Starting phenix.real_space_refine on Thu Mar 5 04:29:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wi4_32521/03_2026/7wi4_32521.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi4_32521/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wi4_32521/03_2026/7wi4_32521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi4_32521/03_2026/7wi4_32521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wi4_32521/03_2026/7wi4_32521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi4_32521/03_2026/7wi4_32521.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.13, per 1000 atoms: 0.42 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: 1.64 Conformation dependent library (CDL) restraints added in 1.3 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: 0.60 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: 3.49 Time building geometry restraints manager: 2.23 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: 10633 19.68 - 39.36: 1062 39.36 - 59.05: 390 59.05 - 78.73: 64 78.73 - 98.41: 19 Dihedral angle restraints: 12168 sinusoidal: 5160 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 12165 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: 0.01 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.810 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 18.321 98.410 7632 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 covalent geometry : bond 0.01245 (19572) covalent geometry : angle 1.08599 (26400) hydrogen bonds : bond 0.23927 ( 832) hydrogen bonds : angle 7.43359 ( 2457) metal coordination : bond 0.01387 ( 12) Misc. bond : bond 0.86074 ( 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 : 0.725 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: 0.1607 time to fit residues: 201.6786 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 : 0.652 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 484 HIS D 178 GLN D 363 ASN A D 363 ASN B D 407 GLN E 178 GLN E 329 GLN E 363 ASN A E 363 ASN B 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124707 restraints weight = 112325.216| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 6.59 r_work: 0.3263 rms_B_bonded: 5.91 restraints_weight: 2.0000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 186 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 246 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 19587 Z= 0.164 Angle : 0.721 9.009 26400 Z= 0.375 Chirality : 0.046 0.337 2958 Planarity : 0.005 0.070 3432 Dihedral : 15.879 99.983 3386 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 12.36 % Allowed : 23.59 % Favored : 64.05 % 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: -1.27 (0.17), residues: 2400 helix: -0.09 (0.14), residues: 1289 sheet: -0.70 (0.51), residues: 113 loop : -1.83 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 176 TYR 0.020 0.002 TYR E 413 PHE 0.022 0.002 PHE D 213 TRP 0.011 0.001 TRP D 507 HIS 0.006 0.001 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00349 (19572) covalent geometry : angle 0.72139 (26400) hydrogen bonds : bond 0.07025 ( 832) hydrogen bonds : angle 4.98491 ( 2457) metal coordination : bond 0.00325 ( 12) Misc. bond : bond 0.00243 ( 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 816 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 568 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8038 (m-30) cc_final: 0.7633 (m-30) REVERT: A 237 PHE cc_start: 0.7942 (m-10) cc_final: 0.7735 (m-80) REVERT: A 293 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7449 (p) REVERT: A 335 MET cc_start: 0.8051 (ttt) cc_final: 0.7751 (tmm) REVERT: A 367 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 382 MET cc_start: 0.7038 (pp-130) cc_final: 0.6500 (pp-130) REVERT: A 398 ARG cc_start: 0.8584 (ttt180) cc_final: 0.8203 (ttp80) REVERT: A 407 GLN cc_start: 0.8681 (mt0) cc_final: 0.8396 (mt0) REVERT: A 554 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: A 566 ASP cc_start: 0.8542 (m-30) cc_final: 0.8243 (m-30) REVERT: A 589 ILE cc_start: 0.8377 (mt) cc_final: 0.8164 (mm) REVERT: A 599 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8463 (ptp-170) REVERT: D 161 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8077 (mmmm) REVERT: D 237 PHE cc_start: 0.7882 (m-80) cc_final: 0.7353 (m-10) REVERT: D 323 ASP cc_start: 0.8075 (p0) cc_final: 0.7469 (p0) REVERT: D 327 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7907 (mtt180) REVERT: D 382 MET cc_start: 0.6780 (ttp) cc_final: 0.6479 (ttp) REVERT: D 397 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: D 443 LEU cc_start: 0.8927 (mm) cc_final: 0.8686 (mt) REVERT: D 451 GLU cc_start: 0.8269 (tt0) cc_final: 0.7767 (tm-30) REVERT: D 456 SER cc_start: 0.8871 (t) cc_final: 0.8573 (p) REVERT: D 483 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: D 494 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8224 (ttmm) REVERT: D 537 MET cc_start: 0.8646 (ptt) cc_final: 0.8419 (ptm) REVERT: D 539 ASP cc_start: 0.8279 (t0) cc_final: 0.7857 (t0) REVERT: D 543 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8121 (ttp-110) REVERT: D 554 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7628 (mm-30) REVERT: D 566 ASP cc_start: 0.8626 (m-30) cc_final: 0.8421 (m-30) REVERT: D 579 MET cc_start: 0.8938 (mmm) cc_final: 0.8582 (mtp) REVERT: D 585 ASP cc_start: 0.7372 (p0) cc_final: 0.7168 (p0) REVERT: D 591 ASP cc_start: 0.7723 (m-30) cc_final: 0.7422 (m-30) REVERT: D 604 TRP cc_start: 0.7502 (OUTLIER) cc_final: 0.6528 (t60) REVERT: E 142 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.5052 (pp) REVERT: E 161 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8289 (mtmm) REVERT: E 186 LYS cc_start: 0.5254 (OUTLIER) cc_final: 0.3925 (mptp) REVERT: E 238 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: E 242 LYS cc_start: 0.2875 (OUTLIER) cc_final: 0.2032 (tptp) REVERT: E 298 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7737 (m-40) REVERT: E 319 VAL cc_start: 0.7528 (t) cc_final: 0.7289 (m) REVERT: E 367 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: E 370 LEU cc_start: 0.8586 (mt) cc_final: 0.8274 (mp) REVERT: E 398 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8177 (mtp180) REVERT: E 439 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8479 (ptp-110) REVERT: E 491 ASN cc_start: 0.8264 (t0) cc_final: 0.7994 (t0) REVERT: E 512 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8753 (ttpp) REVERT: E 589 ILE cc_start: 0.8086 (mt) cc_final: 0.7843 (mm) REVERT: E 591 ASP cc_start: 0.7741 (m-30) cc_final: 0.7481 (m-30) REVERT: F 213 PHE cc_start: 0.4985 (OUTLIER) cc_final: 0.4320 (t80) REVERT: F 237 PHE cc_start: 0.7929 (m-10) cc_final: 0.7320 (m-10) REVERT: F 238 GLU cc_start: 0.8082 (tt0) cc_final: 0.7427 (tp30) REVERT: F 242 LYS cc_start: 0.5173 (OUTLIER) cc_final: 0.4024 (pptt) REVERT: F 281 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.3932 (pt0) REVERT: F 282 MET cc_start: 0.6265 (ptp) cc_final: 0.5868 (ptp) REVERT: F 292 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7636 (mp) REVERT: F 297 THR cc_start: 0.8603 (m) cc_final: 0.8394 (p) REVERT: F 398 ARG cc_start: 0.8338 (ttp-170) cc_final: 0.7808 (ttp80) REVERT: F 401 MET cc_start: 0.6976 (mtp) cc_final: 0.5879 (mtp) REVERT: F 407 GLN cc_start: 0.8689 (tt0) cc_final: 0.8397 (tt0) REVERT: F 408 LYS cc_start: 0.8730 (ptpt) cc_final: 0.8523 (ptpp) REVERT: F 433 LYS cc_start: 0.8679 (tttt) cc_final: 0.8389 (ttmt) REVERT: F 451 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: F 485 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8586 (m) REVERT: F 504 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8700 (t) REVERT: F 511 GLU cc_start: 0.8217 (mp0) cc_final: 0.7974 (mp0) REVERT: F 566 ASP cc_start: 0.8581 (m-30) cc_final: 0.8329 (m-30) REVERT: B 163 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7229 (mt-10) REVERT: B 233 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7492 (p) REVERT: B 236 MET cc_start: 0.7126 (mpt) cc_final: 0.6724 (mpt) REVERT: B 237 PHE cc_start: 0.7980 (m-80) cc_final: 0.7755 (m-80) REVERT: B 247 ILE cc_start: 0.2095 (OUTLIER) cc_final: 0.1491 (mp) REVERT: B 327 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7763 (mtt-85) REVERT: B 351 ARG cc_start: 0.8331 (ttp80) cc_final: 0.8107 (ttm-80) REVERT: B 367 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8022 (mm-30) REVERT: B 413 TYR cc_start: 0.8661 (m-80) cc_final: 0.8235 (m-80) REVERT: B 437 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8532 (pt) REVERT: B 455 ILE cc_start: 