Starting phenix.real_space_refine on Sat Jul 4 07:13:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wi4_32521/07_2026/7wi4_32521.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi4_32521/07_2026/7wi4_32521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wi4_32521/07_2026/7wi4_32521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi4_32521/07_2026/7wi4_32521.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wi4_32521/07_2026/7wi4_32521.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wi4_32521/07_2026/7wi4_32521.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wi4_32521/07_2026/7wi4_32521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi4_32521/07_2026/7wi4_32521.cif" } resolution = 3.4 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= 0.004 sd= 0.046 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 18 5.49 5 Mg 6 5.21 5 S 120 5.16 5 C 12036 2.51 5 N 3462 2.21 5 O 3636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19284 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "D" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "E" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "F" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "B" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "C" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.30, per 1000 atoms: 0.38 Number of scatterers: 19284 At special positions: 0 Unit cell: (137.28, 140.026, 90.6048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 120 16.00 P 18 15.00 Mg 6 11.99 O 3636 8.00 N 3462 7.00 C 12036 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 418 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 414 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 418 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 414 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 414 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 418 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 418 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 414 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 414 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 418 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 418 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 414 " 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 13 sheets defined 56.4% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 157 through 172 removed outlier: 5.000A pdb=" N LEU A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 201 through 208 removed outlier: 3.613A pdb=" N ILE A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 232 through 240 removed outlier: 4.071A pdb=" N MET A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.897A pdb=" N MET A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.752A pdb=" N GLN A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.971A pdb=" N ILE A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 375 removed outlier: 3.769A pdb=" N GLY A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.812A pdb=" N PHE A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.656A pdb=" N SER A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.718A pdb=" N ARG A 423 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 removed outlier: 3.554A pdb=" N TYR A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 474 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 507 removed outlier: 3.502A pdb=" N ILE A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 567 removed outlier: 3.709A pdb=" N ALA A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 543 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 581 removed outlier: 3.790A pdb=" N LEU A 571 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 594 removed outlier: 3.518A pdb=" N ILE A 589 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 4.310A pdb=" N ARG D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 177 Processing helix chain 'D' and resid 199 through 208 removed outlier: 3.644A pdb=" N LYS D 203 " --> pdb=" O THR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 232 through 240 removed outlier: 3.950A pdb=" N MET D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'D' and resid 335 through 338 removed outlier: 3.644A pdb=" N VAL D 338 " --> pdb=" O MET D 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 345 through 352 removed outlier: 3.623A pdb=" N ILE D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 376 removed outlier: 3.596A pdb=" N LEU D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 375 " --> pdb=" O PHE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 404 through 415 Processing helix chain 'D' and resid 417 through 425 removed outlier: 3.953A pdb=" N LEU D 424 " --> pdb=" O ILE D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.852A pdb=" N ILE D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 481 removed outlier: 3.802A pdb=" N ILE D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 507 removed outlier: 3.514A pdb=" N ALA D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP D 507 " --> pdb=" O MET D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 567 removed outlier: 3.764A pdb=" N ASP D 546 " --> pdb=" O ALA D 542 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 566 " --> pdb=" O GLN D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 581 removed outlier: 4.153A pdb=" N LEU D 571 " --> pdb=" O ASN D 567 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D 579 " --> pdb=" O LYS D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 594 Processing helix chain 'E' and resid 157 through 172 removed outlier: 4.494A pdb=" N LEU E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG E 172 " --> pdb=" O VAL E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 removed outlier: 3.740A pdb=" N ARG E 176 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE E 177 " --> pdb=" O PRO E 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 173 through 177' Processing helix chain 'E' and resid 200 through 207 removed outlier: 4.360A pdb=" N ALA E 204 " --> pdb=" O LEU E 200 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 211 removed outlier: 3.845A pdb=" N VAL E 211 " --> pdb=" O GLU E 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 232 through 238 removed outlier: 4.514A pdb=" N MET E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 286 removed outlier: 4.329A pdb=" N VAL E 280 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 334 removed outlier: 4.164A pdb=" N GLU E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 353 removed outlier: 3.929A pdb=" N ILE E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 376 removed outlier: 3.739A pdb=" N GLY E 375 " --> pdb=" O PHE E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 394 removed outlier: 3.993A pdb=" N LYS E 387 " --> pdb=" O VAL E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 425 removed outlier: 3.622A pdb=" N SER E 410 " --> pdb=" O ALA E 406 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY E 417 " --> pdb=" O TYR E 413 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS E 418 " --> pdb=" O HIS E 414 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E 424 " --> pdb=" O ILE E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.928A pdb=" N TYR E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 481 removed outlier: 3.879A pdb=" N LEU E 474 " --> pdb=" O TYR E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 488 No H-bonds generated for 'chain 'E' and resid 486 through 488' Processing helix chain 'E' and resid 489 through 506 removed outlier: 3.585A pdb=" N VAL E 495 " --> pdb=" O ASN E 491 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET E 503 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL E 504 " --> pdb=" O ALA E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 567 removed outlier: 3.864A pdb=" N ASP E 546 " --> pdb=" O ALA E 542 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP E 566 " --> pdb=" O GLN E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 581 removed outlier: 3.914A pdb=" N LEU E 571 " --> pdb=" O ASN E 567 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS E 572 " --> pdb=" O MET E 568 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 577 " --> pdb=" O ALA E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 594 removed outlier: 3.676A pdb=" N ILE E 589 " --> pdb=" O ASP E 585 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP E 590 " --> pdb=" O ALA E 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 4.943A pdb=" N LEU F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 168 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG F 172 " --> pdb=" O VAL F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 177 removed outlier: 3.929A pdb=" N ARG F 176 " --> pdb=" O GLU F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 208 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 232 through 240 removed outlier: 4.580A pdb=" N MET F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 238 " --> pdb=" O ARG F 234 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA F 240 " --> pdb=" O MET F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 284 Processing helix chain 'F' and resid 323 through 335 removed outlier: 3.818A pdb=" N GLN F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS F 334 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 345 through 353 removed outlier: 4.042A pdb=" N ILE F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 376 removed outlier: 3.820A pdb=" N GLY F 375 " --> pdb=" O PHE F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 394 removed outlier: 3.607A pdb=" N LYS F 387 " --> pdb=" O VAL F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 419 removed outlier: 4.001A pdb=" N SER F 410 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN F 415 " --> pdb=" O THR F 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY F 417 " --> pdb=" O TYR F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 425 removed outlier: 3.530A pdb=" N ARG F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 424 " --> pdb=" O ILE F 420 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL F 425 " --> pdb=" O ILE F 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 419 through 425' Processing helix chain 'F' and resid 458 through 481 removed outlier: 4.005A pdb=" N GLY F 472 " --> pdb=" O THR F 468 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG F 473 " --> pdb=" O LEU F 469 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 474 " --> pdb=" O TYR F 470 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA F 475 " --> pdb=" O GLY F 471 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU F 476 " --> pdb=" O GLY F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 485 removed outlier: 3.984A pdb=" N VAL F 485 " --> pdb=" O PRO F 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 482 through 485' Processing helix chain 'F' and resid 493 through 506 removed outlier: 3.753A pdb=" N VAL F 504 " --> pdb=" O ALA F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 567 removed outlier: 3.558A pdb=" N ILE F 545 " --> pdb=" O THR F 541 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU F 564 " --> pdb=" O ALA F 560 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP F 566 " --> pdb=" O GLN F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 581 removed outlier: 3.907A pdb=" N LEU F 571 " --> pdb=" O ASN F 567 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS F 572 " --> pdb=" O MET F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 595 Processing helix chain 'B' and resid 157 through 172 removed outlier: 4.604A pdb=" N LEU B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 197 through 208 removed outlier: 4.257A pdb=" N ALA B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.584A pdb=" N ALA B 240 " --> pdb=" O MET B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 286 removed outlier: 4.446A pdb=" N ASN B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 335 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 345 through 352 removed outlier: 3.743A pdb=" N ILE B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 375 removed outlier: 3.583A pdb=" N LEU B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.696A pdb=" N ALA B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS B 418 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 removed outlier: 3.516A pdb=" N ARG B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.992A pdb=" N ILE B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 481 removed outlier: 3.817A pdb=" N LEU B 474 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 506 removed outlier: 