 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 508 " --> pdb=" O LEU G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 525 removed outlier: 4.201A pdb=" N GLU G 522 " --> pdb=" O ASN G 518 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS G 523 " --> pdb=" O LEU G 519 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 524 " --> pdb=" O LEU G 520 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER G 525 " --> pdb=" O HIS G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 537 removed outlier: 3.608A pdb=" N ASN G 534 " --> pdb=" O LEU G 530 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 536 " --> pdb=" O TYR G 532 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN G 537 " --> pdb=" O ILE G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 553 Processing helix chain 'G' and resid 556 through 566 removed outlier: 3.736A pdb=" N LEU G 561 " --> pdb=" O GLU G 557 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS G 562 " --> pdb=" O GLU G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 566 through 579 removed outlier: 3.621A pdb=" N GLN G 570 " --> pdb=" O SER G 566 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU G 578 " --> pdb=" O MET G 574 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER G 579 " --> pdb=" O ILE G 575 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 279 removed outlier: 6.300A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 356 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLY A 250 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 377 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A 252 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 549 through 552 removed outlier: 3.563A pdb=" N ILE A 550 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 585 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 587 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 524 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY A 523 " --> pdb=" O GLN A 651 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 653 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU A 525 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 277 through 279 removed outlier: 6.222A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 523 through 526 removed outlier: 3.694A pdb=" N VAL B 524 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE B 628 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.053A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 629 through 630 removed outlier: 3.648A pdb=" N GLN C 651 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 527 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 548 through 549 removed outlier: 6.426A pdb=" N ASN C 548 " --> pdb=" O VAL C 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 375 through 378 removed outlier: 3.739A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET G 144 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 278 " --> pdb=" O MET G 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 548 through 551 removed outlier: 5.454A pdb=" N THR D 582 " --> pdb=" O PHE D 628 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE D 630 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL D 584 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA D 632 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 586 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN D 651 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 527 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 275 through 276 removed outlier: 6.551A pdb=" N PHE E 275 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE E 312 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 352 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 311 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 254 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 548 through 553 removed outlier: 6.148A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP E 587 " --> pdb=" O ILE E 550 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL E 552 " --> pdb=" O ASP E 587 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL E 524 " --> pdb=" O GLY E 631 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU E 525 " --> pdb=" O ILE E 653 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 275 through 280 removed outlier: 5.771A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE F 279 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL F 352 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 311 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL F 251 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR F 357 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET F 253 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 523 through 527 removed outlier: 7.137A pdb=" N GLY F 523 " --> pdb=" O LEU F 649 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN F 651 " --> pdb=" O GLY F 523 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 550 through 551 removed outlier: 7.249A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 112 through 116 removed outlier: 3.605A pdb=" N LEU H 115 " --> pdb=" O ILE H 103 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N LEU H 167 " --> pdb=" O GLN H 102 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE H 104 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU H 169 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS H 106 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU H 171 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 212 through 216 removed outlier: 3.672A pdb=" N LEU J 215 " --> pdb=" O ILE J 203 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE J 203 " --> pdb=" O LEU J 215 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLN J 202 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N LEU J 267 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE J 204 " --> pdb=" O LEU J 267 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU J 269 " --> pdb=" O PHE J 204 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS J 206 " --> pdb=" O LEU J 269 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS J 268 " --> pdb=" O ILE J 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 236 through 238 removed outlier: 3.932A pdb=" N HIS G 236 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL G 281 " --> pdb=" O GLU G 238 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE G 277 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR G 270 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA G 279 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER G 268 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL G 281 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER G 266 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY G 261 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU G 324 " --> pdb=" O GLY G 261 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET G 263 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N VAL G 382 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR G 383 " --> pdb=" O TYR G 399 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 422 through 423 720 hydrogen bonds defined for protein. 