3.765A pdb=" N ILE B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 567 removed outlier: 3.864A pdb=" N ASP B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 581 removed outlier: 3.604A pdb=" N LEU B 571 " --> pdb=" O ASN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 594 Processing helix chain 'C' and resid 157 through 171 removed outlier: 3.764A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.520A pdb=" N ARG C 176 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 208 removed outlier: 3.765A pdb=" N LYS C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 232 through 240 removed outlier: 3.821A pdb=" N MET C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 323 through 335 removed outlier: 4.130A pdb=" N GLU C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 329 " --> pdb=" O ARG C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 353 removed outlier: 3.886A pdb=" N ILE C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 376 removed outlier: 4.025A pdb=" N GLY C 375 " --> pdb=" O PHE C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.660A pdb=" N LYS C 387 " --> pdb=" O VAL C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 425 removed outlier: 3.656A pdb=" N SER C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 417 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS C 418 " --> pdb=" O HIS C 414 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 425 " --> pdb=" O ILE C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 470 removed outlier: 3.979A pdb=" N TYR C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 removed outlier: 3.762A pdb=" N LEU C 474 " --> pdb=" O TYR C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 489 through 506 removed outlier: 3.528A pdb=" N LYS C 494 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 495 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 567 removed outlier: 3.573A pdb=" N ASP C 546 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 566 " --> pdb=" O GLN C 562 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 581 removed outlier: 3.864A pdb=" N LEU C 571 " --> pdb=" O ASN C 567 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 594 removed outlier: 3.583A pdb=" N ILE C 589 " --> pdb=" O ASP C 585 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.486A pdb=" N ILE A 248 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA A 296 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 448 removed outlier: 3.971A pdb=" N LYS A 433 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 434 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 247 through 249 removed outlier: 6.266A pdb=" N ILE D 248 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ALA D 296 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL D 188 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 445 through 448 removed outlier: 4.088A pdb=" N LYS D 433 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 248 through 249 removed outlier: 5.840A pdb=" N ILE E 248 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA E 296 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL E 188 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 446 through 448 removed outlier: 6.831A pdb=" N PHE E 447 " --> pdb=" O HIS E 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 188 through 189 Processing sheet with id=AA8, first strand: chain 'F' and resid 248 through 249 removed outlier: 6.446A pdb=" N ILE F 248 " --> pdb=" O ILE F 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 445 through 448 removed outlier: 3.851A pdb=" N LYS F 433 " --> pdb=" O PHE F 447 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 434 " --> pdb=" O ILE F 584 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AB2, first strand: chain 'B' and resid 445 through 448 removed outlier: 3.598A pdb=" N VAL B 445 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS B 433 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 434 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 293 through 296 removed outlier: 3.946A pdb=" N VAL C 188 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 295 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY C 187 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 317 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU C 189 " --> pdb=" O VAL C 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 445 through 448 removed outlier: 3.731A pdb=" N VAL C 445 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS C 433 " --> pdb=" O PHE C 447 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6306 1.33 - 1.46: 3212 1.46 - 1.58: 9817 1.58 - 1.70: 15 1.70 - 1.82: 222 Bond restraints: 19572 Sorted by residual: bond pdb=" O3A ANP F 701 " pdb=" PB ANP F 701 " ideal model delta sigma weight residual 1.700 1.527 0.173 2.00e-02 2.50e+03 7.52e+01 bond pdb=" O3A ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sigma weight residual 1.700 1.527 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" O3A ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sigma weight residual 1.700 1.527 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" O3A ANP D 701 " pdb=" PB ANP D 701 " ideal model delta sigma weight residual 1.700 1.533 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" O3A ANP E 701 " pdb=" PB ANP E 701 " ideal model delta sigma weight residual 1.700 1.535 0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 19567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 26219 4.45 - 8.90: 149 8.90 - 13.35: 21 13.35 - 17.81: 5 17.81 - 22.26: 6 Bond angle restraints: 26400 Sorted by residual: angle pdb=" PB ANP F 701 " pdb=" N3B ANP F 701 " pdb=" PG ANP F 701 " ideal model delta sigma weight residual 126.95 104.69 22.26 3.00e+00 1.11e-01 5.50e+01 angle pdb=" PB ANP C 701 " pdb=" N3B ANP C 701 " pdb=" PG ANP C 701 " ideal model delta sigma weight residual 126.95 105.07 21.88 3.00e+00 1.11e-01 5.32e+01 angle pdb=" PB ANP E 701 " pdb=" N3B ANP E 701 " pdb=" PG ANP E 701 " ideal model delta sigma weight residual 126.95 107.28 19.67 3.00e+00 1.11e-01 4.30e+01 angle pdb=" PA ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sigma weight residual 125.41 106.21 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PA ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sigma weight residual 125.41 107.23 18.18 3.00e+00 1.11e-01 3.67e+01 ... (remaining 26395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.68: 10592 19.68 - 39.36: 1006 39.36 - 59.05: 358 59.05 - 78.73: 30 78.73 - 98.41: 14 Dihedral angle restraints: 12000 sinusoidal: 4992 harmonic: 7008 Sorted by residual: dihedral pdb=" CA ILE A 455 " pdb=" C ILE A 455 " pdb=" N SER A 456 " pdb=" CA SER A 456 " ideal model delta harmonic sigma weight residual -180.00 -124.84 -55.16 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA PHE F 213 " pdb=" C PHE F 213 " pdb=" N PHE F 214 " pdb=" CA PHE F 214 " ideal model delta harmonic sigma weight residual 180.00 135.98 44.02 0 5.00e+00 4.00e-02 7.75e+01 dihedral pdb=" CA THR F 215 " pdb=" C THR F 215 " pdb=" N ILE F 216 " pdb=" CA ILE F 216 " ideal model delta harmonic sigma weight residual -180.00 -144.26 -35.74 0 5.00e+00 4.00e-02 5.11e+01 ... (remaining 11997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2268 0.064 - 0.129: 624 0.129 - 0.193: 57 0.193 - 0.257: 2 0.257 - 0.321: 7 Chirality restraints: 2958 Sorted by residual: chirality pdb=" C3' ANP A 701 " pdb=" C2' ANP A 701 " pdb=" C4' ANP A 701 " pdb=" O3' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ILE C 184 " pdb=" N ILE C 184 " pdb=" C ILE C 184 " pdb=" CB ILE C 184 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' ANP D 701 " pdb=" C2' ANP D 701 " pdb=" C4' ANP D 701 " pdb=" O3' ANP D 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2955 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 425 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO B 426 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 184 " -0.048 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO F 185 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 185 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 185 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 244 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO D 245 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 245 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 245 " -0.038 5.00e-02 4.00e+02 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 164 2.43 - 3.05: 13233 3.05 - 3.67: 27679 3.67 - 4.28: 39519 4.28 - 4.90: 63839 Nonbonded interactions: 144434 Sorted by model distance: nonbonded pdb=" O2G ANP E 701 " pdb="MG MG E 703 " model vdw 1.813 2.170 nonbonded pdb=" OD2 ASP F 492 " pdb="ZN ZN F 702 " model vdw 1.834 2.230 nonbonded pdb=" O2A ANP C 701 " pdb="MG MG C 703 " model vdw 1.853 2.170 nonbonded pdb=" O3A ANP D 701 " pdb="MG MG D 703 " model vdw 1.883 2.170 nonbonded pdb=" N3B ANP C 701 " pdb="MG MG C 703 " model vdw 1.904 2.250 ... (remaining 144429 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 7 \ 03)) selection = (chain 'B' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 7 \ 03)) selection = (chain 'C' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 7 \ 03)) selection = (chain 'D' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 7 \ 03)) selection = (chain 'E' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 7 \ 03)) selection = (chain 'F' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 7 \ 03)) } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 23.080 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.016 0.886 19587 Z= 1.216 Angle : 1.086 22.258 26400 Z= 0.578 Chirality : 0.056 0.321 2958 Planarity : 0.006 0.076 3432 Dihedral : 17.308 98.410 7464 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.29 % Favored : 91.54 % Rotamer: Outliers : 18.40 % Allowed : 16.32 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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 (0.16), residues: 2400 helix: -1.06 (0.13), residues: 1264 sheet: -0.63 (0.54), residues: 101 loop : -2.20 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 232 TYR 0.030 0.004 TYR E 557 PHE 0.022 0.003 PHE C 214 TRP 0.025 0.004 TRP B 507 HIS 0.010 0.002 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.01245 / 0.59 (19572) covalent geometry : angle 1.08599 / 0.58 (26400) hydrogen bonds : bond 0.23927 / 15.82 ( 832) hydrogen bonds : angle 7.43359 / 5.26 ( 2457) metal coordination : bond 0.01387 / 0.98 ( 12) Misc. bond : bond 0.86074 / 43.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 368 poor density : 593 time to evaluate : 0.759 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: A 144 GLU cc_start: 0.7542 (pp20) cc_final: 0.7149 (pp20) REVERT: A 237 PHE cc_start: 0.7550 (m-10) cc_final: 0.7148 (m-80) REVERT: A 238 GLU cc_start: 0.7831 (tt0) cc_final: 0.7561 (tt0) REVERT: A 293 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7768 (p) REVERT: A 323 ASP cc_start: 0.7101 (m-30) cc_final: 0.6888 (m-30) REVERT: A 332 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7954 (mtpp) REVERT: A 367 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 382 MET cc_start: 0.6633 (pp-130) cc_final: 0.6397 (pp-130) REVERT: A 398 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7320 (ttp80) REVERT: A 405 GLU cc_start: 0.7929 (tp30) cc_final: 0.7711 (tm-30) REVERT: A 491 ASN cc_start: 0.7656 (t0) cc_final: 0.7163 (t0) REVERT: A 554 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: A 559 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (ttt180) REVERT: A 562 GLN cc_start: 0.7858 (tp40) cc_final: 0.7654 (tp40) REVERT: A 566 ASP cc_start: 0.8261 (m-30) cc_final: 0.7945 (m-30) REVERT: A 582 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6902 (mt-10) REVERT: D 237 PHE cc_start: 0.7608 (m-80) cc_final: 0.6983 (m-10) REVERT: D 323 ASP cc_start: 0.7531 (p0) cc_final: 0.7010 (p0) REVERT: D 327 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7613 (mtt180) REVERT: D 367 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: D 377 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5714 (mmtm) REVERT: D 403 MET cc_start: 0.7469 (mpp) cc_final: 0.7250 (mpp) REVERT: D 443 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8721 (mm) REVERT: D 451 GLU cc_start: 0.7766 (tt0) cc_final: 0.7377 (tm-30) REVERT: D 456 SER cc_start: 0.8764 (t) cc_final: 0.8520 (p) REVERT: D 491 ASN cc_start: 0.8113 (t0) cc_final: 0.7857 (t0) REVERT: D 495 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7734 (t) REVERT: D 539 ASP cc_start: 0.7833 (t0) cc_final: 0.7504 (t0) REVERT: D 543 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7352 (ttp-110) REVERT: D 554 