2058 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: 6.09 Time building geometry restraints manager: 3.47 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: 5059 1.31 - 1.44: 6993 1.44 - 1.57: 17161 1.57 - 1.69: 48 1.69 - 1.82: 238 Bond restraints: 29499 Sorted by residual: bond pdb=" C4 ATP D 902 " pdb=" C5 ATP D 902 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.02e+01 bond pdb=" C4 ATP C1003 " pdb=" C5 ATP C1003 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.97e+01 bond pdb=" C4 ATP C1002 " pdb=" C5 ATP C1002 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP B 901 " pdb=" C5 ATP B 901 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.89e+01 ... (remaining 29494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.85: 39905 10.85 - 21.70: 26 21.70 - 32.54: 0 32.54 - 43.39: 1 43.39 - 54.24: 1 Bond angle restraints: 39933 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP C1002 " pdb=" O3B ATP C1002 " pdb=" PG ATP C1002 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP C1003 " pdb=" O3B ATP C1003 " pdb=" PG ATP C1003 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 120.49 19.38 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP C1001 " pdb=" O3B ATP C1001 " pdb=" PG ATP C1001 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 ... (remaining 39928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 17561 30.26 - 60.51: 634 60.51 - 90.77: 86 90.77 - 121.03: 0 121.03 - 151.29: 3 Dihedral angle restraints: 18284 sinusoidal: 7626 harmonic: 10658 Sorted by residual: dihedral pdb=" C LEU K 43 " pdb=" N LEU K 43 " pdb=" CA LEU K 43 " pdb=" CB LEU K 43 " ideal model delta harmonic sigma weight residual -122.60 -141.64 19.04 0 2.50e+00 1.60e-01 5.80e+01 dihedral pdb=" CA ASN G 510 " pdb=" C ASN G 510 " pdb=" N VAL G 511 " pdb=" CA VAL G 511 " ideal model delta harmonic sigma weight residual -180.00 -145.37 -34.63 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" N LEU K 43 " pdb=" C LEU K 43 " pdb=" CA LEU K 43 " pdb=" CB LEU K 43 " ideal model delta harmonic sigma weight residual 122.80 139.88 -17.08 0 2.50e+00 1.60e-01 4.67e+01 ... (remaining 18281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 4475 0.196 - 0.391: 8 0.391 - 0.587: 1 0.587 - 0.782: 0 0.782 - 0.978: 1 Chirality restraints: 4485 Sorted by residual: chirality pdb=" CA LEU K 43 " pdb=" N LEU K 43 " pdb=" C LEU K 43 " pdb=" CB LEU K 43 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CG LEU K 43 " pdb=" CB LEU K 43 " pdb=" CD1 LEU K 43 " pdb=" CD2 LEU K 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA ARG K 42 " pdb=" N ARG K 42 " pdb=" C ARG K 42 " pdb=" CB ARG K 42 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4482 not shown) Planarity restraints: 5212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 36 " 0.168 5.00e-02 4.00e+02 2.67e-01 1.14e+02 pdb=" N PRO K 37 " -0.458 5.00e-02 4.00e+02 pdb=" CA PRO K 37 " 0.194 5.00e-02 4.00e+02 pdb=" CD PRO K 37 " 0.096 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 37 " -0.135 5.00e-02 4.00e+02 2.15e-01 7.39e+01 pdb=" N PRO K 38 " 0.371 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " -0.143 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " -0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 41 " -0.014 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLN K 41 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN K 41 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG K 42 " -0.019 2.00e-02 2.50e+03 ... (remaining 5209 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 27 2.25 - 2.91: 11389 2.91 - 3.57: 39352 3.57 - 4.24: 66063 4.24 - 4.90: 105566 Nonbonded interactions: 222397 Sorted by model distance: nonbonded pdb=" O GLY B 531 " pdb=" O5' ATP C1001 " model vdw 1.585 3.040 nonbonded pdb=" NH1 ARG C 645 " pdb=" O1B ATP C1001 " model vdw 1.654 2.496 nonbonded pdb=" OG SER D 559 " pdb=" CE1 TYR E 562 " model vdw 1.865 3.340 nonbonded pdb=" O THR B 532 " pdb=" O2B ATP C1001 " model vdw 1.913 3.040 nonbonded pdb=" CE1 TYR D 562 " pdb=" NH2 ARG D 609 " model vdw 1.917 3.420 ... (remaining 222392 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 209 through 437 or resid 459 through 713 or resid 901)) selection = (chain 'B' and (resid 209 through 437 or resid 459 through 901)) selection = (chain 'C' and (resid 209 through 437 or resid 459 through 713 or resid 1003)) selection = (chain 'D' and (resid 209 through 713 or resid 902)) selection = (chain 'E' and (resid 209 through 437 or resid 459 through 713 or resid 902)) selection = (chain 'F' and (resid 209 through 437 or resid 459 through 713 or resid 901)) } ncs_group { reference = chain 'H' selection = chain 'J' } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.090 Process input model: 30.200 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 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 : 0.015 1.071 29523 Z= 1.346 Angle : 0.991 54.241 39933 Z= 0.642 Chirality : 0.051 0.978 4485 Planarity : 0.007 0.267 5212 Dihedral : 15.455 151.287 11414 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.54 % Favored : 93.24 % Rotamer: Outliers : 0.45 % Allowed : 7.74 % Favored : 91.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.28 (0.10), residues: 3684 helix: -4.93 (0.04), residues: 1291 sheet: -1.97 (0.23), residues: 411 loop : -2.84 (0.11), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 42 TYR 0.009 0.001 TYR E 562 PHE 0.014 0.001 PHE G 340 TRP 0.010 0.001 TRP G 211 HIS 0.004 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00428 (29499) covalent geometry : angle 0.99087 (39933) hydrogen bonds : bond 0.32969 ( 720) hydrogen bonds : angle 9.83645 ( 2058) metal coordination : bond 0.48577 ( 4) Misc. bond : bond 0.49676 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 805 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.8309 (tp) cc_final: 0.8086 (tp) REVERT: A 310 ILE cc_start: 0.8598 (mt) cc_final: 0.8347 (tt) REVERT: A 332 ARG cc_start: 0.7716 (ptt180) cc_final: 0.7347 (ptt-90) REVERT: A 350 ASN cc_start: 0.7779 (p0) cc_final: 0.7506 (p0) REVERT: A 459 MET cc_start: 0.8290 (ptm) cc_final: 0.8043 (ttp) REVERT: A 526 PHE cc_start: 0.9380 (m-80) cc_final: 0.9044 (m-80) REVERT: A 624 LYS cc_start: 0.5578 (tttm) cc_final: 0.4283 (mmtm) REVERT: A 628 PHE cc_start: 0.7928 (m-80) cc_final: 0.7558 (m-80) REVERT: A 784 MET cc_start: 0.1605 (tpp) cc_final: 0.0472 (tpt) REVERT: B 264 MET cc_start: 0.8428 (ttp) cc_final: 0.8099 (ttp) REVERT: B 283 GLU cc_start: 0.7901 (tt0) cc_final: 0.7690 (mt-10) REVERT: B 285 MET cc_start: 0.7216 (tmm) cc_final: 0.6917 (tmm) REVERT: B 301 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 302 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8102 (tp30) REVERT: B 326 THR cc_start: 0.5101 (t) cc_final: 0.4525 (m) REVERT: B 331 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8649 (tp30) REVERT: B 420 ASP cc_start: 0.8266 (m-30) cc_final: 0.7980 (m-30) REVERT: B 427 GLU cc_start: 0.8376 (tt0) cc_final: 0.8161 (tp30) REVERT: B 477 THR cc_start: 0.6772 (t) cc_final: 0.6317 (m) REVERT: B 496 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8280 (mtpt) REVERT: B 560 MET cc_start: 0.4957 (ttt) cc_final: 0.4736 (tpt) REVERT: B 614 LEU cc_start: 0.8865 (mt) cc_final: 0.8246 (pp) REVERT: C 229 MET cc_start: 0.7522 (mtm) cc_final: 0.7120 (tmm) REVERT: C 236 HIS cc_start: 0.5438 (t-170) cc_final: 0.5080 (t-170) REVERT: C 264 MET cc_start: 0.8750 (tpt) cc_final: 0.8448 (tpp) REVERT: C 304 GLU cc_start: 0.8161 (tt0) cc_final: 0.7895 (tt0) REVERT: C 324 ASP cc_start: 0.8446 (p0) cc_final: 0.7961 (t0) REVERT: C 430 MET cc_start: 0.8485 (mmt) cc_final: 0.8245 (mmm) REVERT: C 474 LEU cc_start: 0.6596 (mt) cc_final: 