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7046 (mm-30) REVERT: D 566 ASP cc_start: 0.8286 (m-30) cc_final: 0.7980 (m-30) REVERT: D 579 MET cc_start: 0.8554 (mmm) cc_final: 0.8251 (mtp) REVERT: D 582 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6766 (mt-10) REVERT: D 591 ASP cc_start: 0.7227 (m-30) cc_final: 0.6992 (m-30) REVERT: D 604 TRP cc_start: 0.7225 (OUTLIER) cc_final: 0.6050 (t60) REVERT: E 141 MET cc_start: 0.6556 (ttm) cc_final: 0.6351 (ttm) REVERT: E 142 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5251 (pp) REVERT: E 163 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7063 (mm-30) REVERT: E 186 LYS cc_start: 0.5389 (OUTLIER) cc_final: 0.3940 (mptp) REVERT: E 233 VAL cc_start: 0.8562 (m) cc_final: 0.8298 (p) REVERT: E 238 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: E 242 LYS cc_start: 0.2312 (OUTLIER) cc_final: 0.1719 (tptp) REVERT: E 298 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7908 (m-40) REVERT: E 319 VAL cc_start: 0.7568 (t) cc_final: 0.7257 (m) REVERT: E 331 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8300 (mp) REVERT: E 367 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: E 370 LEU cc_start: 0.8383 (mt) cc_final: 0.8110 (mp) REVERT: E 377 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5702 (mmtm) REVERT: E 425 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7954 (t) REVERT: E 491 ASN cc_start: 0.8235 (t0) cc_final: 0.7869 (t0) REVERT: E 498 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.7833 (m110) REVERT: E 540 GLU cc_start: 0.7377 (tp30) cc_final: 0.7171 (tp30) REVERT: E 566 ASP cc_start: 0.7992 (m-30) cc_final: 0.7775 (m-30) REVERT: F 213 PHE cc_start: 0.4505 (OUTLIER) cc_final: 0.3700 (t80) REVERT: F 237 PHE cc_start: 0.7754 (m-10) cc_final: 0.6364 (m-10) REVERT: F 238 GLU cc_start: 0.7996 (tt0) cc_final: 0.7261 (tt0) REVERT: F 281 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.4419 (pt0) REVERT: F 293 VAL cc_start: 0.8053 (m) cc_final: 0.7821 (p) REVERT: F 367 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7718 (mm-30) REVERT: F 398 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.6990 (ttp80) REVERT: F 401 MET cc_start: 0.5624 (mtp) cc_final: 0.4437 (mtp) REVERT: F 407 GLN cc_start: 0.8051 (tt0) cc_final: 0.7692 (tt0) REVERT: F 408 LYS cc_start: 0.8612 (ptpt) cc_final: 0.8302 (ptpp) REVERT: F 413 TYR cc_start: 0.8929 (m-80) cc_final: 0.8585 (m-80) REVERT: F 433 LYS cc_start: 0.8266 (tttt) cc_final: 0.7869 (ttmm) REVERT: F 467 SER cc_start: 0.8817 (m) cc_final: 0.8515 (t) REVERT: F 511 GLU cc_start: 0.7351 (mp0) cc_final: 0.7032 (mp0) REVERT: F 562 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6546 (tm-30) REVERT: F 566 ASP cc_start: 0.8075 (m-30) cc_final: 0.7180 (m-30) REVERT: B 233 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 236 MET cc_start: 0.6384 (mpt) cc_final: 0.5961 (mpt) REVERT: B 238 GLU cc_start: 0.7890 (pt0) cc_final: 0.7525 (pp20) REVERT: B 247 ILE cc_start: 0.2390 (OUTLIER) cc_final: 0.1931 (mp) REVERT: B 319 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7636 (m) REVERT: B 353 THR cc_start: 0.7968 (p) cc_final: 0.7757 (p) REVERT: B 367 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 455 ILE cc_start: 0.8383 (mm) cc_final: 0.8028 (mp) REVERT: B 462 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7781 (mp) REVERT: B 504 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8213 (t) REVERT: B 512 LYS cc_start: 0.8489 (tptp) cc_final: 0.8280 (tptp) REVERT: B 539 ASP cc_start: 0.7807 (t70) cc_final: 0.7366 (t0) REVERT: B 543 ARG cc_start: 0.7439 (ttp-170) cc_final: 0.7129 (ttp80) REVERT: B 547 GLN cc_start: 0.7385 (mt0) cc_final: 0.7130 (mt0) REVERT: B 556 ASN cc_start: 0.8555 (m-40) cc_final: 0.8199 (m110) REVERT: B 566 ASP cc_start: 0.7864 (m-30) cc_final: 0.7618 (m-30) REVERT: B 579 MET cc_start: 0.8523 (mmm) cc_final: 0.8243 (mtp) REVERT: B 604 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.6591 (t60) REVERT: C 161 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7801 (tptp) REVERT: C 248 ILE cc_start: 0.4825 (OUTLIER) cc_final: 0.4540 (mp) REVERT: C 250 ILE cc_start: 0.7986 (mm) cc_final: 0.7683 (mm) REVERT: C 252 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.5687 (mp10) REVERT: C 319 VAL cc_start: 0.7820 (t) cc_final: 0.7445 (m) REVERT: C 329 GLN cc_start: 0.8159 (tp40) cc_final: 0.7729 (mm-40) REVERT: C 370 LEU cc_start: 0.8585 (mt) cc_final: 0.8288 (mp) REVERT: C 390 ASP cc_start: 0.7338 (m-30) cc_final: 0.6902 (m-30) REVERT: C 397 GLU cc_start: 0.7044 (pm20) cc_final: 0.6441 (pm20) REVERT: C 398 ARG cc_start: 0.7274 (mtp180) cc_final: 0.6794 (ttt180) REVERT: C 415 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: C 433 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8157 (ttpp) REVERT: C 491 ASN cc_start: 0.8425 (t0) cc_final: 0.8085 (t0) REVERT: C 543 ARG cc_start: 0.7432 (ttm110) cc_final: 0.6967 (ttp80) REVERT: C 544 ILE cc_start: 0.8673 (mm) cc_final: 0.8459 (mt) REVERT: C 547 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: C 554 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: C 562 GLN cc_start: 0.8089 (tp40) cc_final: 0.7060 (tp-100) REVERT: C 566 ASP cc_start: 0.8089 (m-30) cc_final: 0.7206 (m-30) REVERT: C 575 LYS cc_start: 0.7896 (tmtp) cc_final: 0.7652 (tmmt) outliers start: 368 outliers final: 223 residues processed: 868 average time/residue: 0.1643 time to fit residues: 206.6501 Evaluate side-chains 822 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 567 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 410 SER Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 439 ARG Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 561 ARG Chi-restraints excluded: chain E residue 568 MET Chi-restraints excluded: chain E residue 580 LYS Chi-restraints excluded: chain E residue 597 ASP Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 548 GLU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 596 ARG Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 581 TYR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 484 HIS D 178 GLN D 363 ASN A D 363 ASN B D 407 GLN E 178 GLN E 329 GLN F 588 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.159820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125983 restraints weight = 112449.074| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 6.83 r_work: 0.3269 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 186 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 246 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 12 (20 function evaluations) r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 19587 Z= 0.160 Angle : 0.714 9.003 26400 Z= 0.371 Chirality : 0.046 0.352 2958 Planarity : 0.006 0.072 3432 Dihedral : 14.182 97.961 3218 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.29 % Rotamer: Outliers : 12.17 % Allowed : 23.49 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.25 (0.17), residues: 2400 helix: -0.07 (0.14), residues: 1294 sheet: -0.68 (0.51), residues: 113 loop : -1.82 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 176 TYR 0.021 0.002 TYR E 413 PHE 0.021 0.002 PHE D 213 TRP 0.010 0.001 TRP D 507 HIS 0.006 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (19572) covalent geometry : angle 0.71361 / 0.37 (26400) hydrogen bonds : bond 0.06488 / 4.17 ( 832) hydrogen bonds : angle 4.91760 / 3.47 ( 2457) metal coordination : bond 0.00362 / 0.20 ( 12) Misc. bond : bond 0.00502 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 569 time to evaluate : 0.707 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: A 153 ASP cc_start: 0.8063 (m-30) cc_final: 0.7662 (m-30) REVERT: A 249 PHE cc_start: 0.6726 (t80) cc_final: 0.6385 (t80) REVERT: A 293 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7378 (p) REVERT: A 335 MET cc_start: 0.8130 (ttt) cc_final: 0.7811 (tmm) REVERT: A 354 PRO cc_start: 0.8570 (Cg_endo) cc_final: 0.8367 (Cg_exo) REVERT: A 382 MET cc_start: 0.7075 (pp-130) cc_final: 0.6566 (pp-130) REVERT: A 397 GLU cc_start: 0.8379 (mp0) cc_final: 0.8153 (mp0) REVERT: A 398 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8217 (ttp80) REVERT: A 407 GLN cc_start: 0.8703 (mt0) cc_final: 0.8401 (mt0) REVERT: A 554 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 562 GLN cc_start: 0.8328 (tp40) cc_final: 0.8084 (tp40) REVERT: A 566 ASP cc_start: 0.8526 (m-30) cc_final: 0.8176 (m-30) REVERT: A 589 ILE cc_start: 0.8350 (mt) cc_final: 0.8122 (mm) REVERT: A 599 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8484 (ptp-170) REVERT: D 161 LYS cc_start: 0.8275 (mtpp) cc_final: 0.8056 (mmmm) REVERT: D 237 PHE cc_start: 0.7887 (m-80) cc_final: 0.7360 (m-10) REVERT: D 323 ASP cc_start: 0.8076 (p0) cc_final: 0.7507 (p0) REVERT: D 327 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7874 (mtt180) REVERT: D 382 MET cc_start: 0.6792 (ttp) cc_final: 0.6489 (ttp) REVERT: D 397 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: D 443 LEU cc_start: 0.8904 (mm) cc_final: 0.8695 (mt) REVERT: D 451 GLU cc_start: 0.8314 (tt0) cc_final: 0.7818 (tm-30) REVERT: D 456 SER cc_start: 0.8869 (t) cc_final: 0.8565 (p) REVERT: D 483 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: D 491 ASN cc_start: 0.7952 (t0) cc_final: 0.7709 (t0) REVERT: D 494 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8210 (ttmm) REVERT: D 537 MET cc_start: 0.8621 (ptt) cc_final: 0.8381 (ptm) REVERT: D 539 ASP cc_start: 0.8275 (t0) cc_final: 0.7878 (t0) REVERT: D 543 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8020 (ttp-110) REVERT: D 554 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7620 (mm-30) REVERT: D 566 ASP cc_start: 0.8579 (m-30) cc_final: 0.8378 (m-30) REVERT: D 579 MET cc_start: 0.8946 (mmm) cc_final: 0.8595 (mtp) REVERT: D 591 ASP cc_start: 0.7754 (m-30) cc_final: 0.7520 (m-30) REVERT: D 604 TRP cc_start: 0.7520 (OUTLIER) cc_final: 0.6601 (t60) REVERT: E 142 LEU cc_start: 0.5280 (OUTLIER) cc_final: 0.5044 (pp) REVERT: E 161 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8336 (mtmm) REVERT: E 186 LYS cc_start: 0.5173 (OUTLIER) cc_final: 0.3939 (mptp) REVERT: E 238 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8209 (mm-30) REVERT: E 242 LYS cc_start: 0.2840 (OUTLIER) cc_final: 0.2037 (tptp) REVERT: E 298 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7749 (m-40) REVERT: E 319 VAL cc_start: 0.7523 (t) cc_final: 0.7292 (m) REVERT: E 367 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8128 (mm-30) REVERT: E 370 LEU cc_start: 0.8581 (mt) cc_final: 0.8256 (mp) REVERT: E 384 GLU cc_start: 0.8107 (pt0) cc_final: 0.7901 (pt0) REVERT: E 491 ASN cc_start: 0.8225 (t0) cc_final: 0.7947 (t0) REVERT: E 512 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8735 (ttpp) REVERT: E 574 MET cc_start: 0.8624 (ttm) cc_final: 0.8321 (ttp) REVERT: E 589 ILE cc_start: 0.8069 (mt) cc_final: 0.7847 (mm) REVERT: E 591 ASP cc_start: 0.7722 (m-30) cc_final: 0.7437 (m-30) REVERT: F 213 PHE cc_start: 0.4949 (OUTLIER) cc_final: 0.4201 (t80) REVERT: F 237 PHE cc_start: 0.7884 (m-10) cc_final: 0.7355 (m-10) REVERT: F 238 GLU cc_start: 0.8050 (tt0) cc_final: 0.7463 (tp30) REVERT: F 242 LYS cc_start: 0.5363 (OUTLIER) cc_final: 0.4262 (pptt) REVERT: F 281 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.4893 (pt0) REVERT: F 292 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7501 (mp) REVERT: F 297 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8364 (p) REVERT: F 397 GLU cc_start: 0.8115 (mp0) cc_final: 0.7851 (mp0) REVERT: F 398 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.7942 (ttp80) REVERT: F 407 GLN cc_start: 0.8657 (tt0) cc_final: 0.8373 (tt0) REVERT: F 433 LYS cc_start: 0.8683 (tttt) cc_final: 0.8393 (ttmt) REVERT: F 451 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: F 485 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8570 (m) REVERT: F 511 GLU cc_start: 0.8249 (mp0) cc_final: 0.7994 (mp0) REVERT: F 562 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8148 (tp-100) REVERT: F 566 ASP cc_start: 0.8559 (m-30) cc_final: 0.8303 (m-30) REVERT: B 163 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 233 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7537 (p) REVERT: B 236 MET cc_start: 0.7115 (mpt) cc_final: 0.6711 (mpt) REVERT: B 247 ILE cc_start: 0.2053 (OUTLIER) cc_final: 0.1435 (mp) REVERT: B 351 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8120 (ttm-80) REVERT: B 367 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 413 TYR cc_start: 0.8613 (m-80) cc_final: 0.8216 (m-80) REVERT: B 437 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8520 (pt) REVERT: B 455 ILE cc_start: 0.8282 (mm) cc_final: 0.7945 (mp) REVERT: B 543 ARG cc_start: 0.8288 (ttp-170) cc_final: 