0.6168 (tt) REVERT: C 513 TYR cc_start: 0.8244 (m-80) cc_final: 0.7482 (m-80) REVERT: C 518 LEU cc_start: 0.7972 (tp) cc_final: 0.7681 (mt) REVERT: C 574 ASP cc_start: 0.8604 (t0) cc_final: 0.8083 (t0) REVERT: C 621 MET cc_start: 0.6042 (mmm) cc_final: 0.5815 (mmm) REVERT: D 251 VAL cc_start: 0.9005 (p) cc_final: 0.8795 (p) REVERT: D 302 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7837 (mm-30) REVERT: D 513 TYR cc_start: 0.6817 (m-80) cc_final: 0.6366 (m-10) REVERT: D 621 MET cc_start: 0.8449 (ppp) cc_final: 0.8047 (ppp) REVERT: D 698 LEU cc_start: 0.7778 (mt) cc_final: 0.7417 (mt) REVERT: E 278 LEU cc_start: 0.8514 (mt) cc_final: 0.8308 (mt) REVERT: E 342 MET cc_start: 0.8385 (mmm) cc_final: 0.8105 (ttm) REVERT: E 345 MET cc_start: 0.7482 (ptp) cc_final: 0.6897 (ptt) REVERT: E 513 TYR cc_start: 0.7864 (p90) cc_final: 0.7494 (p90) REVERT: E 636 PRO cc_start: 0.6352 (Cg_endo) cc_final: 0.6115 (Cg_exo) REVERT: F 264 MET cc_start: 0.9034 (ptp) cc_final: 0.8678 (ptm) REVERT: F 285 MET cc_start: 0.8812 (tpp) cc_final: 0.7525 (tpp) REVERT: F 291 GLU cc_start: 0.8675 (tp30) cc_final: 0.8289 (tp30) REVERT: F 324 ASP cc_start: 0.9069 (m-30) cc_final: 0.8471 (p0) REVERT: F 367 LEU cc_start: 0.8875 (mp) cc_final: 0.8657 (mp) REVERT: F 398 MET cc_start: 0.8702 (mmm) cc_final: 0.8474 (mmm) REVERT: F 504 GLU cc_start: 0.7612 (pp20) cc_final: 0.6982 (mp0) REVERT: F 618 MET cc_start: 0.6639 (ttm) cc_final: 0.6218 (ttm) REVERT: K 6 LYS cc_start: 0.5042 (mmmm) cc_final: 0.4735 (mmmt) REVERT: K 15 LEU cc_start: 0.7750 (mm) cc_final: 0.7497 (mm) REVERT: H 118 GLU cc_start: 0.9231 (mp0) cc_final: 0.8971 (mp0) REVERT: H 123 ILE cc_start: 0.8329 (mm) cc_final: 0.8115 (mm) REVERT: H 141 GLN cc_start: 0.7117 (mt0) cc_final: 0.6040 (mt0) REVERT: J 201 MET cc_start: 0.8336 (ptt) cc_final: 0.7844 (ppp) REVERT: J 221 ASP cc_start: 0.6979 (t0) cc_final: 0.6261 (t0) REVERT: J 250 LEU cc_start: 0.6912 (mt) cc_final: 0.6293 (tt) REVERT: G 121 GLU cc_start: 0.8340 (tt0) cc_final: 0.8026 (tp30) REVERT: G 161 LYS cc_start: 0.8446 (tmtt) cc_final: 0.8149 (ttmt) REVERT: G 191 SER cc_start: 0.7506 (t) cc_final: 0.6929 (p) REVERT: G 257 MET cc_start: 0.8586 (mmt) cc_final: 0.8283 (mmm) REVERT: G 370 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7006 (tptt) REVERT: G 406 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7980 (tm-30) REVERT: G 424 TYR cc_start: 0.6077 (t80) cc_final: 0.5612 (t80) REVERT: G 429 THR cc_start: 0.7752 (p) cc_final: 0.7537 (t) REVERT: G 430 ASP cc_start: 0.7765 (t0) cc_final: 0.6901 (t0) REVERT: G 485 THR cc_start: 0.5565 (p) cc_final: 0.5220 (m) REVERT: G 539 LEU cc_start: 0.7747 (mt) cc_final: 0.7528 (tp) outliers start: 14 outliers final: 5 residues processed: 815 average time/residue: 0.1919 time to fit residues: 239.1355 Evaluate side-chains 461 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 456 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 562 TYR Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 562 TYR Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN A 757 HIS B 238 GLN B 432 GLN B 626 ASN C 238 GLN C 270 ASN C 337 GLN C 394 HIS D 295 ASN D 468 ASN D 702 GLN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 HIS E 432 GLN ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN E 548 ASN E 568 ASN E 612 ASN F 270 ASN F 337 GLN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 468 ASN F 509 HIS F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN K 2 GLN K 25 ASN K 31 GLN H 125 ASN H 149 GLN H 162 GLN G 162 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 ASN G 293 GLN G 305 ASN G 491 ASN G 577 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.133920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104496 restraints weight = 88066.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102597 restraints weight = 53896.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.103486 restraints weight = 46767.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103861 restraints weight = 35699.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.103973 restraints weight = 33665.031| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 29523 Z= 0.236 Angle : 0.791 18.828 39933 Z= 0.402 Chirality : 0.047 0.160 4485 Planarity : 0.007 0.173 5212 Dihedral : 12.086 144.089 4332 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 2.69 % Allowed : 16.16 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.12), residues: 3684 helix: -3.00 (0.10), residues: 1311 sheet: -1.39 (0.24), residues: 384 loop : -2.28 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 672 TYR 0.024 0.002 TYR A 213 PHE 0.022 0.002 PHE B 277 TRP 0.026 0.002 TRP D 561 HIS 0.013 0.002 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00528 (29499) covalent geometry : angle 0.79103 (39933) hydrogen bonds : bond 0.04755 ( 720) hydrogen bonds : angle 5.61176 ( 2058) metal coordination : bond 0.01141 ( 4) Misc. bond : bond 0.00347 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 456 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ILE cc_start: 0.9380 (pt) cc_final: 0.8835 (pt) REVERT: A 287 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8740 (mttm) REVERT: A 406 LEU cc_start: 0.6821 (mm) cc_final: 0.6501 (mt) REVERT: A 493 ASP cc_start: 0.9083 (t0) cc_final: 0.8589 (t0) REVERT: A 621 MET cc_start: 0.7448 (mmp) cc_final: 0.7044 (mmm) REVERT: A 624 LYS cc_start: 0.3891 (tttm) cc_final: 0.3004 (mppt) REVERT: A 784 MET cc_start: 0.0610 (tpp) cc_final: -0.0201 (tpt) REVERT: B 264 MET cc_start: 0.8167 (ttp) cc_final: 0.7713 (ttp) REVERT: B 285 MET cc_start: 0.8527 (tmm) cc_final: 0.7913 (tmm) REVERT: B 302 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7842 (tp30) REVERT: B 327 ASN cc_start: 0.8020 (p0) cc_final: 0.7747 (p0) REVERT: B 331 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7524 (tp30) REVERT: B 667 LEU cc_start: 0.8437 (mt) cc_final: 0.8186 (mt) REVERT: C 288 MET cc_start: 0.8933 (tpp) cc_final: 0.8554 (tpp) REVERT: C 324 ASP cc_start: 0.7892 (p0) cc_final: 0.7669 (t0) REVERT: C 339 LEU cc_start: 0.9169 (mt) cc_final: 0.8782 (mt) REVERT: C 383 ASP cc_start: 0.7204 (m-30) cc_final: 0.6974 (m-30) REVERT: D 513 TYR cc_start: 0.7924 (m-80) cc_final: 0.7500 (m-80) REVERT: E 229 MET cc_start: 0.8264 (mpp) cc_final: 0.7647 (mtm) REVERT: E 278 LEU cc_start: 0.8224 (mt) cc_final: 0.8011 (mt) REVERT: E 398 MET cc_start: 0.4701 (ttp) cc_final: 0.3050 (tpp) REVERT: E 501 GLU cc_start: 0.7950 (mp0) cc_final: 0.7538 (pm20) REVERT: E 527 TYR cc_start: 0.6715 (p90) cc_final: 0.6431 (p90) REVERT: E 661 ASN cc_start: 0.7984 (p0) cc_final: 0.7604 (p0) REVERT: F 285 MET cc_start: 0.8619 (tpp) cc_final: 0.8051 (tpp) REVERT: F 291 GLU cc_start: 0.8641 (tp30) cc_final: 0.8406 (tp30) REVERT: F 324 ASP cc_start: 0.8692 (m-30) cc_final: 0.7987 (p0) REVERT: F 564 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6483 (mp0) REVERT: K 15 LEU cc_start: 0.8254 (mm) cc_final: 0.8028 (mt) REVERT: K 16 GLU cc_start: 0.7673 (mp0) cc_final: 0.7285 (mp0) REVERT: H 163 LYS cc_start: 0.8644 (tppp) cc_final: 0.8375 (mmmm) REVERT: J 201 MET cc_start: 0.8412 (ptt) cc_final: 0.7575 (ppp) REVERT: J 245 PHE cc_start: 0.6961 (t80) cc_final: 0.6754 (t80) REVERT: G 233 MET cc_start: 0.8924 (mmm) cc_final: 0.8657 (mmm) outliers start: 83 outliers final: 48 residues processed: 516 average time/residue: 0.1712 time to fit residues: 142.1185 Evaluate side-chains 403 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 354 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 526 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 544 TRP Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 341 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 668 ASN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 782 GLN K 2 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.144767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.124435 restraints weight = 99901.