0.7911 (ttp80) REVERT: B 547 GLN cc_start: 0.8137 (mt0) cc_final: 0.7890 (mt0) REVERT: B 582 GLU cc_start: 0.7913 (tp30) cc_final: 0.7569 (tm-30) REVERT: B 604 TRP cc_start: 0.7841 (OUTLIER) cc_final: 0.6689 (t60) REVERT: C 161 LYS cc_start: 0.8440 (ttmt) cc_final: 0.7603 (tptp) REVERT: C 236 MET cc_start: 0.8038 (mmt) cc_final: 0.7631 (mmt) REVERT: C 319 VAL cc_start: 0.7581 (t) cc_final: 0.7305 (m) REVERT: C 324 VAL cc_start: 0.8270 (p) cc_final: 0.8028 (t) REVERT: C 329 GLN cc_start: 0.8720 (tp40) cc_final: 0.8143 (mm-40) REVERT: C 357 SER cc_start: 0.7540 (m) cc_final: 0.7188 (p) REVERT: C 370 LEU cc_start: 0.8511 (mt) cc_final: 0.8266 (mp) REVERT: C 385 PHE cc_start: 0.7941 (m-10) cc_final: 0.7593 (m-80) REVERT: C 390 ASP cc_start: 0.7906 (m-30) cc_final: 0.7642 (m-30) REVERT: C 397 GLU cc_start: 0.7937 (pm20) cc_final: 0.7335 (pm20) REVERT: C 398 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7953 (mtm110) REVERT: C 433 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8503 (ttpp) REVERT: C 491 ASN cc_start: 0.8632 (t0) cc_final: 0.8341 (t0) REVERT: C 512 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8553 (ttpp) REVERT: C 562 GLN cc_start: 0.8759 (tp40) cc_final: 0.7984 (tp-100) REVERT: C 566 ASP cc_start: 0.8725 (m-30) cc_final: 0.7983 (m-30) outliers start: 242 outliers final: 153 residues processed: 742 average time/residue: 0.1643 time to fit residues: 177.2258 Evaluate side-chains 720 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 541 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 564 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 167 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 407 GLN D 562 GLN E 329 GLN E 363 ASN A E 363 ASN B E 414 HIS F 572 HIS F 588 GLN B 178 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.157563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123281 restraints weight = 103599.478| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 6.18 r_work: 0.3257 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 246 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 255 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.719 19587 Z= 0.229 Angle : 0.652 9.248 26400 Z= 0.337 Chirality : 0.044 0.237 2958 Planarity : 0.005 0.070 3432 Dihedral : 12.500 89.393 3006 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 10.14 % Allowed : 25.47 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2400 helix: 0.23 (0.14), residues: 1301 sheet: -0.70 (0.52), residues: 113 loop : -1.72 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 234 TYR 0.016 0.002 TYR D 557 PHE 0.030 0.002 PHE B 237 TRP 0.011 0.001 TRP D 507 HIS 0.005 0.001 HIS C 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (19572) covalent geometry : angle 0.65181 / 0.34 (26400) hydrogen bonds : bond 0.06121 / 3.98 ( 832) hydrogen bonds : angle 4.65677 / 3.28 ( 2457) metal coordination : bond 0.20770 / 14.42 ( 12) Misc. bond : bond 0.00096 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 556 time to evaluate : 0.612 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: A 141 MET cc_start: 0.6655 (tpp) cc_final: 0.6351 (tpp) REVERT: A 153 ASP cc_start: 0.8053 (m-30) cc_final: 0.7640 (m-30) REVERT: A 236 MET cc_start: 0.7659 (mpt) cc_final: 0.7163 (mmt) REVERT: A 275 LEU cc_start: 0.3393 (OUTLIER) cc_final: 0.3126 (pp) REVERT: A 293 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7308 (p) REVERT: A 382 MET cc_start: 0.7122 (pp-130) cc_final: 0.6608 (pp-130) REVERT: A 398 ARG cc_start: 0.8516 (ttt180) cc_final: 0.8139 (ttp80) REVERT: A 407 GLN cc_start: 0.8684 (mt0) cc_final: 0.8344 (mt0) REVERT: A 547 GLN cc_start: 0.8104 (mt0) cc_final: 0.7887 (mt0) REVERT: A 554 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: A 562 GLN cc_start: 0.8421 (tp40) cc_final: 0.8037 (tp40) REVERT: A 566 ASP cc_start: 0.8395 (m-30) cc_final: 0.8187 (m-30) REVERT: A 588 GLN cc_start: 0.8152 (mt0) cc_final: 0.7827 (mt0) REVERT: A 589 ILE cc_start: 0.8310 (mt) cc_final: 0.8044 (mm) REVERT: D 179 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7901 (mmtp) REVERT: D 237 PHE cc_start: 0.7863 (m-80) cc_final: 0.7472 (m-10) REVERT: D 323 ASP cc_start: 0.7986 (p0) cc_final: 0.7481 (p0) REVERT: D 327 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7883 (mtt180) REVERT: D 382 MET cc_start: 0.6783 (ttp) cc_final: 0.6487 (ttp) REVERT: D 397 GLU cc_start: 0.7758 (mp0) cc_final: 0.7456 (mp0) REVERT: D 443 LEU cc_start: 0.8978 (mm) cc_final: 0.8714 (mt) REVERT: D 451 GLU cc_start: 0.8233 (tt0) cc_final: 0.7717 (tm-30) REVERT: D 483 GLU cc_start: 0.8338 (pt0) cc_final: 0.8131 (pm20) REVERT: D 491 ASN cc_start: 0.7813 (t0) cc_final: 0.7592 (t0) REVERT: D 494 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8229 (tttt) REVERT: D 537 MET cc_start: 0.8621 (ptt) cc_final: 0.8396 (ptm) REVERT: D 539 ASP cc_start: 0.8284 (t0) cc_final: 0.7839 (t0) REVERT: D 543 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8164 (ttp-170) REVERT: D 554 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7662 (mm-30) REVERT: D 562 GLN cc_start: 0.8653 (tp40) cc_final: 0.8397 (tp-100) REVERT: D 579 MET cc_start: 0.8807 (mmm) cc_final: 0.8504 (mtp) REVERT: D 591 ASP cc_start: 0.7763 (m-30) cc_final: 0.7339 (m-30) REVERT: D 604 TRP cc_start: 0.7481 (OUTLIER) cc_final: 0.6422 (t60) REVERT: E 142 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.5001 (pp) REVERT: E 158 ASP cc_start: 0.7893 (t0) cc_final: 0.7633 (t0) REVERT: E 161 LYS cc_start: 0.8642 (mmmm) cc_final: 0.8270 (mtmm) REVERT: E 186 LYS cc_start: 0.5116 (OUTLIER) cc_final: 0.3982 (mptp) REVERT: E 242 LYS cc_start: 0.3063 (OUTLIER) cc_final: 0.2291 (tptp) REVERT: E 319 VAL cc_start: 0.7515 (t) cc_final: 0.7196 (m) REVERT: E 329 GLN cc_start: 0.8550 (mm110) cc_final: 0.8243 (mm-40) REVERT: E 330 ILE cc_start: 0.8853 (mt) cc_final: 0.8570 (mp) REVERT: E 331 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8439 (mp) REVERT: E 367 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8021 (mm-30) REVERT: E 377 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.6223 (mmtm) REVERT: E 384 GLU cc_start: 0.8111 (pt0) cc_final: 0.7882 (pt0) REVERT: E 401 MET cc_start: 0.7601 (mtt) cc_final: 0.7340 (mtt) REVERT: E 491 ASN cc_start: 0.8219 (t0) cc_final: 0.7887 (t0) REVERT: E 512 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8672 (ttpp) REVERT: E 574 MET cc_start: 0.8600 (ttm) cc_final: 0.8283 (ttp) REVERT: E 591 ASP cc_start: 0.7820 (m-30) cc_final: 0.7571 (m-30) REVERT: F 161 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8192 (mttt) REVERT: F 190 MET cc_start: 0.6479 (mtm) cc_final: 0.6033 (ptp) REVERT: F 237 PHE cc_start: 0.7933 (m-10) cc_final: 0.7287 (m-10) REVERT: F 238 GLU cc_start: 0.8087 (tt0) cc_final: 0.7485 (tp30) REVERT: F 281 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.4761 (pt0) REVERT: F 292 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7393 (mp) REVERT: F 293 VAL cc_start: 0.7954 (m) cc_final: 0.7603 (p) REVERT: F 332 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8504 (mttp) REVERT: F 398 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.7871 (ttp80) REVERT: F 407 GLN cc_start: 0.8673 (tt0) cc_final: 0.8446 (tt0) REVERT: F 433 LYS cc_start: 0.8678 (tttt) cc_final: 0.8394 (ttmt) REVERT: F 485 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8584 (m) REVERT: F 511 GLU cc_start: 0.8208 (mp0) cc_final: 0.7951 (mp0) REVERT: F 590 ASP cc_start: 0.8429 (t0) cc_final: 0.8213 (t0) REVERT: F 604 TRP cc_start: 0.7190 (OUTLIER) cc_final: 0.6802 (t60) REVERT: B 233 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.6987 (p) REVERT: B 236 MET cc_start: 0.6977 (mpt) cc_final: 0.6350 (mpt) REVERT: B 238 GLU cc_start: 0.8160 (tp30) cc_final: 0.7933 (pp20) REVERT: B 247 ILE cc_start: 0.1901 (OUTLIER) cc_final: 0.1164 (mp) REVERT: B 351 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8080 (ttm-80) REVERT: B 367 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7974 (mm-30) REVERT: B 403 MET cc_start: 0.8051 (mpp) cc_final: 0.7830 (mpp) REVERT: B 413 TYR cc_start: 0.8650 (m-80) cc_final: 0.8207 (m-80) REVERT: B 437 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8413 (pt) REVERT: B 455 ILE cc_start: 0.8311 (mm) cc_final: 0.8034 (mp) REVERT: B 547 GLN cc_start: 0.8045 (mt0) cc_final: 0.7799 (mt0) REVERT: B 562 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7438 (tm-30) REVERT: B 579 MET cc_start: 0.8688 (mmm) cc_final: 0.8319 (mmt) REVERT: B 582 GLU cc_start: 0.7899 (tp30) cc_final: 0.7555 (tm-30) REVERT: B 604 TRP cc_start: 0.7843 (OUTLIER) cc_final: 0.6634 (t60) REVERT: C 200 LEU cc_start: 0.7162 (tp) cc_final: 0.6931 (tp) REVERT: C 203 LYS cc_start: 0.6470 (tmmt) cc_final: 0.6204 (tmmt) REVERT: C 236 MET cc_start: 0.7721 (mmt) cc_final: 0.7319 (mmt) REVERT: C 237 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5951 (t80) REVERT: C 247 ILE cc_start: -0.1423 (OUTLIER) cc_final: -0.1638 (mp) REVERT: C 319 VAL cc_start: 0.7630 (t) cc_final: 0.7375 (m) REVERT: C 324 VAL cc_start: 0.8276 (p) cc_final: 0.7996 (t) REVERT: C 329 GLN cc_start: 0.8668 (tp40) cc_final: 0.8099 (mm-40) REVERT: C 367 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: C 370 LEU cc_start: 0.8483 (mt) cc_final: 0.8227 (mp) REVERT: C 390 ASP cc_start: 0.7903 (m-30) cc_final: 0.7633 (m-30) REVERT: C 397 GLU cc_start: 0.7877 (pm20) cc_final: 0.7263 (pm20) REVERT: C 398 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7921 (mtm110) REVERT: C 433 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8487 (ttpp) REVERT: C 491 ASN cc_start: 0.8615 (t0) cc_final: 0.8277 (t0) REVERT: C 546 ASP cc_start: 0.7879 (m-30) cc_final: 0.7657 (m-30) REVERT: C 562 GLN cc_start: 0.8737 (tp40) cc_final: 0.7980 (tp-100) REVERT: C 566 ASP cc_start: 0.8729 (m-30) cc_final: 0.8019 (m-30) outliers start: 203 outliers final: 157 residues processed: 701 average time/residue: 0.1709 time to fit residues: 173.3333 Evaluate side-chains 720 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 541 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 41 optimal weight: 10.0000 chunk 195 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 93 optimal weight: 9.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 HIS D 407 GLN F 414 HIS F 562 GLN F 588 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.159756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126148 restraints weight = 120463.230| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 6.98 r_work: 0.3271 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 255 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 261 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.498 19587 Z= 0.183 Angle : 0.643 9.588 26400 Z= 0.331 Chirality : 0.043 0.191 2958 Planarity : 0.005 0.070 3432 Dihedral : 11.650 91.500 2964 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.12 % Rotamer: Outliers : 9.79 % Allowed : 26.95 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2400 helix: 0.43 (0.15), residues: 1306 sheet: -0.76 (0.51), residues: 113 loop : -1.56 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 234 TYR 0.015 0.001 TYR D 557 PHE 0.043 0.001 PHE A 237 TRP 0.011 0.001 TRP D 507 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (19572) covalent geometry : angle 0.64341 / 0.33 (26400) hydrogen bonds : bond 0.05469 / 3.53 ( 832) hydrogen bonds : angle 4.48883 / 3.18 ( 2457) metal coordination : bond 0.14417 / 5.79 ( 12) Misc. bond : bond 0.00047 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 537 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.6946 (tpp) cc_final: 0.6712 (tpp) REVERT: A 179 LYS cc_start: 0.7475 (mmtp) cc_final: 0.7267 (mmtp) REVERT: A 236 MET cc_start: 0.7572 (mpt) cc_final: 0.7325 (mmt) REVERT: A 293 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7427 (p) REVERT: A 382 MET cc_start: 0.7079 (pp-130) cc_final: 0.6595 (pp-130) REVERT: A 398 ARG cc_start: 0.8536 (ttt180) cc_final: 0.8198 (ttp80) REVERT: A 407 GLN cc_start: 0.8741 (mt0) cc_final: 0.8385 (mt0) REVERT: A 554 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: A 562 GLN cc_start: 0.8510 (tp40) cc_final: 0.8163 (tp40) REVERT: A 566 ASP cc_start: 0.8284 (m-30) cc_final: 0.8052 (m-30) REVERT: A 589 ILE cc_start: 0.8263 (mt) cc_final: 0.8036 (mm) REVERT: D 179 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7821 (mmtp) REVERT: D 237 PHE cc_start: 0.7822 (m-80) cc_final: 0.7496 (m-10) REVERT: D 323 ASP cc_start: 0.8140 (p0) cc_final: 0.7677 (p0) REVERT: D 327 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7847 (mtt180) REVERT: D 382 MET cc_start: 0.6757 (ttp) cc_final: 0.6474 (ttp) REVERT: D 397 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: D 443 LEU cc_start: 0.8966 (mm) cc_final: 0.8730 (mt) REVERT: D 451 GLU cc_start: 0.8182 (tt0) cc_final: 0.7755 (tm-30) REVERT: D 470 TYR cc_start: 0.9011 (m-80) cc_final: 0.8758 (m-80) REVERT: D 537 MET cc_start: 0.8671 (ptt) cc_final: 0.8458 (ptm) REVERT: D 539 ASP cc_start: 0.8279 (t0) cc_final: 0.7835 (t0) REVERT: D 543 ARG cc_start: 0.8353 (ttp80) cc_final: 0.8146 (ttp-170) REVERT: D 554 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7911 (mm-30) REVERT: D 579 MET cc_start: 0.8775 (mmm) cc_final: 0.8530 (mtp) REVERT: D 591 ASP cc_start: 0.7741 (m-30) cc_final: 0.7428 (m-30) REVERT: D 595 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8178 (mpt90) REVERT: D 604 TRP cc_start: 0.7574 (OUTLIER) cc_final: 0.6548 (t60) REVERT: E 158 ASP cc_start: 0.7756 (t0) cc_final: 0.7451 (t0) REVERT: E 161 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8279 (mtmm) REVERT: E 186 LYS cc_start: 0.5205 (OUTLIER) cc_final: 0.4042 (mptp) REVERT: E 242 LYS cc_start: 0.3165 (OUTLIER) cc_final: 0.2354 (tptp) REVERT: E 327 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7824 (mtt-85) REVERT: E 330 ILE cc_start: 0.8894 (mt) cc_final: 0.8591 (mp) REVERT: E 335 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7408 (tmt) REVERT: E 367 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8001 (mm-30) REVERT: E 377 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6030 (mmtm) REVERT: E 384 GLU cc_start: 0.8113 (pt0) cc_final: 0.7902 (pt0) REVERT: E 398 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7894 (ptm-80) REVERT: E 401 MET cc_start: 0.7721 (mtt) cc_final: 0.7276 (mtp) REVERT: E 468 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8532 (t) REVERT: E 491 ASN cc_start: 0.8295 (t0) cc_final: 0.7952 (t0) REVERT: E 591 ASP cc_start: 0.7708 (m-30) cc_final: 0.7474 (m-30) REVERT: F 161 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8251 (mttt) REVERT: F 190 MET cc_start: 0.6613 (mtm) cc_final: 0.6265 (ptp) REVERT: F 237 PHE cc_start: 0.7812 (m-10) cc_final: 0.7360 (m-10) REVERT: F 238 GLU cc_start: 0.8038 (tt0) cc_final: 0.7444 (tp30) REVERT: F 239 GLN cc_start: 0.5886 (OUTLIER) cc_final: 0.5164 (tp40) REVERT: F 281 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.4296 (pt0) REVERT: F 292 ILE cc_start: 0.7642 (pt) cc_final: 0.7433 (pt) REVERT: F 293 VAL cc_start: 0.7972 (m) cc_final: 0.7642 (p) REVERT: F 327 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7808 (mtp180) REVERT: F 377 LYS cc_start: 0.6381 (OUTLIER) cc_final: 0.6179 (mmtm) REVERT: F 398 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.7855 (ttp80) REVERT: F 399 ARG cc_start: 0.8443 (ttp-110) cc_final: 0.8242 (ttm110) REVERT: F 401 MET cc_start: 0.7000 (mtp) cc_final: 0.6053 (mtp) REVERT: F 407 GLN cc_start: 0.8684 (tt0) cc_final: 0.8462 (tt0) REVERT: F 433 LYS cc_start: 0.8648 (tttt) cc_final: 0.8411 (ttmt) REVERT: F 451 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: F 485 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8551 (m) REVERT: F 511 GLU cc_start: 0.8261 (mp0) cc_final: 0.8033 (mp0) REVERT: F 590 ASP cc_start: 0.8488 (t0) cc_final: 0.8264 (t0) REVERT: F 604 TRP cc_start: 0.7164 (OUTLIER) cc_final: 0.6898 (t60) REVERT: B 233 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7082 (p) REVERT: B 236 MET cc_start: 0.7031 (mpt) cc_final: 0.6509 (mpt) REVERT: B 238 GLU cc_start: 0.8158 (tp30) cc_final: 0.7814 (pp20) REVERT: B 247 ILE cc_start: 0.1777 (OUTLIER) cc_final: 0.1177 (mp) REVERT: B 351 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8163 (ttm-80) REVERT: B 367 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 394 MET cc_start: 0.7282 (ptp) cc_final: 0.6897 (ptm) REVERT: B 413 TYR cc_start: 0.8680 (m-80) cc_final: 0.8177 (m-80) REVERT: B 437 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8486 (pt) REVERT: B 455 ILE cc_start: 0.8293 (mm) cc_final: 0.8009 (mp) REVERT: B 547 GLN cc_start: 0.7921 (mt0) cc_final: 0.7666 (mt0) REVERT: B 562 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7538 (tm-30) REVERT: B 579 MET cc_start: 0.8636 (mmm) cc_final: 0.8379 (mmt) REVERT: B 582 GLU cc_start: 0.7828 (tp30) cc_final: 0.7568 (tm-30) REVERT: B 599 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8108 (pmm-80) REVERT: B 604 TRP cc_start: 0.7862 (OUTLIER) cc_final: 0.6546 (t60) REVERT: C 161 LYS cc_start: 0.8479 (ttpt) cc_final: 0.7762 (tptp) REVERT: C 203 LYS cc_start: 0.6557 (tmmt) cc_final: 0.6301 (tmmt) REVERT: C 216 ILE cc_start: 0.8052 (mm) cc_final: 0.7550 (mm) REVERT: C 236 MET cc_start: 0.7315 (mmt) cc_final: 0.6643 (tpp) REVERT: C 281 GLU cc_start: 0.3876 (OUTLIER) cc_final: 0.3639 (mp0) REVERT: C 319 VAL cc_start: 0.7696 (t) cc_final: 0.7455 (m) REVERT: C 329 GLN cc_start: 0.8769 (tp40) cc_final: 0.8242 (mm-40) REVERT: C 367 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8169 (mm-30) REVERT: C 370 LEU cc_start: 0.8495 (mt) cc_final: 0.8213 (mm) REVERT: C 390 ASP cc_start: 0.7948 (m-30) cc_final: 0.7674 (m-30) REVERT: C 397 GLU cc_start: 0.8006 (pm20) cc_final: 0.7367 (pm20) REVERT: C 398 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7999 (mtm110) REVERT: C 433 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8534 (ttpp) REVERT: C 547 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7388 (mt0) REVERT: C 562 GLN cc_start: 0.8823 (tp40) cc_final: 0.8102 (tp-100) REVERT: C 566 ASP cc_start: 0.8758 (m-30) cc_final: 0.8074 (m-30) outliers start: 196 outliers final: 136 residues processed: 673 average time/residue: 0.1687 time to fit residues: 164.2279 Evaluate side-chains 693 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 531 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 126 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 233 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 overall best weight: 1.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 407 GLN D 562 GLN E 239 GLN E 329 GLN F 178 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN F 588 GLN B 562 GLN B 567 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.159278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125476 restraints weight = 101954.090| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 5.87 r_work: 0.3287 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 261 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 263 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19587 Z= 0.148 Angle : 0.635 10.322 26400 Z= 0.327 Chirality : 0.043 0.237 2958 Planarity : 0.005 0.118 3432 Dihedral : 11.008 94.445 2918 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 9.25 % Allowed : 26.81 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2400 helix: 0.54 (0.14), residues: 1311 sheet: -0.84 (0.50), residues: 113 loop : -1.48 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 439 TYR 0.016 0.002 TYR D 557 PHE 0.043 0.001 PHE A 237 TRP 0.011 0.001 TRP D 507 HIS 0.008 0.001 HIS F 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (19572) covalent geometry : angle 0.63531 / 0.33 (26400) hydrogen bonds : bond 0.05535 / 3.58 ( 832) hydrogen bonds : angle 4.44011 / 3.14 ( 2457) metal coordination : bond 0.01010 / 0.52 ( 12) Misc. bond : bond 0.00067 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 530 time to evaluate : 0.502 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: A 144 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7393 (pp20) REVERT: A 236 MET cc_start: 0.7407 (mpt) cc_final: 0.7115 (mmt) REVERT: A 293 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7399 (p) REVERT: A 327 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.6978 (mtm-85) REVERT: A 335 MET cc_start: 0.8178 (tpp) cc_final: 0.7974 (tpp) REVERT: A 382 MET cc_start: 0.7009 (pp-130) cc_final: 0.6530 (pp-130) REVERT: A 398 ARG cc_start: 0.8452 (ttt180) cc_final: 0.8247 (mtp180) REVERT: A 407 GLN cc_start: 0.8693 (mt0) cc_final: 0.8332 (mt0) REVERT: A 539 ASP cc_start: 0.7806 (t70) cc_final: 0.7426 (t0) REVERT: A 554 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: A 566 ASP cc_start: 0.8223 (m-30) cc_final: 0.8018 (m-30) REVERT: A 589 ILE cc_start: 0.8255 (mt) cc_final: 0.8029 (mm) REVERT: D 158 ASP cc_start: 0.8188 (t0) cc_final: 0.7956 (t70) REVERT: D 179 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7833 (mmtp) REVERT: D 190 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.5416 (mmt) REVERT: D 237 PHE cc_start: 0.7768 (m-80) cc_final: 0.7441 (m-10) REVERT: D 323 ASP cc_start: 0.8080 (p0) cc_final: 0.7617 (p0) REVERT: D 382 MET cc_start: 0.6708 (ttp) cc_final: 0.6436 (ttp) REVERT: D 397 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: D 403 MET cc_start: 0.8032 (mtm) cc_final: 0.7733 (mtm) REVERT: D 443 LEU cc_start: 0.8989 (mm) cc_final: 0.8761 (mt) REVERT: D 451 GLU cc_start: 0.8176 (tt0) cc_final: 0.7750 (tm-30) REVERT: D 462 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7931 (mp) REVERT: D 470 TYR cc_start: 0.9065 (m-80) cc_final: 0.8828 (m-80) REVERT: D 537 MET cc_start: 0.8654 (ptt) cc_final: 0.8426 (ptm) REVERT: D 539 ASP cc_start: 0.8217 (t0) cc_final: 0.7854 (t0) REVERT: D 554 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7721 (mm-30) REVERT: D 579 MET cc_start: 0.8790 (mmm) cc_final: 0.8511 (mtp) REVERT: D 591 ASP cc_start: 0.7710 (m-30) cc_final: 0.7389 (m-30) REVERT: D 595 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8184 (mpt90) REVERT: D 604 TRP cc_start: 0.7508 (OUTLIER) cc_final: 0.6394 (t60) REVERT: E 161 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8251 (mtmm) REVERT: E 186 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4004 (mptp) REVERT: E 242 LYS cc_start: 0.3438 (OUTLIER) cc_final: 0.2625 (tptp) REVERT: E 330 ILE cc_start: 0.8898 (mt) cc_final: 0.8634 (mp) REVERT: E 367 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7984 (mm-30) REVERT: E 377 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.5983 (mmtm) REVERT: E 398 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7948 (mtm110) REVERT: E 491 ASN cc_start: 0.8268 (t0) cc_final: 0.7908 (t0) REVERT: E 546 ASP cc_start: 0.7796 (m-30) cc_final: 0.7489 (m-30) REVERT: E 591 ASP cc_start: 0.7733 (m-30) cc_final: 0.7489 (m-30) REVERT: F 161 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8270 (mttt) REVERT: F 190 MET cc_start: 0.6525 (mtm) cc_final: 0.6276 (ptp) REVERT: F 237 PHE cc_start: 0.7778 (m-10) cc_final: 0.7336 (m-10) REVERT: F 238 GLU cc_start: 0.8045 (tt0) cc_final: 0.7330 (tm-30) REVERT: F 239 GLN cc_start: 0.5941 (OUTLIER) cc_final: 0.5278 (tp40) REVERT: F 281 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.4379 (pt0) REVERT: F 293 VAL cc_start: 0.8062 (m) cc_final: 0.7744 (p) REVERT: F 377 LYS cc_start: 0.6250 (OUTLIER) cc_final: 0.6010 (mmtm) REVERT: F 398 ARG cc_start: 0.8311 (ttp-170) cc_final: 0.7790 (ttp80) REVERT: F 401 MET cc_start: 0.6926 (mtp) cc_final: 0.5948 (mtp) REVERT: F 433 LYS cc_start: 0.8625 (tttt) cc_final: 0.8385 (ttmt) REVERT: F 451 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: F 485 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8568 (m) REVERT: F 511 GLU cc_start: 0.8178 (mp0) cc_final: 0.7955 (mp0) REVERT: F 590 ASP cc_start: 0.8418 (t0) cc_final: 0.8183 (t0) REVERT: F 604 TRP cc_start: 0.7136 (OUTLIER) cc_final: 0.6913 (t60) REVERT: B 233 VAL cc_start: 0.7555 (m) cc_final: 0.7116 (p) REVERT: B 236 MET cc_start: 0.7056 (mpt) cc_final: 0.6574 (mpt) REVERT: B 247 ILE cc_start: 0.1709 (OUTLIER) cc_final: 0.1116 (mp) REVERT: B 367 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 394 MET cc_start: 0.7232 (ptp) cc_final: 0.6875 (ptm) REVERT: B 413 TYR cc_start: 0.8646 (m-80) cc_final: 0.8091 (m-80) REVERT: B 437 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8474 (pt) REVERT: B 455 ILE cc_start: 0.8295 (mm) cc_final: 0.8028 (mp) REVERT: B 492 ASP cc_start: 0.8082 (m-30) cc_final: 0.7499 (m-30) REVERT: B 547 GLN cc_start: 0.7873 (mt0) cc_final: 0.7623 (mt0) REVERT: B 562 GLN cc_start: 0.8314 (tp40) cc_final: 0.7492 (tm-30) REVERT: B 579 MET cc_start: 0.8553 (mmm) cc_final: 0.8286 (mmt) REVERT: B 582 GLU cc_start: 0.7771 (tp30) cc_final: 0.7526 (tm-30) REVERT: B 599 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8026 (pmm-80) REVERT: B 604 TRP cc_start: 0.7799 (OUTLIER) cc_final: 0.6451 (t60) REVERT: C 161 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7630 (tptp) REVERT: C 203 LYS cc_start: 0.6766 (tmmt) cc_final: 0.6560 (tmmt) REVERT: C 216 ILE cc_start: 0.8052 (mm) cc_final: 0.7544 (mm) REVERT: C 236 MET cc_start: 0.7276 (mmt) cc_final: 0.6660 (tpp) REVERT: C 237 PHE cc_start: 0.6004 (t80) cc_final: 0.4759 (t80) REVERT: C 319 VAL cc_start: 0.7671 (t) cc_final: 0.7414 (m) REVERT: C 329 GLN cc_start: 0.8684 (tp40) cc_final: 0.8156 (mm-40) REVERT: C 367 GLU cc_start: 0.8498 (tp30) cc_final: 0.8129 (mm-30) REVERT: C 370 LEU cc_start: 0.8479 (mt) cc_final: 0.8189 (mm) REVERT: C 390 ASP cc_start: 0.7908 (m-30) cc_final: 0.7630 (m-30) REVERT: C 397 GLU cc_start: 0.7924 (pm20) cc_final: 0.7298 (pm20) REVERT: C 398 ARG cc_start: 0.8170 (mtp180) cc_final: 0.7906 (mtm110) REVERT: C 433 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8517 (ttpp) REVERT: C 562 GLN cc_start: 0.8771 (tp40) cc_final: 0.8042 (tp-100) REVERT: C 566 ASP cc_start: 0.8722 (m-30) cc_final: 0.8033 (m-30) outliers start: 185 outliers final: 147 residues processed: 656 average time/residue: 0.1662 time to fit residues: 158.0690 Evaluate side-chains 690 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 521 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 179 LYS Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 503 MET Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 244 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 chunk 212 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 407 GLN D 562 GLN F 407 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN F 588 GLN B 567 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127233 restraints weight = 113212.821| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 6.66 r_work: 0.3297 rms_B_bonded: 5.89 restraints_weight: 2.0000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 263 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 268 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19587 Z= 0.129 Angle : 0.622 8.499 26400 Z= 0.319 Chirality : 0.043 0.171 2958 Planarity : 0.005 0.073 3432 Dihedral : 10.512 96.360 2904 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 8.85 % Allowed : 27.55 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2400 helix: 0.86 (0.15), residues: 1271 sheet: -0.81 (0.50), residues: 113 loop : -1.42 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 327 TYR 0.016 0.001 TYR C 557 PHE 0.039 0.001 PHE B 237 TRP 0.010 0.001 TRP D 507 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19572) covalent geometry : angle 0.62211 / 0.32 (26400) hydrogen bonds : bond 0.05021 / 3.25 ( 832) hydrogen bonds : angle 4.34136 / 3.08 ( 2457) metal coordination : bond 0.00616 / 0.35 ( 12) Misc. bond : bond 0.00037 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 522 time to evaluate : 0.709 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: A 141 MET cc_start: 0.6832 (tpp) cc_final: 0.6520 (tpp) REVERT: A 161 LYS cc_start: 0.8291 (mmmm) cc_final: 0.7679 (mttm) REVERT: A 236 MET cc_start: 0.7393 (mpt) cc_final: 0.6835 (mmt) REVERT: A 327 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.6961 (mtm-85) REVERT: A 382 MET cc_start: 0.7053 (pp-130) cc_final: 0.6666 (pp-130) REVERT: A 397 GLU cc_start: 0.8289 (mp0) cc_final: 0.8030 (mm-30) REVERT: A 554 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: A 562 GLN cc_start: 0.8507 (tp40) cc_final: 0.8121 (tp-100) REVERT: A 566 ASP cc_start: 0.8141 (m-30) cc_final: 0.7932 (m-30) REVERT: A 589 ILE cc_start: 0.8247 (mt) cc_final: 0.8023 (mm) REVERT: D 158 ASP cc_start: 0.8008 (t0) cc_final: 0.7800 (t0) REVERT: D 179 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7821 (tptt) REVERT: D 190 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.5816 (mmt) REVERT: D 327 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7588 (ptp-170) REVERT: D 382 MET cc_start: 0.6666 (ttp) cc_final: 0.6393 (ttp) REVERT: D 397 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: D 443 LEU cc_start: 0.8965 (mm) cc_final: 0.8745 (mt) REVERT: D 451 GLU cc_start: 0.8174 (tt0) cc_final: 0.7754 (tm-30) REVERT: D 462 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7977 (mp) REVERT: D 470 TYR cc_start: 0.9037 (m-80) cc_final: 0.8812 (m-80) REVERT: D 537 MET cc_start: 0.8668 (ptt) cc_final: 0.8457 (ptm) REVERT: D 539 ASP cc_start: 0.8161 (t0) cc_final: 0.7738 (t0) REVERT: D 554 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7794 (mm-30) REVERT: D 579 MET cc_start: 0.8772 (mmm) cc_final: 0.8427 (mtp) REVERT: D 595 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8187 (mpt90) REVERT: D 604 TRP cc_start: 0.7446 (OUTLIER) cc_final: 0.6279 (t60) REVERT: E 161 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8287 (ttmt) REVERT: E 186 LYS cc_start: 0.4949 (OUTLIER) cc_final: 0.3989 (mptp) REVERT: E 190 MET cc_start: 0.7073 (mtm) cc_final: 0.6768 (mtm) REVERT: E 242 LYS cc_start: 0.3556 (OUTLIER) cc_final: 0.2728 (tptp) REVERT: E 331 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8495 (mp) REVERT: E 366 ASN cc_start: 0.8836 (t0) cc_final: 0.8564 (t0) REVERT: E 367 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7939 (mm-30) REVERT: E 377 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.5510 (mptt) REVERT: E 398 ARG cc_start: 0.8315 (mtp-110) cc_final: 0.7981 (ptm-80) REVERT: E 491 ASN cc_start: 0.8272 (t0) cc_final: 0.7908 (t0) REVERT: E 546 ASP cc_start: 0.7806 (m-30) cc_final: 0.7511 (m-30) REVERT: E 591 ASP cc_start: 0.7791 (m-30) cc_final: 0.7541 (m-30) REVERT: F 161 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8239 (mttt) REVERT: F 237 PHE cc_start: 0.7952 (m-10) cc_final: 0.7468 (m-10) REVERT: F 238 GLU cc_start: 0.7987 (tt0) cc_final: 0.7209 (tm-30) REVERT: F 281 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.4280 (pt0) REVERT: F 293 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7795 (p) REVERT: F 377 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.6115 (mmtm) REVERT: F 398 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.7866 (ttp80) REVERT: F 401 MET cc_start: 0.7089 (mtp) cc_final: 0.6097 (mtp) REVERT: F 407 GLN cc_start: 0.8568 (tt0) cc_final: 0.8291 (tt0) REVERT: F 433 LYS cc_start: 0.8641 (tttt) cc_final: 0.8385 (ttmt) REVERT: F 451 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: F 511 GLU cc_start: 0.8238 (mp0) cc_final: 0.7978 (mp0) REVERT: F 513 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8643 (mp) REVERT: F 590 ASP cc_start: 0.8447 (t0) cc_final: 0.8140 (t0) REVERT: B 233 VAL cc_start: 0.7495 (m) cc_final: 0.7280 (p) REVERT: B 236 MET cc_start: 0.7003 (mpt) cc_final: 0.6579 (mpt) REVERT: B 238 GLU cc_start: 0.7620 (pp20) cc_final: 0.7358 (pp20) REVERT: B 247 ILE cc_start: 0.1713 (OUTLIER) cc_final: 0.1112 (mp) REVERT: B 327 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7512 (mtt-85) REVERT: B 394 MET cc_start: 0.7270 (ptp) cc_final: 0.6859 (ptm) REVERT: B 413 TYR cc_start: 0.8608 (m-80) cc_final: 0.8055 (m-80) REVERT: B 463 GLU cc_start: 0.8266 (tt0) cc_final: 0.8040 (mt-10) REVERT: B 492 ASP cc_start: 0.8108 (m-30) cc_final: 0.7528 (m-30) REVERT: B 543 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7914 (ttp80) REVERT: B 547 GLN cc_start: 0.7861 (mt0) cc_final: 0.7602 (mt0) REVERT: B 562 GLN cc_start: 0.8410 (tp40) cc_final: 0.7536 (tm-30) REVERT: B 579 MET cc_start: 0.8544 (mmm) cc_final: 0.8243 (mmt) REVERT: B 599 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8086 (pmm-80) REVERT: B 604 TRP cc_start: 0.7769 (OUTLIER) cc_final: 0.6338 (t60) REVERT: C 161 LYS cc_start: 0.8449 (ttpt) cc_final: 0.7678 (tptp) REVERT: C 216 ILE cc_start: 0.8027 (mm) cc_final: 0.7507 (mm) REVERT: C 235 ASP cc_start: 0.7553 (m-30) cc_final: 0.7271 (m-30) REVERT: C 236 MET cc_start: 0.7204 (mmt) cc_final: 0.6622 (tpp) REVERT: C 237 PHE cc_start: 0.6087 (t80) cc_final: 0.4641 (t80) REVERT: C 319 VAL cc_start: 0.7602 (t) cc_final: 0.7320 (m) REVERT: C 329 GLN cc_start: 0.8743 (tp40) cc_final: 0.8238 (mm-40) REVERT: C 367 GLU cc_start: 0.8544 (tp30) cc_final: 0.8180 (mm-30) REVERT: C 370 LEU cc_start: 0.8474 (mt) cc_final: 0.8184 (mp) REVERT: C 390 ASP cc_start: 0.7943 (m-30) cc_final: 0.7654 (m-30) REVERT: C 397 GLU cc_start: 0.7979 (pm20) cc_final: 0.7365 (pm20) REVERT: C 398 ARG cc_start: 0.8188 (mtp180) cc_final: 0.7927 (mtm110) REVERT: C 433 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8564 (ttpp) REVERT: C 434 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8329 (m) REVERT: C 562 GLN cc_start: 0.8594 (tp40) cc_final: 0.7929 (tp-100) REVERT: C 566 ASP cc_start: 0.8719 (m-30) cc_final: 0.8053 (m-30) outliers start: 177 outliers final: 131 residues processed: 639 average time/residue: 0.1628 time to fit residues: 150.4777 Evaluate side-chains 669 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 518 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 407 GLN D 418 HIS D 562 GLN E 276 ASN F 407 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN F 588 GLN C 418 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126575 restraints weight = 113526.903| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 6.72 r_work: 0.3286 rms_B_bonded: 5.91 restraints_weight: 2.0000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 268 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 273 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.571 19587 Z= 0.230 Angle : 0.634 8.517 26400 Z= 0.327 Chirality : 0.043 0.238 2958 Planarity : 0.004 0.072 3432 Dihedral : 9.977 95.983 2867 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 8.46 % Allowed : 27.50 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2400 helix: 0.73 (0.15), residues: 1308 sheet: -0.76 (0.51), residues: 113 loop : -1.40 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 398 TYR 0.016 0.001 TYR D 557 PHE 0.042 0.001 PHE B 237 TRP 0.010 0.001 TRP D 507 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (19572) covalent geometry : angle 0.63436 / 0.33 (26400) hydrogen bonds : bond 0.05324 / 3.45 ( 832) hydrogen bonds : angle 4.35235 / 3.08 ( 2457) metal coordination : bond 0.21367 / 14.23 ( 12) Misc. bond : bond 0.00034 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 526 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.6884 (tpp) cc_final: 0.6561 (tpp) REVERT: A 161 LYS cc_start: 0.8304 (mmmm) cc_final: 0.7688 (mttm) REVERT: A 236 MET cc_start: 0.7435 (mpt) cc_final: 0.6867 (mmt) REVERT: A 327 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.6966 (mtm-85) REVERT: A 335 MET cc_start: 0.8221 (tpp) cc_final: 0.7852 (mmm) REVERT: A 382 MET cc_start: 0.7010 (pp-130) cc_final: 0.6631 (pp-130) REVERT: A 397 GLU cc_start: 0.8326 (mp0) cc_final: 0.8015 (mm-30) REVERT: A 491 ASN cc_start: 0.7475 (t0) cc_final: 0.7173 (t0) REVERT: A 554 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: A 562 GLN cc_start: 0.8520 (tp40) cc_final: 0.8131 (tp-100) REVERT: A 589 ILE cc_start: 0.8242 (mt) cc_final: 0.8015 (mm) REVERT: D 158 ASP cc_start: 0.7995 (t0) cc_final: 0.7761 (t0) REVERT: D 179 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7851 (tptt) REVERT: D 327 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7689 (ptp-170) REVERT: D 382 MET cc_start: 0.6717 (ttp) cc_final: 0.6444 (ttp) REVERT: D 397 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: D 443 LEU cc_start: 0.9001 (mm) cc_final: 0.8707 (mt) REVERT: D 451 GLU cc_start: 0.8151 (tt0) cc_final: 0.7740 (tm-30) REVERT: D 470 TYR cc_start: 0.9097 (m-80) cc_final: 0.8890 (m-80) REVERT: D 537 MET cc_start: 0.8681 (ptt) cc_final: 0.8469 (ptm) REVERT: D 539 ASP cc_start: 0.8196 (t0) cc_final: 0.7789 (t0) REVERT: D 547 GLN cc_start: 0.7770 (mt0) cc_final: 0.7524 (mt0) REVERT: D 554 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7874 (mm-30) REVERT: D 579 MET cc_start: 0.8791 (mmm) cc_final: 0.8548 (mtp) REVERT: D 591 ASP cc_start: 0.7577 (m-30) cc_final: 0.7053 (m-30) REVERT: D 595 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8189 (mpt90) REVERT: D 604 TRP cc_start: 0.7385 (OUTLIER) cc_final: 0.6202 (t60) REVERT: E 161 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8288 (ttmt) REVERT: E 186 LYS cc_start: 0.5051 (OUTLIER) cc_final: 0.4120 (mptp) REVERT: E 239 GLN cc_start: 0.7125 (mm-40) cc_final: 0.6675 (tt0) REVERT: E 242 LYS cc_start: 0.3578 (OUTLIER) cc_final: 0.2710 (tptp) REVERT: E 278 MET cc_start: 0.3969 (tpt) cc_final: 0.2806 (tpt) REVERT: E 366 ASN cc_start: 0.8802 (t0) cc_final: 0.8527 (t0) REVERT: E 367 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: E 377 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.5453 (mptt) REVERT: E 491 ASN cc_start: 0.8301 (t0) cc_final: 0.8001 (t0) REVERT: E 591 ASP cc_start: 0.7847 (m-30) cc_final: 0.7601 (m-30) REVERT: F 161 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8260 (mttp) REVERT: F 190 MET cc_start: 0.7152 (ptp) cc_final: 0.6692 (ptp) REVERT: F 237 PHE cc_start: 0.7964 (m-10) cc_final: 0.7461 (m-10) REVERT: F 238 GLU cc_start: 0.8034 (tt0) cc_final: 0.7283 (tm-30) REVERT: F 281 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.4339 (pt0) REVERT: F 293 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7790 (p) REVERT: F 331 LEU cc_start: 0.8944 (mt) cc_final: 0.8014 (mm) REVERT: F 335 MET cc_start: 