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.123243 restraints weight = 127316.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.124191 restraints weight = 110806.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.124166 restraints weight = 76086.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.124747 restraints weight = 69824.471| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29523 Z= 0.119 Angle : 0.660 16.774 39933 Z= 0.322 Chirality : 0.044 0.170 4485 Planarity : 0.005 0.161 5212 Dihedral : 11.955 150.915 4321 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 2.49 % Allowed : 18.26 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.83 (0.13), residues: 3684 helix: -1.96 (0.13), residues: 1316 sheet: -1.09 (0.24), residues: 424 loop : -1.99 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 609 TYR 0.016 0.001 TYR E 527 PHE 0.023 0.001 PHE C 370 TRP 0.013 0.001 TRP E 561 HIS 0.010 0.001 HIS G 521 Details of bonding type rmsd covalent geometry : bond 0.00266 (29499) covalent geometry : angle 0.66003 (39933) hydrogen bonds : bond 0.03630 ( 720) hydrogen bonds : angle 4.99523 ( 2058) metal coordination : bond 0.00130 ( 4) Misc. bond : bond 0.00137 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 392 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8560 (mttm) REVERT: A 332 ARG cc_start: 0.7517 (ptt90) cc_final: 0.7168 (ptt90) REVERT: A 350 ASN cc_start: 0.7675 (p0) cc_final: 0.7398 (p0) REVERT: A 493 ASP cc_start: 0.8107 (t0) cc_final: 0.7728 (t0) REVERT: A 621 MET cc_start: 0.6938 (mmp) cc_final: 0.6699 (mmm) REVERT: A 624 LYS cc_start: 0.3445 (tttm) cc_final: 0.3102 (mptt) REVERT: A 784 MET cc_start: 0.0412 (tpp) cc_final: -0.0164 (tpt) REVERT: B 264 MET cc_start: 0.8164 (ttp) cc_final: 0.7640 (ttp) REVERT: B 285 MET cc_start: 0.8474 (tmm) cc_final: 0.8264 (tmm) REVERT: B 424 LEU cc_start: 0.8523 (tp) cc_final: 0.8065 (tt) REVERT: B 553 LYS cc_start: 0.5685 (mmtt) cc_final: 0.5340 (mmtt) REVERT: B 614 LEU cc_start: 0.7950 (mt) cc_final: 0.7402 (pp) REVERT: C 288 MET cc_start: 0.8651 (tpp) cc_final: 0.8027 (tpp) REVERT: C 324 ASP cc_start: 0.8279 (p0) cc_final: 0.7857 (t0) REVERT: D 285 MET cc_start: 0.8587 (tpt) cc_final: 0.8356 (tpt) REVERT: D 391 LEU cc_start: 0.8838 (mm) cc_final: 0.8629 (mm) REVERT: D 513 TYR cc_start: 0.7659 (m-80) cc_final: 0.7323 (m-80) REVERT: E 223 MET cc_start: 0.8375 (ppp) cc_final: 0.7926 (ppp) REVERT: E 229 MET cc_start: 0.8063 (mpp) cc_final: 0.7434 (mtm) REVERT: E 234 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8028 (pp) REVERT: E 261 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8288 (mttm) REVERT: E 278 LEU cc_start: 0.8240 (mt) cc_final: 0.8034 (mp) REVERT: E 398 MET cc_start: 0.4665 (ttp) cc_final: 0.3151 (tpp) REVERT: F 219 CYS cc_start: 0.4654 (m) cc_final: 0.3789 (p) REVERT: F 324 ASP cc_start: 0.8336 (m-30) cc_final: 0.7746 (p0) REVERT: K 15 LEU cc_start: 0.8358 (mm) cc_final: 0.8107 (mt) REVERT: K 16 GLU cc_start: 0.7539 (mp0) cc_final: 0.7067 (mp0) REVERT: H 104 PHE cc_start: 0.6859 (m-10) cc_final: 0.6522 (m-10) REVERT: H 163 LYS cc_start: 0.8597 (tppp) cc_final: 0.7280 (tppp) REVERT: J 201 MET cc_start: 0.7709 (ptt) cc_final: 0.7207 (ppp) REVERT: J 239 ASP cc_start: 0.7816 (p0) cc_final: 0.7550 (p0) REVERT: G 157 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6713 (tm-30) REVERT: G 233 MET cc_start: 0.9027 (mmm) cc_final: 0.8783 (mmm) REVERT: G 414 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7378 (mm) REVERT: G 546 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7126 (pp) outliers start: 77 outliers final: 48 residues processed: 447 average time/residue: 0.1626 time to fit residues: 118.8131 Evaluate side-chains 401 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 544 TRP Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 220 optimal weight: 9.9990 chunk 29 optimal weight: 0.0050 chunk 162 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 268 optimal weight: 0.3980 chunk 360 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 282 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 HIS ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 HIS F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.142695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.121942 restraints weight = 100019.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.121531 restraints weight = 128260.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.122142 restraints weight = 115288.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.122142 restraints weight = 75450.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.122438 restraints weight = 71382.833| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29523 Z= 0.133 Angle : 0.636 14.838 39933 Z= 0.312 Chirality : 0.044 0.149 4485 Planarity : 0.005 0.151 5212 Dihedral : 11.793 154.619 4321 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.00 % Favored : 92.94 % Rotamer: Outliers : 3.30 % Allowed : 19.01 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.33 (0.13), residues: 3684 helix: -1.37 (0.14), residues: 1325 sheet: -0.93 (0.25), residues: 419 loop : -1.79 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 323 TYR 0.020 0.001 TYR A 513 PHE 0.018 0.001 PHE C 370 TRP 0.008 0.001 TRP B 486 HIS 0.009 0.001 HIS G 521 Details of bonding type rmsd covalent geometry : bond 0.00305 (29499) covalent geometry : angle 0.63641 (39933) hydrogen bonds : bond 0.03241 ( 720) hydrogen bonds : angle 4.73804 ( 2058) metal coordination : bond 0.00211 ( 4) Misc. bond : bond 0.00124 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 379 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8074 (mmp) cc_final: 0.7833 (mmp) REVERT: A 332 ARG cc_start: 0.7679 (ptt90) cc_final: 0.7230 (ptt90) REVERT: A 345 MET cc_start: 0.7426 (ppp) cc_final: 0.7148 (ppp) REVERT: A 621 MET cc_start: 0.6940 (mmp) cc_final: 0.6679 (mmm) REVERT: A 624 LYS cc_start: 0.3457 (tttm) cc_final: 0.3063 (mmtm) REVERT: A 784 MET cc_start: 0.0362 (tpp) cc_final: -0.0185 (tpt) REVERT: B 264 MET cc_start: 0.7967 (ttp) cc_final: 0.7569 (ttp) REVERT: B 416 TYR cc_start: 0.8183 (m-10) cc_final: 0.7966 (m-10) REVERT: B 424 LEU cc_start: 0.8451 (tp) cc_final: 0.8023 (tt) REVERT: B 486 TRP cc_start: 0.5857 (m100) cc_final: 0.5559 (m100) REVERT: B 496 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6402 (mtmt) REVERT: B 553 LYS cc_start: 0.5323 (mmtt) cc_final: 0.5119 (mmtt) REVERT: B 560 MET cc_start: 0.5508 (mmm) cc_final: 0.4994 (tpt) REVERT: B 614 LEU cc_start: 0.7910 (mt) cc_final: 0.7413 (pp) REVERT: C 288 MET cc_start: 0.8773 (tpp) cc_final: 0.8568 (tpp) REVERT: C 324 ASP cc_start: 0.8063 (p0) cc_final: 0.7690 (t0) REVERT: C 339 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8570 (mt) REVERT: C 342 MET cc_start: 0.9017 (ttm) cc_final: 0.8668 (mtp) REVERT: D 437 MET cc_start: 0.6594 (mmm) cc_final: 0.6237 (mmm) REVERT: D 513 TYR cc_start: 0.7449 (m-80) cc_final: 0.7154 (m-80) REVERT: E 223 MET cc_start: 0.8150 (ppp) cc_final: 0.7775 (ppp) REVERT: E 229 MET cc_start: 0.8119 (mpp) cc_final: 0.7472 (mtm) REVERT: E 234 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7934 (pp) REVERT: E 261 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8399 (mttm) REVERT: E 278 LEU cc_start: 0.8240 (mt) cc_final: 0.8010 (mt) REVERT: E 398 MET cc_start: 0.4852 (ttp) cc_final: 0.3232 (tpp) REVERT: F 324 ASP cc_start: 0.8289 (m-30) cc_final: 0.7642 (p0) REVERT: F 354 ILE cc_start: 0.8127 (mm) cc_final: 0.7911 (tp) REVERT: K 15 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7921 (mt) REVERT: K 18 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: J 201 MET cc_start: 0.7572 (ptt) cc_final: 0.7103 (ppp) REVERT: J 239 ASP cc_start: 0.7904 (p0) cc_final: 0.7628 (p0) REVERT: J 250 LEU cc_start: 0.5792 (mt) cc_final: 0.5480 (mp) REVERT: G 233 MET cc_start: 0.9024 (mmm) cc_final: 0.8791 (mmm) REVERT: G 363 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8635 (m) REVERT: G 546 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6857 (pp) outliers start: 102 outliers final: 63 residues processed: 456 average time/residue: 0.1603 time to fit residues: 120.2707 Evaluate side-chains 405 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 334 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 544 TRP Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 145 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 0.0570 chunk 92 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 163 optimal weight: 0.5980 chunk 308 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.143551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.121248 restraints weight = 99730.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.121420 restraints weight = 111324.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.118215 restraints weight = 70893.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.117804 restraints weight = 86982.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.118218 restraints weight = 80543.523| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29523 Z= 0.107 Angle : 0.624 14.643 39933 Z= 0.301 Chirality : 0.043 0.151 4485 Planarity : 0.005 0.140 5212 Dihedral : 11.508 154.124 4321 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 3.08 % Allowed : 19.95 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.14), residues: 3684 helix: -1.00 (0.14), residues: 1322 sheet: -0.77 (0.25), residues: 433 loop : -1.65 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 387 TYR 0.023 0.001 TYR C 513 PHE 0.018 0.001 PHE D 585 TRP 0.019 0.001 TRP D 486 HIS 0.009 0.001 HIS G 521 Details of bonding type rmsd covalent geometry : bond 0.00241 (29499) covalent geometry : angle 0.62427 (39933) hydrogen bonds : bond 0.02884 ( 720) hydrogen bonds : angle 4.52785 ( 2058) metal coordination : bond 0.00094 ( 4) Misc. bond : bond 0.00113 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 365 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 MET cc_start: 0.7441 (mmp) cc_final: 0.7027 (mmm) REVERT: A 624 LYS cc_start: 0.3714 (tttm) cc_final: 0.3173 (mmtm) REVERT: A 784 MET cc_start: 0.0474 (tpp) cc_final: -0.0283 (tpt) REVERT: B 264 MET cc_start: 0.7862 (ttp) cc_final: 0.7454 (ttp) REVERT: B 331 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 424 LEU cc_start: 0.8479 (tp) cc_final: 0.8037 (tt) REVERT: B 486 TRP cc_start: 0.6147 (m100) cc_final: 0.5839 (m100) REVERT: B 553 LYS cc_start: 0.5726 (mmtt) cc_final: 0.5451 (mmtt) REVERT: B 560 MET cc_start: 0.5417 (mmm) cc_final: 0.5004 (tpt) REVERT: B 614 LEU cc_start: 0.8160 (mt) cc_final: 0.7548 (pp) REVERT: B 621 MET cc_start: 0.6644 (tpt) cc_final: 0.6375 (tpt) REVERT: C 324 ASP cc_start: 0.8151 (p0) cc_final: 0.7814 (t0) REVERT: D 391 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8637 (mm) REVERT: D 437 MET cc_start: 0.6875 (mmm) cc_final: 0.6566 (mmm) REVERT: D 513 TYR cc_start: 0.7976 (m-80) cc_final: 0.7576 (m-80) REVERT: D 562 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7475 (t80) REVERT: D 621 MET cc_start: 0.8894 (tmm) cc_final: 0.8633 (tmm) REVERT: E 223 MET cc_start: 0.8116 (ppp) cc_final: 0.7664 (ppp) REVERT: E 229 MET cc_start: 0.8359 (mpp) cc_final: 0.7862 (mtm) REVERT: E 234 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7876 (pp) REVERT: E 261 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8419 (mttm) REVERT: E 345 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.5179 (ptt) REVERT: E 398 MET cc_start: 0.4707 (ttp) cc_final: 0.3029 (tpp) REVERT: F 291 GLU cc_start: 0.7874 (tt0) cc_final: 0.7462 (pt0) REVERT: F 324 ASP cc_start: 0.8473 (m-30) cc_final: 0.7831 (p0) REVERT: F 333 ARG cc_start: 0.8301 (tpm170) cc_final: 0.8072 (tpm170) REVERT: F 354 ILE cc_start: 0.8109 (mm) cc_final: 0.7853 (tp) REVERT: K 15 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7682 (mt) REVERT: K 18 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: K 36 ILE cc_start: 0.9376 (mm) cc_final: 0.8576 (tp) REVERT: K 37 PRO cc_start: 0.9314 (OUTLIER) cc_final: 0.9038 (Cg_endo) REVERT: H 129 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8579 (mmtm) REVERT: J 201 MET cc_start: 0.8343 (ptt) cc_final: 0.7544 (ppp) REVERT: J 239 ASP cc_start: 0.7928 (p0) cc_final: 0.7684 (p0) REVERT: J 250 LEU cc_start: 0.5939 (mt) cc_final: 0.5649 (mp) REVERT: G 157 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7092 (tm-30) REVERT: G 233 MET cc_start: 0.9143 (mmm) cc_final: 0.8928 (mmm) REVERT: G 255 THR cc_start: 0.8213 (t) cc_final: 0.7684 (t) REVERT: G 546 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6994 (pp) outliers start: 95 outliers final: 63 residues processed: 436 average time/residue: 0.1594 time to fit residues: 114.8661 Evaluate side-chains 399 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 327 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 544 TRP Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 310 optimal weight: 3.9990 chunk 165 optimal weight: 0.2980 chunk 200 optimal weight: 20.0000 chunk 123 optimal weight: 0.0980 chunk 317 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 HIS F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.140615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.117558 restraints weight = 99641.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.117187 restraints weight = 102809.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.115814 restraints weight = 77114.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.115509 restraints weight = 73883.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115806 restraints weight = 71557.916| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29523 Z= 0.152 Angle : 0.656 13.818 39933 Z= 0.323 Chirality : 0.044 0.194 4485 Planarity : 0.005 0.140 5212 Dihedral : 11.311 149.146 4321 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.55 % Favored : 92.43 % Rotamer: Outliers : 3.43 % Allowed : 20.34 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3684 helix: -0.84 (0.14), residues: 1348 sheet: -0.81 (0.25), residues: 426 loop : -1.54 (0.15), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 645 TYR 0.024 0.001 TYR C 513 PHE 0.028 0.001 PHE J 204 TRP 0.017 0.001 TRP D 561 HIS 0.005 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00347 (29499) covalent geometry : angle 0.65633 (39933) hydrogen bonds : bond 0.03175 ( 720) hydrogen bonds : angle 4.54512 ( 2058) metal coordination : bond 0.00319 ( 4) Misc. bond : bond 0.00302 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 336 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 MET cc_start: 0.7501 (mmp) cc_final: 0.7125 (mmm) REVERT: A 784 MET cc_start: 0.0497 (tpp) cc_final: -0.0275 (tpt) REVERT: B 264 MET cc_start: 0.7986 (ttp) cc_final: 0.7574 (ttp) REVERT: B 424 LEU cc_start: 0.8633 (tp) cc_final: 0.8252 (tt) REVERT: B 553 LYS cc_start: 0.5650 (mmtt) cc_final: 0.5348 (mmtt) REVERT: B 621 MET cc_start: 0.6799 (tpt) cc_final: 0.6592 (tpt) REVERT: C 324 ASP cc_start: 0.8204 (p0) cc_final: 0.7906 (t0) REVERT: C 618 MET cc_start: 0.7492 (ppp) cc_final: 0.7207 (ppp) REVERT: D 341 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9068 (mp) REVERT: D 391 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8692 (mm) REVERT: D 437 MET cc_start: 0.7380 (mmm) cc_final: 0.7075 (mmm) REVERT: D 513 TYR cc_start: 0.7956 (m-80) cc_final: 0.7608 (m-80) REVERT: D 558 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6495 (tp) REVERT: D 621 MET cc_start: 0.8922 (tmm) cc_final: 0.8706 (tmm) REVERT: E 223 MET cc_start: 0.8194 (ppp) cc_final: 0.7596 (ppp) REVERT: E 229 MET cc_start: 0.8232 (mpp) cc_final: 0.7628 (mpp) REVERT: E 234 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8128 (pp) REVERT: E 278 LEU cc_start: 0.8436 (mt) cc_final: 0.8201 (mt) REVERT: E 345 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.5364 (ptp) REVERT: E 698 LEU cc_start: 0.8434 (tt) cc_final: 0.8219 (tp) REVERT: F 285 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7847 (ttp) REVERT: F 291 GLU cc_start: 0.7895 (tt0) cc_final: 0.7463 (pt0) REVERT: F 324 ASP cc_start: 0.8227 (m-30) cc_final: 0.7684 (p0) REVERT: F 354 ILE cc_start: 0.8140 (mm) cc_final: 0.7886 (tp) REVERT: F 398 MET cc_start: 0.7892 (mmm) cc_final: 0.7607 (mmp) REVERT: K 15 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8035 (mt) REVERT: K 18 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7461 (pp20) REVERT: K 36 ILE cc_start: 0.9290 (mm) cc_final: 0.8630 (tp) REVERT: K 37 PRO cc_start: 0.9076 (OUTLIER) cc_final: 0.8568 (Cg_endo) REVERT: H 129 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8687 (mmtm) REVERT: J 201 MET cc_start: 0.8106 (ptt) cc_final: 0.7552 (ppp) REVERT: J 239 ASP cc_start: 0.8153 (p0) cc_final: 0.7842 (p0) REVERT: J 250 LEU cc_start: 0.5940 (mt) cc_final: 0.5711 (mp) REVERT: G 255 THR cc_start: 0.8378 (t) cc_final: 0.7795 (t) REVERT: G 400 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8852 (pt0) REVERT: G 414 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8428 (mm) REVERT: G 478 ASN cc_start: 0.7611 (t0) cc_final: 0.7376 (t0) REVERT: G 546 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6950 (pp) outliers start: 106 outliers final: 73 residues processed: 417 average time/residue: 0.1548 time to fit residues: 107.5538 Evaluate side-chains 400 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 315 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 654 TYR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 400 GLN Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 544 TRP Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 151 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 360 optimal weight: 0.9980 chunk 319 optimal weight: 20.0000 chunk 239 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 322 optimal weight: 0.0770 chunk 253 optimal weight: 0.0000 chunk 11 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 GLN C 270 ASN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.142767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.122047 restraints weight = 99598.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.121568 restraints weight = 125948.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122201 restraints weight = 111892.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122398 restraints weight = 73599.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.122570 restraints weight = 71990.342| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29523 Z= 0.103 Angle : 0.627 13.677 39933 Z= 0.302 Chirality : 0.043 0.184 4485 Planarity : 0.004 0.140 5212 Dihedral : 11.077 147.092 4321 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 3.01 % Allowed : 20.73 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3684 helix: -0.66 (0.14), residues: 1337 sheet: -0.66 (0.24), residues: 427 loop : -1.48 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 333 TYR 0.021 0.001 TYR C 513 PHE 0.020 0.001 PHE D 585 TRP 0.012 0.001 TRP B 486 HIS 0.003 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00232 (29499) covalent geometry : angle 0.62704 (39933) hydrogen bonds : bond 0.02666 ( 720) hydrogen bonds : angle 4.36407 ( 2058) metal coordination : bond 0.00057 ( 4) Misc. bond : bond 0.00139 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 347 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.7321 (ppp) cc_final: 0.7103 (ppp) REVERT: A 481 SER cc_start: 0.3803 (OUTLIER) cc_final: 0.3504 (p) REVERT: A 621 MET cc_start: 0.7304 (mmp) cc_final: 0.7004 (mmm) REVERT: A 784 MET cc_start: 0.0475 (tpp) cc_final: -0.0245 (tpt) REVERT: B 264 MET cc_start: 0.8075 (ttp) cc_final: 0.7676 (ttp) REVERT: B 331 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 424 LEU cc_start: 0.8602 (tp) cc_final: 0.8230 (tt) REVERT: B 560 MET cc_start: 0.5129 (mmm) cc_final: 0.4912 (mmm) REVERT: C 324 ASP cc_start: 0.8088 (p0) cc_final: 0.7846 (t0) REVERT: C 618 MET cc_start: 0.7847 (ppp) cc_final: 0.7563 (ppp) REVERT: D 302 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7049 (mp0) REVERT: D 391 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8698 (mm) REVERT: D 437 MET cc_start: 0.7362 (mmm) cc_final: 0.7075 (mmm) REVERT: D 513 TYR cc_start: 0.7632 (m-80) cc_final: 0.7268 (m-10) REVERT: D 558 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6686 (tp) REVERT: D 562 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7513 (t80) REVERT: E 229 MET cc_start: 0.8296 (mpp) cc_final: 0.7790 (mpp) REVERT: E 234 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7953 (pp) REVERT: E 261 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8420 (mttm) REVERT: E 341 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8899 (tt) REVERT: E 430 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7374 (ttm) REVERT: E 698 LEU cc_start: 0.8130 (tt) cc_final: 0.7918 (tp) REVERT: F 291 GLU cc_start: 0.7939 (tt0) cc_final: 0.7668 (pt0) REVERT: F 324 ASP cc_start: 0.8087 (m-30) cc_final: 0.7590 (p0) REVERT: F 354 ILE cc_start: 0.8035 (mm) cc_final: 0.7834 (tp) REVERT: K 15 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7859 (mt) REVERT: K 18 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7451 (pp20) REVERT: K 36 ILE cc_start: 0.9204 (mm) cc_final: 0.8513 (tp) REVERT: K 37 PRO cc_start: 0.8810 (OUTLIER) cc_final: 0.8272 (Cg_endo) REVERT: H 129 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8590 (mmtm) REVERT: J 201 MET cc_start: 0.7650 (ptt) cc_final: 0.7284 (ppp) REVERT: J 239 ASP cc_start: 0.8129 (p0) cc_final: 0.7770 (p0) REVERT: J 250 LEU cc_start: 0.5742 (mt) cc_final: 0.5472 (mp) REVERT: G 242 SER cc_start: 0.9529 (m) cc_final: 0.8913 (p) REVERT: G 427 ASP cc_start: 0.7934 (t0) cc_final: 0.7571 (t0) REVERT: G 546 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6865 (pp) outliers start: 93 outliers final: 59 residues processed: 417 average time/residue: 0.1565 time to fit residues: 108.1970 Evaluate side-chains 393 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 322 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 430 MET Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 237 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 224 optimal weight: 0.3980 chunk 144 optimal weight: 0.8980 chunk 151 optimal weight: 0.1980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS D 225 GLN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.141126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.118654 restraints weight = 99580.