0.7237 (ptt) cc_final: 0.6926 (pmm) REVERT: F 377 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.6176 (mmtm) REVERT: F 398 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7880 (ttp80) REVERT: F 401 MET cc_start: 0.7057 (mtp) cc_final: 0.6064 (mtp) REVERT: F 433 LYS cc_start: 0.8647 (tttt) cc_final: 0.8400 (ttmt) REVERT: F 451 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: F 483 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: F 511 GLU cc_start: 0.8254 (mp0) cc_final: 0.7996 (mp0) REVERT: F 513 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8718 (mp) REVERT: F 590 ASP cc_start: 0.8431 (t0) cc_final: 0.8206 (t0) REVERT: B 236 MET cc_start: 0.7090 (mpt) cc_final: 0.6695 (mpt) REVERT: B 247 ILE cc_start: 0.1626 (OUTLIER) cc_final: 0.1063 (mp) REVERT: B 327 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7532 (mtt-85) REVERT: B 367 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7798 (mm-30) REVERT: B 394 MET cc_start: 0.7233 (ptp) cc_final: 0.6845 (ptm) REVERT: B 401 MET cc_start: 0.7141 (mtt) cc_final: 0.6913 (mtp) REVERT: B 413 TYR cc_start: 0.8608 (m-80) cc_final: 0.8004 (m-80) REVERT: B 463 GLU cc_start: 0.8260 (tt0) cc_final: 0.8043 (mt-10) REVERT: B 547 GLN cc_start: 0.7919 (mt0) cc_final: 0.7711 (mt0) REVERT: B 562 GLN cc_start: 0.8388 (tp40) cc_final: 0.7477 (tm-30) REVERT: B 579 MET cc_start: 0.8544 (mmm) cc_final: 0.8282 (mmt) REVERT: B 599 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8105 (pmm-80) REVERT: B 604 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.6260 (t60) REVERT: C 161 LYS cc_start: 0.8438 (ttpt) cc_final: 0.7661 (tptp) REVERT: C 203 LYS cc_start: 0.6795 (tmmt) cc_final: 0.6576 (tmmt) REVERT: C 216 ILE cc_start: 0.8050 (mm) cc_final: 0.7520 (mm) REVERT: C 236 MET cc_start: 0.7120 (mmt) cc_final: 0.6623 (tpp) REVERT: C 237 PHE cc_start: 0.5745 (t80) cc_final: 0.4182 (t80) REVERT: C 319 VAL cc_start: 0.7625 (t) cc_final: 0.7307 (m) REVERT: C 329 GLN cc_start: 0.8758 (tp40) cc_final: 0.8249 (mm-40) REVERT: C 367 GLU cc_start: 0.8567 (tp30) cc_final: 0.8188 (mm-30) REVERT: C 370 LEU cc_start: 0.8537 (mt) cc_final: 0.8225 (mm) REVERT: C 390 ASP cc_start: 0.7937 (m-30) cc_final: 0.7667 (m-30) REVERT: C 397 GLU cc_start: 0.7964 (pm20) cc_final: 0.7366 (pm20) REVERT: C 398 ARG cc_start: 0.8202 (mtp180) cc_final: 0.7869 (mtm110) REVERT: C 433 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8554 (ttpp) REVERT: C 434 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8280 (m) REVERT: C 562 GLN cc_start: 0.8625 (tp40) cc_final: 0.7938 (tp-100) REVERT: C 566 ASP cc_start: 0.8725 (m-30) cc_final: 0.8083 (m-30) outliers start: 169 outliers final: 139 residues processed: 640 average time/residue: 0.1521 time to fit residues: 141.4825 Evaluate side-chains 677 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 520 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 503 MET Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 550 LYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 142 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 407 GLN D 418 HIS D 562 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 588 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125923 restraints weight = 106020.221| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 6.40 r_work: 0.3282 rms_B_bonded: 6.13 restraints_weight: 2.0000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 273 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 274 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.466 19587 Z= 0.175 Angle : 0.630 8.604 26400 Z= 0.325 Chirality : 0.043 0.211 2958 Planarity : 0.004 0.070 3432 Dihedral : 9.676 97.157 2859 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 7.57 % Allowed : 28.83 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 2400 helix: 0.98 (0.15), residues: 1277 sheet: -0.73 (0.51), residues: 113 loop : -1.36 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 327 TYR 0.014 0.001 TYR C 557 PHE 0.044 0.001 PHE B 237 TRP 0.008 0.001 TRP B 507 HIS 0.009 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (19572) covalent geometry : angle 0.62970 / 0.32 (26400) hydrogen bonds : bond 0.04895 / 3.15 ( 832) hydrogen bonds : angle 4.32672 / 3.08 ( 2457) metal coordination : bond 0.14795 / 8.51 ( 12) Misc. bond : bond 0.00029 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 515 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.6931 (tpp) cc_final: 0.6659 (tpp) REVERT: A 161 LYS cc_start: 0.8212 (mmmm) cc_final: 0.7631 (mttm) REVERT: A 327 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.6949 (mtm-85) REVERT: A 382 MET cc_start: 0.7063 (pp-130) cc_final: 0.6643 (pp-130) REVERT: A 397 GLU cc_start: 0.8294 (mp0) cc_final: 0.8005 (mm-30) REVERT: A 498 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8403 (t0) REVERT: A 554 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: A 562 GLN cc_start: 0.8322 (tp40) cc_final: 0.8010 (tp-100) REVERT: A 589 ILE cc_start: 0.8219 (mt) cc_final: 0.7964 (mm) REVERT: D 158 ASP cc_start: 0.7980 (t0) cc_final: 0.7763 (t0) REVERT: D 179 LYS cc_start: 0.8203 (mmtp) cc_final: 0.7904 (mmtt) REVERT: D 327 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7655 (ptp-170) REVERT: D 382 MET cc_start: 0.6746 (ttp) cc_final: 0.6468 (ttp) REVERT: D 397 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: D 443 LEU cc_start: 0.8903 (mm) cc_final: 0.8639 (mt) REVERT: D 451 GLU cc_start: 0.8200 (tt0) cc_final: 0.7736 (tm-30) REVERT: D 470 TYR cc_start: 0.9068 (m-80) cc_final: 0.8846 (m-80) REVERT: D 537 MET cc_start: 0.8674 (ptt) cc_final: 0.8449 (ptm) REVERT: D 539 ASP cc_start: 0.8165 (t0) cc_final: 0.7779 (t0) REVERT: D 547 GLN cc_start: 0.7809 (mt0) cc_final: 0.7538 (mt0) REVERT: D 554 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7720 (mm-30) REVERT: D 562 GLN cc_start: 0.8357 (tp40) cc_final: 0.8131 (tp-100) REVERT: D 566 ASP cc_start: 0.8005 (m-30) cc_final: 0.7788 (m-30) REVERT: D 579 MET cc_start: 0.8743 (mmm) cc_final: 0.8443 (mtp) REVERT: D 591 ASP cc_start: 0.7610 (m-30) cc_final: 0.7073 (m-30) REVERT: D 595 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8161 (mpt90) REVERT: D 604 TRP cc_start: 0.7480 (OUTLIER) cc_final: 0.6250 (t60) REVERT: E 161 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8258 (ttmt) REVERT: E 186 LYS cc_start: 0.4845 (OUTLIER) cc_final: 0.3986 (mptp) REVERT: E 239 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6976 (tt0) REVERT: E 242 LYS cc_start: 0.3578 (OUTLIER) cc_final: 0.2721 (tptp) REVERT: E 278 MET cc_start: 0.3959 (tpt) cc_final: 0.2770 (tpt) REVERT: E 366 ASN cc_start: 0.8803 (t0) cc_final: 0.8531 (t0) REVERT: E 367 GLU cc_start: 0.8294 (tp30) cc_final: 0.7927 (mm-30) REVERT: E 491 ASN cc_start: 0.8235 (t0) cc_final: 0.7876 (t0) REVERT: E 591 ASP cc_start: 0.7946 (m-30) cc_final: 0.7686 (m-30) REVERT: F 161 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8239 (mttp) REVERT: F 237 PHE cc_start: 0.7909 (m-10) cc_final: 0.7392 (m-10) REVERT: F 238 GLU cc_start: 0.8071 (tt0) cc_final: 0.7387 (tm-30) REVERT: F 281 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.4363 (pt0) REVERT: F 293 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7681 (p) REVERT: F 298 ASN cc_start: 0.8105 (p0) cc_final: 0.7839 (p0) REVERT: F 331 LEU cc_start: 0.8982 (mt) cc_final: 0.8682 (mm) REVERT: F 335 MET cc_start: 0.7450 (ptt) cc_final: 0.7246 (ptt) REVERT: F 377 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.6074 (mmtm) REVERT: F 398 ARG cc_start: 0.8438 (ttp-170) cc_final: 0.7880 (ttp80) REVERT: F 401 MET cc_start: 0.7224 (mtp) cc_final: 0.6224 (mtp) REVERT: F 433 LYS cc_start: 0.8701 (tttt) cc_final: 0.8406 (ttmt) REVERT: F 451 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: F 483 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: F 511 GLU cc_start: 0.8262 (mp0) cc_final: 0.7993 (mp0) REVERT: F 590 ASP cc_start: 0.8417 (t0) cc_final: 0.8193 (t0) REVERT: B 236 MET cc_start: 0.6997 (mpt) cc_final: 0.6637 (mpt) REVERT: B 247 ILE cc_start: 0.1788 (OUTLIER) cc_final: 0.1194 (mp) REVERT: B 327 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7509 (mtt-85) REVERT: B 413 TYR cc_start: 0.8579 (m-80) cc_final: 0.7952 (m-80) REVERT: B 463 GLU cc_start: 0.8263 (tt0) cc_final: 0.8049 (mt-10) REVERT: B 492 ASP cc_start: 0.8080 (m-30) cc_final: 0.7450 (m-30) REVERT: B 562 GLN cc_start: 0.8310 (tp40) cc_final: 0.7400 (tm-30) REVERT: B 579 MET cc_start: 0.8547 (mmm) cc_final: 0.8324 (mmt) REVERT: B 604 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.6293 (t60) REVERT: C 161 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7541 (tptp) REVERT: C 216 ILE cc_start: 0.8042 (mm) cc_final: 0.7584 (mm) REVERT: C 236 MET cc_start: 0.6996 (mmt) cc_final: 0.6522 (tpp) REVERT: C 237 PHE cc_start: 0.6172 (t80) cc_final: 0.5175 (t80) REVERT: C 319 VAL cc_start: 0.7400 (t) cc_final: 0.7088 (m) REVERT: C 329 GLN cc_start: 0.8705 (tp40) cc_final: 0.8183 (mm-40) REVERT: C 367 GLU cc_start: 0.8538 (tp30) cc_final: 0.8147 (mm-30) REVERT: C 370 LEU cc_start: 0.8473 (mt) cc_final: 0.8175 (mp) REVERT: C 397 GLU cc_start: 0.8013 (pm20) cc_final: 0.7454 (pm20) REVERT: C 398 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7844 (mtm110) REVERT: C 433 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8521 (ttpp) REVERT: C 434 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8206 (m) REVERT: C 562 GLN cc_start: 0.8574 (tp40) cc_final: 0.7906 (tp-100) REVERT: C 566 ASP cc_start: 0.8772 (m-30) cc_final: 0.8130 (m-30) outliers start: 151 outliers final: 122 residues processed: 616 average time/residue: 0.1545 time to fit residues: 138.6762 Evaluate side-chains 645 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 508 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 538 SER Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 550 LYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 102 optimal weight: 8.9990 chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 210 optimal weight: 0.0270 chunk 90 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 115 optimal weight: 0.0370 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 407 GLN D 418 HIS ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 ASN F 558 ASN F 588 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.161142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126319 restraints weight = 107921.766| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 6.45 r_work: 0.3287 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 274 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 276 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.538 19587 Z= 0.179 Angle : 0.627 8.996 26400 Z= 0.323 Chirality : 0.043 0.214 2958 Planarity : 0.004 0.070 3432 Dihedral : 9.337 97.525 2840 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 7.22 % Allowed : 29.28 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2400 helix: 1.02 (0.15), residues: 1283 sheet: -0.73 (0.51), residues: 113 loop : -1.34 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 327 TYR 0.014 0.001 TYR C 557 PHE 0.045 0.001 PHE B 237 TRP 0.007 0.001 TRP B 507 HIS 0.012 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (19572) covalent geometry : angle 0.62730 / 0.32 (26400) hydrogen bonds : bond 0.04759 / 3.06 ( 832) hydrogen bonds : angle 4.31993 / 3.08 ( 2457) metal coordination : bond 0.15551 / 7.78 ( 12) Misc. bond : bond 0.00024 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 509 time to evaluate : 0.708 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: A 141 MET cc_start: 0.7007 (tpp) cc_final: 0.6712 (tpp) REVERT: A 161 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7825 (mmmm) REVERT: A 236 MET cc_start: 0.7283 (mmt) cc_final: 0.6868 (mmp) REVERT: A 327 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.6962 (mtm-85) REVERT: A 382 MET cc_start: 0.7092 (pp-130) cc_final: 0.6628 (pp-130) REVERT: A 397 GLU cc_start: 0.8281 (mp0) cc_final: 0.7989 (mm-30) REVERT: A 498 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8397 (t0) REVERT: A 554 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: A 562 GLN cc_start: 0.8330 (tp40) cc_final: 0.8048 (tp-100) REVERT: A 589 ILE cc_start: 0.8238 (mt) cc_final: 0.7982 (mm) REVERT: D 179 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7926 (mmtt) REVERT: D 327 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7601 (ptp-170) REVERT: D 382 MET cc_start: 0.6754 (ttp) cc_final: 0.6474 (ttp) REVERT: D 397 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: D 408 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8546 (mtpp) REVERT: D 443 LEU cc_start: 0.8900 (mm) cc_final: 0.8645 (mt) REVERT: D 451 GLU cc_start: 0.8154 (tt0) cc_final: 0.7708 (tm-30) REVERT: D 537 MET cc_start: 0.8644 (ptt) cc_final: 0.8422 (ptm) REVERT: D 539 ASP cc_start: 0.8175 (t0) cc_final: 0.7806 (t0) REVERT: D 547 GLN cc_start: 0.7814 (mt0) cc_final: 0.7576 (mt0) REVERT: D 554 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7752 (mm-30) REVERT: D 579 MET cc_start: 0.8748 (mmm) cc_final: 0.8388 (mtp) REVERT: D 595 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8306 (mpt90) REVERT: D 604 TRP cc_start: 0.7494 (OUTLIER) cc_final: 0.6216 (t60) REVERT: E 161 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8231 (ttmt) REVERT: E 186 LYS cc_start: 0.4733 (OUTLIER) cc_final: 0.3915 (mptp) REVERT: E 242 LYS cc_start: 0.3580 (OUTLIER) cc_final: 0.2749 (tptp) REVERT: E 278 MET cc_start: 0.3867 (tpt) cc_final: 0.2679 (tpt) REVERT: E 324 VAL cc_start: 0.8211 (p) cc_final: 0.7900 (t) REVERT: E 366 ASN cc_start: 0.8762 (t0) cc_final: 0.8487 (t0) REVERT: E 367 GLU cc_start: 0.8288 (tp30) cc_final: 0.7914 (mm-30) REVERT: E 398 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.8080 (ptm-80) REVERT: E 491 ASN cc_start: 0.8236 (t0) cc_final: 0.7880 (t0) REVERT: E 591 ASP cc_start: 0.7955 (m-30) cc_final: 0.7690 (m-30) REVERT: F 161 LYS cc_start: 0.8479 (mmmm) cc_final: 0.8225 (mttp) REVERT: F 237 PHE cc_start: 0.7891 (m-10) cc_final: 0.7386 (m-10) REVERT: F 238 GLU cc_start: 0.8065 (tt0) cc_final: 0.7409 (tm-30) REVERT: F 281 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.4259 (pt0) REVERT: F 293 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7696 (p) REVERT: F 298 ASN cc_start: 0.8260 (p0) cc_final: 0.7931 (p0) REVERT: F 331 LEU cc_start: 0.8916 (mt) cc_final: 0.8598 (mm) REVERT: F 377 LYS cc_start: 0.6372 (OUTLIER) cc_final: 0.6023 (mmtm) REVERT: F 398 ARG cc_start: 0.8445 (ttp-170) cc_final: 0.7890 (ttp80) REVERT: F 401 MET cc_start: 0.7270 (mtp) cc_final: 0.6135 (mtp) REVERT: F 433 LYS cc_start: 0.8705 (tttt) cc_final: 0.8406 (ttmt) REVERT: F 451 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: F 483 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: F 511 GLU cc_start: 0.8246 (mp0) cc_final: 0.8034 (mp0) REVERT: F 590 ASP cc_start: 0.8408 (t0) cc_final: 0.8196 (t0) REVERT: B 236 MET cc_start: 0.7076 (mpt) cc_final: 0.6769 (mpt) REVERT: B 247 ILE cc_start: 0.1563 (OUTLIER) cc_final: 0.1015 (mp) REVERT: B 282 MET cc_start: 0.5443 (mpp) cc_final: 0.5071 (mpp) REVERT: B 327 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.7437 (mtt-85) REVERT: B 329 GLN cc_start: 0.8696 (tp40) cc_final: 0.8066 (mp10) REVERT: B 413 TYR cc_start: 0.8570 (m-80) cc_final: 0.7947 (m-80) REVERT: B 463 GLU cc_start: 0.8250 (tt0) cc_final: 0.8047 (mt-10) REVERT: B 492 ASP cc_start: 0.8052 (m-30) cc_final: 0.7443 (m-30) REVERT: B 562 GLN cc_start: 0.8314 (tp40) cc_final: 0.7392 (tm-30) REVERT: B 579 MET cc_start: 0.8551 (mmm) cc_final: 0.8326 (mmt) REVERT: B 599 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8210 (pmm-80) REVERT: B 604 TRP cc_start: 0.7737 (OUTLIER) cc_final: 0.6163 (t60) REVERT: C 161 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7458 (tptp) REVERT: C 216 ILE cc_start: 0.8027 (mm) cc_final: 0.7518 (mm) REVERT: C 236 MET cc_start: 0.6871 (mmt) cc_final: 0.6388 (tpp) REVERT: C 319 VAL cc_start: 0.7372 (t) cc_final: 0.7105 (m) REVERT: C 329 GLN cc_start: 0.8710 (tp40) cc_final: 0.8189 (mm-40) REVERT: C 367 GLU cc_start: 0.8552 (tp30) cc_final: 0.8155 (mm-30) REVERT: C 370 LEU cc_start: 0.8463 (mt) cc_final: 0.8160 (mp) REVERT: C 397 GLU cc_start: 0.7990 (pm20) cc_final: 0.7422 (pm20) REVERT: C 398 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7855 (mtm110) REVERT: C 433 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8526 (ttpp) REVERT: C 434 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8181 (m) REVERT: C 547 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7748 (mt0) REVERT: C 562 GLN cc_start: 0.8566 (tp40) cc_final: 0.7933 (tp-100) REVERT: C 566 ASP cc_start: 0.8752 (m-30) cc_final: 0.8129 (m-30) outliers start: 144 outliers final: 120 residues processed: 604 average time/residue: 0.1571 time to fit residues: 137.6886 Evaluate side-chains 645 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 509 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 538 SER Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 550 LYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 66 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 150 optimal weight: 0.2980 chunk 215 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 407 GLN D 418 HIS F 239 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 588 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.159628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125248 restraints weight = 108823.103| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 6.65 r_work: 0.3268 rms_B_bonded: 6.06 restraints_weight: 2.0000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 276 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 280 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.459 19587 Z= 0.185 Angle : 0.644 9.710 26400 Z= 0.330 Chirality : 0.043 0.200 2958 Planarity : 0.004 0.071 3432 Dihedral : 9.292 96.853 2837 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.71 % Rotamer: Outliers : 7.02 % Allowed : 29.67 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2400 helix: 0.97 (0.15), residues: 1278 sheet: -1.73 (0.59), residues: 78 loop : -1.29 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 176 TYR 0.016 0.001 TYR C 557 PHE 0.043 0.001 PHE B 237 TRP 0.010 0.001 TRP B 507 HIS 0.007 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (19572) covalent geometry : angle 0.64368 / 0.33 (26400) hydrogen bonds : bond 0.05246 / 3.39 ( 832) hydrogen bonds : angle 4.35871 / 3.11 ( 2457) metal coordination : bond 0.13285 / 6.64 ( 12) Misc. bond : bond 0.00042 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 520 time to evaluate : 0.868 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: A 141 MET cc_start: 0.7099 (tpp) cc_final: 0.6831 (tpp) REVERT: A 161 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7776 (mmmm) REVERT: A 327 ARG cc_start: 0.7857 (mtm-85) cc_final: 0.7000 (mtm-85) REVERT: A 382 MET cc_start: 0.7093 (pp-130) cc_final: 0.6629 (pp-130) REVERT: A 407 GLN cc_start: 0.8692 (mt0) cc_final: 0.8352 (mt0) REVERT: A 491 ASN cc_start: 0.7564 (t0) cc_final: 0.7309 (t0) REVERT: A 539 ASP cc_start: 0.7798 (t70) cc_final: 0.7433 (t0) REVERT: A 554 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: A 562 GLN cc_start: 0.8342 (tp40) cc_final: 0.8009 (tp-100) REVERT: A 588 GLN cc_start: 0.8116 (mt0) cc_final: 0.7893 (mt0) REVERT: A 589 ILE cc_start: 0.8228 (mt) cc_final: 0.7958 (mm) REVERT: D 179 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7944 (tptt) REVERT: D 327 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7662 (ptp-170) REVERT: D 382 MET cc_start: 0.6788 (ttp) cc_final: 0.6505 (ttp) REVERT: D 443 LEU cc_start: 0.8915 (mm) cc_final: 0.8662 (mt) REVERT: D 451 GLU cc_start: 0.8225 (tt0) cc_final: 0.7732 (tm-30) REVERT: D 537 MET cc_start: 0.8634 (ptt) cc_final: 0.8400 (ptm) REVERT: D 539 ASP cc_start: 0.8232 (t0) cc_final: 0.7889 (t0) REVERT: D 554 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7814 (mm-30) REVERT: D 579 MET cc_start: 0.8754 (mmm) cc_final: 0.8381 (mtp) REVERT: D 595 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8160 (mpt90) REVERT: D 604 TRP cc_start: 0.7491 (OUTLIER) cc_final: 0.6232 (t60) REVERT: E 161 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8231 (ttmt) REVERT: E 186 LYS cc_start: 0.4724 (OUTLIER) cc_final: 0.3936 (mptp) REVERT: E 242 LYS cc_start: 0.3583 (OUTLIER) cc_final: 0.2739 (tptp) REVERT: E 278 MET cc_start: 0.4020 (tpt) cc_final: 0.2900 (tpt) REVERT: E 324 VAL cc_start: 0.8178 (p) cc_final: 0.7893 (t) REVERT: E 366 ASN cc_start: 0.8758 (t0) cc_final: 0.8478 (t0) REVERT: E 367 GLU cc_start: 0.8294 (tp30) cc_final: 0.7912 (mm-30) REVERT: E 398 ARG cc_start: 0.8327 (mtp-110) cc_final: 0.8012 (ptm-80) REVERT: E 491 ASN cc_start: 0.8267 (t0) cc_final: 0.7911 (t0) REVERT: F 161 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8232 (mttp) REVERT: F 237 PHE cc_start: 0.7941 (m-10) cc_final: 0.7429 (m-10) REVERT: F 238 GLU cc_start: 0.8121 (tt0) cc_final: 0.7415 (tm-30) REVERT: F 281 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.4314 (pt0) REVERT: F 293 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7760 (p) REVERT: F 331 LEU cc_start: 0.8946 (mt) cc_final: 0.8728 (mm) REVERT: F 377 LYS cc_start: 0.6381 (OUTLIER) cc_final: 0.6072 (mmtm) REVERT: F 398 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8097 (ttt90) REVERT: F 401 MET cc_start: 0.7311 (mtp) cc_final: 0.6328 (mtp) REVERT: F 433 LYS cc_start: 0.8715 (tttt) cc_final: 0.8431 (ttmt) REVERT: F 451 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: F 483 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: F 511 GLU cc_start: 0.8222 (mp0) cc_final: 0.7995 (mp0) REVERT: F 590 ASP cc_start: 0.8422 (t0) cc_final: 0.8211 (t0) REVERT: B 161 LYS cc_start: 0.8378 (mmmm) cc_final: 0.7915 (mttp) REVERT: B 247 ILE cc_start: 0.1741 (OUTLIER) cc_final: 0.1172 (mp) REVERT: B 282 MET cc_start: 0.5317 (mpp) cc_final: 0.4896 (mpp) REVERT: B 327 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7489 (mtt-85) REVERT: B 329 GLN cc_start: 0.8697 (tp40) cc_final: 0.8099 (mp10) REVERT: B 413 TYR cc_start: 0.8568 (m-80) cc_final: 0.7962 (m-80) REVERT: B 463 GLU cc_start: 0.8262 (tt0) cc_final: 0.8058 (mt-10) REVERT: B 562 GLN cc_start: 0.8341 (tp40) cc_final: 0.7416 (tm-30) REVERT: B 579 MET cc_start: 0.8566 (mmm) cc_final: 0.8342 (mmt) REVERT: B 599 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8221 (pmm-80) REVERT: B 604 TRP cc_start: 0.7753 (OUTLIER) cc_final: 0.6112 (t60) REVERT: C 161 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7410 (tptp) REVERT: C 216 ILE cc_start: 0.8052 (mm) cc_final: 0.7567 (mm) REVERT: C 236 MET cc_start: 0.6861 (mmt) cc_final: 0.6350 (tpp) REVERT: C 329 GLN cc_start: 0.8729 (tp40) cc_final: 0.8199 (mm-40) REVERT: C 367 GLU cc_start: 0.8579 (tp30) cc_final: 0.8172 (mm-30) REVERT: C 370 LEU cc_start: 0.8496 (mt) cc_final: 0.8184 (mp) REVERT: C 397 GLU cc_start: 0.7987 (pm20) cc_final: 0.7425 (pm20) REVERT: C 398 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7868 (mtm110) REVERT: C 433 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8483 (ttpp) REVERT: C 547 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7785 (mt0) REVERT: C 562 GLN cc_start: 0.8596 (tp40) cc_final: 0.7932 (tp-100) REVERT: C 566 ASP cc_start: 0.8736 (m-30) cc_final: 0.8099 (m-30) outliers start: 140 outliers final: 121 residues processed: 616 average time/residue: 0.1528 time to fit residues: 136.4649 Evaluate side-chains 650 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 516 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 503 MET Chi-restraints excluded: chain F residue 538 SER Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 550 LYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 227 optimal weight: 0.0970 chunk 21 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 22 optimal weight: 0.0170 chunk 200 optimal weight: 1.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 407 GLN D 556 ASN D 562 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 588 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN C 572 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.163152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128973 restraints weight = 101414.777| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 6.29 r_work: 0.3337 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 280 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 283 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19587 Z= 0.117 Angle : 0.619 9.241 26400 Z= 0.316 Chirality : 0.042 0.209 2958 Planarity : 0.004 0.070 3432 Dihedral : 8.968 99.429 2834 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.93 % Allowed : 30.66 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2400 helix: 1.15 (0.15), residues: 1282 sheet: -1.73 (0.59), residues: 78 loop : -1.18 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 399 TYR 0.013 0.001 TYR C 557 PHE 0.048 0.001 PHE B 237 TRP 0.006 0.001 TRP A 507 HIS 0.006 0.001 HIS D 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (19572) covalent geometry : angle 0.61871 / 0.32 (26400) hydrogen bonds : bond 0.04307 / 2.77 ( 832) hydrogen bonds : angle 4.22303 / 3.02 ( 2457) metal coordination : bond 0.00965 / 0.50 ( 12) Misc. bond : bond 0.00027 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5168.96 seconds wall clock time: 89 minutes 3.77 seconds (5343.77 seconds total)