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.118333 restraints weight = 125565.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.115681 restraints weight = 91466.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.115611 restraints weight = 89135.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115953 restraints weight = 74835.293| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29523 Z= 0.125 Angle : 0.653 14.505 39933 Z= 0.316 Chirality : 0.044 0.175 4485 Planarity : 0.005 0.143 5212 Dihedral : 10.957 141.775 4321 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.14 % Favored : 92.83 % Rotamer: Outliers : 2.85 % Allowed : 21.34 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3684 helix: -0.59 (0.14), residues: 1350 sheet: -0.69 (0.24), residues: 439 loop : -1.39 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 570 TYR 0.012 0.001 TYR B 707 PHE 0.031 0.001 PHE C 573 TRP 0.021 0.001 TRP F 486 HIS 0.005 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00289 (29499) covalent geometry : angle 0.65316 (39933) hydrogen bonds : bond 0.02944 ( 720) hydrogen bonds : angle 4.38643 ( 2058) metal coordination : bond 0.00199 ( 4) Misc. bond : bond 0.00178 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 331 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 SER cc_start: 0.3943 (OUTLIER) cc_final: 0.3584 (p) REVERT: A 621 MET cc_start: 0.7688 (mmp) cc_final: 0.7253 (mmm) REVERT: A 784 MET cc_start: 0.0400 (tpp) cc_final: -0.0049 (tpt) REVERT: B 424 LEU cc_start: 0.8656 (tp) cc_final: 0.8293 (tt) REVERT: B 430 MET cc_start: 0.7322 (tpp) cc_final: 0.7023 (tpp) REVERT: B 560 MET cc_start: 0.5020 (mmm) cc_final: 0.4769 (mmm) REVERT: C 213 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: C 324 ASP cc_start: 0.8172 (p0) cc_final: 0.7856 (t0) REVERT: C 569 ILE cc_start: 0.8782 (mm) cc_final: 0.8406 (mp) REVERT: C 577 ARG cc_start: 0.5772 (ttt180) cc_final: 0.5431 (mtp-110) REVERT: C 618 MET cc_start: 0.7738 (ppp) cc_final: 0.7470 (ppp) REVERT: D 391 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8699 (mm) REVERT: D 437 MET cc_start: 0.7680 (mmm) cc_final: 0.7393 (mmm) REVERT: D 513 TYR cc_start: 0.8040 (m-80) cc_final: 0.7636 (m-10) REVERT: D 558 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6741 (tp) REVERT: D 562 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7923 (t80) REVERT: E 223 MET cc_start: 0.8004 (ppp) cc_final: 0.7737 (ppp) REVERT: E 229 MET cc_start: 0.8349 (mpp) cc_final: 0.7735 (mpp) REVERT: E 234 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7981 (pp) REVERT: F 291 GLU cc_start: 0.8029 (tt0) cc_final: 0.7720 (pt0) REVERT: F 354 ILE cc_start: 0.8049 (mm) cc_final: 0.7826 (tp) REVERT: K 15 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8004 (mt) REVERT: K 18 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: K 37 PRO cc_start: 0.8709 (OUTLIER) cc_final: 0.8196 (Cg_endo) REVERT: H 129 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8724 (mmtm) REVERT: J 201 MET cc_start: 0.8097 (ptt) cc_final: 0.7523 (ppp) REVERT: J 239 ASP cc_start: 0.8102 (p0) cc_final: 0.7772 (p0) REVERT: J 250 LEU cc_start: 0.5928 (mt) cc_final: 0.5694 (mp) REVERT: G 160 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7595 (pm20) REVERT: G 400 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8802 (pt0) REVERT: G 427 ASP cc_start: 0.8017 (t0) cc_final: 0.7690 (t0) REVERT: G 430 ASP cc_start: 0.7344 (t0) cc_final: 0.7103 (t0) REVERT: G 546 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7014 (pp) outliers start: 88 outliers final: 65 residues processed: 396 average time/residue: 0.1551 time to fit residues: 102.4780 Evaluate side-chains 392 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 315 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 400 GLN Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 213 optimal weight: 9.9990 chunk 353 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 120 optimal weight: 0.0570 chunk 104 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 228 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.142373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.121790 restraints weight = 99920.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.121367 restraints weight = 126135.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121786 restraints weight = 112886.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121856 restraints weight = 73566.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.122028 restraints weight = 71918.051| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 29523 Z= 0.107 Angle : 0.659 14.314 39933 Z= 0.316 Chirality : 0.044 0.195 4485 Planarity : 0.004 0.145 5212 Dihedral : 10.724 138.705 4321 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 2.49 % Allowed : 22.22 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.14), residues: 3684 helix: -0.46 (0.15), residues: 1334 sheet: -0.64 (0.24), residues: 442 loop : -1.33 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 645 TYR 0.018 0.001 TYR C 513 PHE 0.034 0.001 PHE C 573 TRP 0.019 0.001 TRP F 486 HIS 0.003 0.001 HIS G 166 Details of bonding type rmsd covalent geometry : bond 0.00246 (29499) covalent geometry : angle 0.65927 (39933) hydrogen bonds : bond 0.02747 ( 720) hydrogen bonds : angle 4.33220 ( 2058) metal coordination : bond 0.00095 ( 4) Misc. bond : bond 0.00125 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 336 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 SER cc_start: 0.3449 (OUTLIER) cc_final: 0.3039 (p) REVERT: A 621 MET cc_start: 0.7444 (mmp) cc_final: 0.7081 (mmm) REVERT: A 784 MET cc_start: 0.0360 (tpp) cc_final: -0.0271 (tpt) REVERT: B 264 MET cc_start: 0.7895 (ttp) cc_final: 0.7648 (ttp) REVERT: B 416 TYR cc_start: 0.8256 (m-10) cc_final: 0.8036 (m-10) REVERT: B 424 LEU cc_start: 0.8618 (tp) cc_final: 0.8292 (tt) REVERT: B 430 MET cc_start: 0.7332 (tpp) cc_final: 0.7088 (tpp) REVERT: B 556 GLU cc_start: 0.6038 (mp0) cc_final: 0.5731 (tm-30) REVERT: C 213 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7492 (m-10) REVERT: C 324 ASP cc_start: 0.8056 (p0) cc_final: 0.7853 (t0) REVERT: C 569 ILE cc_start: 0.8512 (mm) cc_final: 0.8292 (mp) REVERT: C 577 ARG cc_start: 0.5652 (ttt180) cc_final: 0.5367 (mtp-110) REVERT: C 618 MET cc_start: 0.7843 (ppp) cc_final: 0.7564 (ppp) REVERT: C 652 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8336 (mp) REVERT: D 302 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7264 (mm-30) REVERT: D 391 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8718 (mm) REVERT: D 437 MET cc_start: 0.7597 (mmm) cc_final: 0.7336 (mmm) REVERT: D 513 TYR cc_start: 0.7737 (m-80) cc_final: 0.7317 (m-10) REVERT: D 558 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6696 (tp) REVERT: E 229 MET cc_start: 0.8351 (mpp) cc_final: 0.7534 (mpp) REVERT: E 234 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7957 (pp) REVERT: E 430 MET cc_start: 0.7956 (ttm) cc_final: 0.7639 (ttm) REVERT: E 596 ARG cc_start: 0.7470 (tpp-160) cc_final: 0.7222 (tpp-160) REVERT: F 291 GLU cc_start: 0.7890 (tt0) cc_final: 0.7659 (pt0) REVERT: F 459 MET cc_start: 0.7436 (tpp) cc_final: 0.7144 (tmm) REVERT: K 15 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7918 (mt) REVERT: K 18 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: K 37 PRO cc_start: 0.8611 (OUTLIER) cc_final: 0.8065 (Cg_endo) REVERT: J 201 MET cc_start: 0.7601 (ptt) cc_final: 0.7313 (ppp) REVERT: J 239 ASP cc_start: 0.8017 (p0) cc_final: 0.7643 (p0) REVERT: J 250 LEU cc_start: 0.5679 (mt) cc_final: 0.5452 (mp) REVERT: G 160 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: G 242 SER cc_start: 0.9590 (m) cc_final: 0.8989 (p) REVERT: G 400 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: G 427 ASP cc_start: 0.8091 (t0) cc_final: 0.7723 (t0) REVERT: G 546 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6974 (pp) outliers start: 77 outliers final: 54 residues processed: 394 average time/residue: 0.1476 time to fit residues: 98.3098 Evaluate side-chains 385 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 400 GLN Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 544 TRP Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 0.0170 chunk 261 optimal weight: 4.9990 chunk 328 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 ASN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.141869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.121276 restraints weight = 99331.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.120597 restraints weight = 129837.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.121318 restraints weight = 116883.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.121314 restraints weight = 78627.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.121624 restraints weight = 75478.957| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29523 Z= 0.113 Angle : 0.668 14.958 39933 Z= 0.320 Chirality : 0.044 0.178 4485 Planarity : 0.004 0.146 5212 Dihedral : 10.612 134.397 4321 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.11 % Favored : 92.86 % Rotamer: Outliers : 2.30 % Allowed : 22.60 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3684 helix: -0.48 (0.15), residues: 1337 sheet: -0.58 (0.24), residues: 442 loop : -1.30 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 375 TYR 0.022 0.001 TYR D 505 PHE 0.036 0.001 PHE C 573 TRP 0.038 0.002 TRP A 486 HIS 0.003 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00263 (29499) covalent geometry : angle 0.66774 (39933) hydrogen bonds : bond 0.02804 ( 720) hydrogen bonds : angle 4.32015 ( 2058) metal coordination : bond 0.00111 ( 4) Misc. bond : bond 0.00121 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 322 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.7722 (ppp) cc_final: 0.7377 (ppp) REVERT: A 481 SER cc_start: 0.3382 (OUTLIER) cc_final: 0.2994 (p) REVERT: A 621 MET cc_start: 0.7400 (mmp) cc_final: 0.7065 (mmm) REVERT: A 784 MET cc_start: 0.0387 (tpp) cc_final: 0.0020 (tpt) REVERT: B 264 MET cc_start: 0.8044 (ttp) cc_final: 0.7704 (ttp) REVERT: B 430 MET cc_start: 0.7223 (tpp) cc_final: 0.6965 (tpp) REVERT: B 560 MET cc_start: 0.5100 (mmm) cc_final: 0.4634 (tpt) REVERT: C 213 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7497 (m-10) REVERT: C 324 ASP cc_start: 0.7929 (p0) cc_final: 0.7727 (t0) REVERT: C 569 ILE cc_start: 0.8415 (mm) cc_final: 0.8202 (mp) REVERT: C 618 MET cc_start: 0.7837 (ppp) cc_final: 0.7559 (ppp) REVERT: C 652 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8367 (mp) REVERT: D 391 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8682 (mm) REVERT: D 437 MET cc_start: 0.7050 (mmm) cc_final: 0.6839 (mmm) REVERT: D 513 TYR cc_start: 0.7704 (m-80) cc_final: 0.7359 (m-10) REVERT: D 558 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6714 (tp) REVERT: E 229 MET cc_start: 0.8331 (mpp) cc_final: 0.7581 (mpp) REVERT: E 234 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7715 (pp) REVERT: E 430 MET cc_start: 0.7900 (ttm) cc_final: 0.7615 (ttm) REVERT: E 596 ARG cc_start: 0.7413 (tpp-160) cc_final: 0.7192 (tpp-160) REVERT: E 698 LEU cc_start: 0.8132 (tt) cc_final: 0.7896 (tp) REVERT: F 291 GLU cc_start: 0.7795 (tt0) cc_final: 0.7581 (pt0) REVERT: K 15 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8041 (mt) REVERT: K 18 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7509 (pp20) REVERT: K 37 PRO cc_start: 0.8548 (OUTLIER) cc_final: 0.7981 (Cg_endo) REVERT: H 129 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8626 (mmtm) REVERT: J 239 ASP cc_start: 0.7905 (p0) cc_final: 0.7555 (p0) REVERT: J 250 LEU cc_start: 0.5651 (mt) cc_final: 0.5425 (mp) REVERT: G 160 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: G 400 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8637 (pt0) REVERT: G 427 ASP cc_start: 0.8095 (t0) cc_final: 0.7801 (t0) REVERT: G 546 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6963 (pp) outliers start: 71 outliers final: 53 residues processed: 376 average time/residue: 0.1578 time to fit residues: 98.9422 Evaluate side-chains 377 residues out of total 3088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 312 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 512 GLN Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 400 GLN Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 544 TRP Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 221 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 175 optimal weight: 0.0020 chunk 12 optimal weight: 0.6980 chunk 296 optimal weight: 40.0000 chunk 239 optimal weight: 5.9990 chunk 164 optimal weight: 0.0980 chunk 186 optimal weight: 4.9990 chunk 334 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 361 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 ASN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.141867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.121534 restraints weight = 99866.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.121063 restraints weight = 135954.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.121614 restraints weight = 121962.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.121558 restraints weight = 81814.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.121916 restraints weight = 75837.833| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 29523 Z= 0.161 Angle : 0.796 59.196 39933 Z= 0.409 Chirality : 0.044 0.479 4485 Planarity : 0.004 0.147 5212 Dihedral : 10.612 134.377 4321 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.11 % Favored : 92.86 % Rotamer: Outliers : 2.33 % Allowed : 22.60 % Favored : 75.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3684 helix: -0.47 (0.15), residues: 1337 sheet: -0.58 (0.24), residues: 442 loop : -1.29 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 375 TYR 0.017 0.001 TYR D 505 PHE 0.035 0.001 PHE C 573 TRP 0.032 0.002 TRP A 486 HIS 0.008 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00372 (29499) covalent geometry : angle 0.79552 (39933) hydrogen bonds : bond 0.02796 ( 720) hydrogen bonds : angle 4.31681 ( 2058) metal coordination : bond 0.00118 ( 4) Misc. bond : bond 0.00120 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4531.56 seconds wall clock time: 79 minutes 11.32 seconds (4751.32 seconds total)