0.8270 (mm) cc_final: 0.7909 (mp) REVERT: B 543 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.8008 (ttp80) REVERT: B 547 GLN cc_start: 0.8169 (mt0) cc_final: 0.7946 (mt0) REVERT: B 582 GLU cc_start: 0.7932 (tp30) cc_final: 0.7592 (tm-30) REVERT: B 604 TRP cc_start: 0.7851 (OUTLIER) cc_final: 0.6689 (t60) REVERT: C 161 LYS cc_start: 0.8446 (ttmt) cc_final: 0.7619 (tptp) REVERT: C 236 MET cc_start: 0.8039 (mmt) cc_final: 0.7735 (mmt) REVERT: C 247 ILE cc_start: -0.1840 (OUTLIER) cc_final: -0.2042 (mp) REVERT: C 252 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6455 (mp10) REVERT: C 319 VAL cc_start: 0.7598 (t) cc_final: 0.7319 (m) REVERT: C 324 VAL cc_start: 0.8317 (p) cc_final: 0.8087 (t) REVERT: C 329 GLN cc_start: 0.8712 (tp40) cc_final: 0.8133 (mm-40) REVERT: C 357 SER cc_start: 0.7629 (m) cc_final: 0.7276 (p) REVERT: C 370 LEU cc_start: 0.8540 (mt) cc_final: 0.8292 (mp) REVERT: C 385 PHE cc_start: 0.7926 (m-10) cc_final: 0.7582 (m-80) REVERT: C 390 ASP cc_start: 0.7899 (m-30) cc_final: 0.7592 (m-30) REVERT: C 397 GLU cc_start: 0.7910 (pm20) cc_final: 0.7324 (pm20) REVERT: C 398 ARG cc_start: 0.8184 (mtp180) cc_final: 0.7921 (mtm110) REVERT: C 433 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8486 (ttpp) REVERT: C 491 ASN cc_start: 0.8702 (t0) cc_final: 0.8415 (t0) REVERT: C 543 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7237 (ttp80) REVERT: C 547 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: C 562 GLN cc_start: 0.8763 (tp40) cc_final: 0.7967 (tp-100) REVERT: C 566 ASP cc_start: 0.8646 (m-30) cc_final: 0.7866 (m-30) outliers start: 248 outliers final: 154 residues processed: 750 average time/residue: 0.1512 time to fit residues: 164.3420 Evaluate side-chains 727 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 544 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 565 THR 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 292 ILE Chi-restraints excluded: chain D residue 293 VAL 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 410 SER 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 485 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 SER 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 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 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 398 ARG Chi-restraints excluded: chain E residue 418 HIS 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 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 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 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 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 504 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR 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 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 464 SER 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 247 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 167 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 chunk 147 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 562 GLN E 329 GLN E 414 HIS F 562 GLN F 588 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126619 restraints weight = 104026.825| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 5.64 r_work: 0.3319 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 246 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 260 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.714 19587 Z= 0.223 Angle : 0.662 8.670 26400 Z= 0.339 Chirality : 0.044 0.240 2958 Planarity : 0.005 0.070 3432 Dihedral : 13.687 91.074 3193 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.04 % Favored : 94.92 % Rotamer: Outliers : 10.19 % Allowed : 25.32 % Favored : 64.49 % 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: -0.86 (0.17), residues: 2400 helix: 0.29 (0.14), residues: 1301 sheet: -0.64 (0.52), residues: 113 loop : -1.69 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 325 TYR 0.015 0.002 TYR D 557 PHE 0.024 0.001 PHE B 313 TRP 0.011 0.001 TRP D 507 HIS 0.005 0.001 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00314 (19572) covalent geometry : angle 0.66232 (26400) hydrogen bonds : bond 0.05928 ( 832) hydrogen bonds : angle 4.61636 ( 2457) metal coordination : bond 0.20628 ( 12) Misc. bond : bond 0.00133 ( 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: 204 poor density : 555 time to evaluate : 0.647 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: 0.6618 (tpp) cc_final: 0.6359 (tpp) REVERT: A 153 ASP cc_start: 0.7999 (m-30) cc_final: 0.7605 (m-30) REVERT: A 275 LEU cc_start: 0.3420 (OUTLIER) cc_final: 0.3172 (pp) REVERT: A 293 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7389 (p) REVERT: A 367 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 382 MET cc_start: 0.6940 (pp-130) cc_final: 0.6452 (pp-130) REVERT: A 398 ARG cc_start: 0.8436 (ttt180) cc_final: 0.8086 (ttp80) REVERT: A 407 GLN cc_start: 0.8651 (mt0) cc_final: 0.8299 (mt0) REVERT: A 547 GLN cc_start: 0.7892 (mt0) cc_final: 0.7683 (mt0) REVERT: A 554 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: A 562 GLN cc_start: 0.8285 (tp40) cc_final: 0.8011 (tp40) REVERT: A 566 ASP cc_start: 0.8384 (m-30) cc_final: 0.8131 (m-30) REVERT: A 589 ILE cc_start: 0.8345 (mt) cc_final: 0.8121 (mm) REVERT: D 237 PHE cc_start: 0.7817 (m-80) cc_final: 0.7412 (m-10) REVERT: D 323 ASP cc_start: 0.8040 (p0) cc_final: 0.7568 (p0) REVERT: D 327 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7827 (mtt180) REVERT: D 382 MET cc_start: 0.6651 (ttp) cc_final: 0.6374 (ttp) REVERT: D 397 GLU cc_start: 0.7616 (mp0) cc_final: 0.7315 (mp0) REVERT: D 408 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8489 (mtpp) REVERT: D 443 LEU cc_start: 0.8944 (mm) cc_final: 0.8692 (mt) REVERT: D 451 GLU cc_start: 0.8201 (tt0) cc_final: 0.7772 (tm-30) REVERT: D 537 MET cc_start: 0.8599 (ptt) cc_final: 0.8363 (ptm) REVERT: D 539 ASP cc_start: 0.8197 (t0) cc_final: 0.7733 (t0) REVERT: D 543 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7951 (ttp-110) REVERT: D 554 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7659 (mm-30) REVERT: D 562 GLN cc_start: 0.8707 (tp40) cc_final: 0.8475 (tp-100) REVERT: D 566 ASP cc_start: 0.8241 (m-30) cc_final: 0.8039 (m-30) REVERT: D 579 MET cc_start: 0.8722 (mmm) cc_final: 0.8337 (mtp) REVERT: D 591 ASP cc_start: 0.7685 (m-30) cc_final: 0.7423 (m-30) REVERT: D 604 TRP cc_start: 0.7429 (OUTLIER) cc_final: 0.6374 (t60) REVERT: E 142 LEU cc_start: 0.5117 (OUTLIER) cc_final: 0.4835 (pp) REVERT: E 161 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8268 (mtmm) REVERT: E 186 LYS cc_start: 0.5212 (OUTLIER) cc_final: 0.4056 (mptp) REVERT: E 203 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7118 (tptp) REVERT: E 242 LYS cc_start: 0.3115 (OUTLIER) cc_final: 0.2266 (tptp) REVERT: E 319 VAL cc_start: 0.7724 (t) cc_final: 0.7405 (m) REVERT: E 329 GLN cc_start: 0.8516 (mm110) cc_final: 0.8207 (mm-40) REVERT: E 330 ILE cc_start: 0.8869 (mt) cc_final: 0.8579 (mp) REVERT: E 331 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8394 (mp) REVERT: E 367 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: E 370 LEU cc_start: 0.8497 (mt) cc_final: 0.8220 (mp) REVERT: E 377 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.6180 (mmtm) REVERT: E 409 GLU cc_start: 0.8502 (tt0) cc_final: 0.8284 (mt-10) REVERT: E 491 ASN cc_start: 0.8109 (t0) cc_final: 0.7810 (t0) REVERT: E 562 GLN cc_start: 0.8838 (tp40) cc_final: 0.8099 (tp-100) REVERT: E 591 ASP cc_start: 0.7680 (m-30) cc_final: 0.7426 (m-30) REVERT: F 161 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8192 (mttp) REVERT: F 190 MET cc_start: 0.6431 (mtm) cc_final: 0.6081 (ptp) REVERT: F 237 PHE cc_start: 0.7789 (m-10) cc_final: 0.7193 (m-10) REVERT: F 238 GLU cc_start: 0.7959 (tt0) cc_final: 0.7260 (tm-30) REVERT: F 281 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.4911 (pt0) REVERT: F 292 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7467 (mp) REVERT: F 293 VAL cc_start: 0.7944 (m) cc_final: 0.7546 (p) REVERT: F 332 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8533 (mtmm) REVERT: F 366 ASN cc_start: 0.8662 (t0) cc_final: 0.8414 (t0) REVERT: F 398 ARG cc_start: 0.8276 (ttp-170) cc_final: 0.7818 (ttp80) REVERT: F 407 GLN cc_start: 0.8649 (tt0) cc_final: 0.8363 (tt0) REVERT: F 433 LYS cc_start: 0.8607 (tttt) cc_final: 0.8341 (ttmt) REVERT: F 451 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: F 485 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8583 (m) REVERT: F 511 GLU cc_start: 0.8173 (mp0) cc_final: 0.7952 (mp0) REVERT: F 562 GLN cc_start: 0.8565 (tp40) cc_final: 0.8240 (tp-100) REVERT: F 590 ASP cc_start: 0.8391 (t0) cc_final: 0.8064 (t0) REVERT: F 604 TRP cc_start: 0.7137 (OUTLIER) cc_final: 0.6765 (t60) REVERT: B 233 VAL cc_start: 0.7918 (m) cc_final: 0.7323 (p) REVERT: B 236 MET cc_start: 0.7022 (mpt) cc_final: 0.6437 (mpt) REVERT: B 237 PHE cc_start: 0.7924 (m-80) cc_final: 0.7607 (m-80) REVERT: B 238 GLU cc_start: 0.8169 (tp30) cc_final: 0.7671 (pp20) REVERT: B 247 ILE cc_start: 0.1654 (OUTLIER) cc_final: 0.0933 (mp) REVERT: B 351 ARG cc_start: 0.8298 (ttp80) cc_final: 0.8097 (ttm-80) REVERT: B 367 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 413 TYR cc_start: 0.8673 (m-80) cc_final: 0.8217 (m-80) REVERT: B 437 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8358 (pt) REVERT: B 455 ILE cc_start: 0.8305 (mm) cc_final: 0.7941 (mp) REVERT: B 547 GLN cc_start: 0.7950 (mt0) cc_final: 0.7727 (mt0) REVERT: B 579 MET cc_start: 0.8649 (mmm) cc_final: 0.8325 (mmt) REVERT: B 582 GLU cc_start: 0.7701 (tp30) cc_final: 0.7491 (tm-30) REVERT: B 604 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.6627 (t60) REVERT: C 200 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6813 (mm) REVERT: C 203 LYS cc_start: 0.6442 (tmmt) cc_final: 0.6139 (tmmt) REVERT: C 237 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.5655 (t80) REVERT: C 319 VAL cc_start: 0.7800 (t) cc_final: 0.7577 (m) REVERT: C 324 VAL cc_start: 0.8295 (p) cc_final: 0.8017 (t) REVERT: C 329 GLN cc_start: 0.8692 (tp40) cc_final: 0.8146 (mm-40) REVERT: C 367 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: C 370 LEU cc_start: 0.8473 (mt) cc_final: 0.8191 (mm) REVERT: C 390 ASP cc_start: 0.7824 (m-30) cc_final: 0.7549 (m-30) REVERT: C 397 GLU cc_start: 0.7847 (pm20) cc_final: 0.7224 (pm20) REVERT: C 398 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7784 (mtm110) REVERT: C 433 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8494 (ttpp) REVERT: C 491 ASN cc_start: 0.8535 (t0) cc_final: 0.8188 (t0) REVERT: C 547 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7040 (mt0) REVERT: C 562 GLN cc_start: 0.8645 (tp40) cc_final: 0.7840 (tp-100) REVERT: C 566 ASP cc_start: 0.8705 (m-30) cc_final: 0.7975 (m-30) outliers start: 204 outliers final: 146 residues processed: 700 average time/residue: 0.1482 time to fit residues: 149.1503 Evaluate side-chains 710 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 541 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 294 ILE 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 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 294 ILE Chi-restraints excluded: chain D residue 317 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 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 563 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 203 LYS 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 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 397 GLU 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 468 THR 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 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 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 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 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 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 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS 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 565 THR 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 200 LEU Chi-restraints excluded: chain C residue 237 PHE 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 367 GLU 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 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 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: 4.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.0980 chunk 224 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS D 407 GLN D 418 HIS F 588 GLN B 178 GLN C 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.156516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124589 restraints weight = 120569.751| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 6.62 r_work: 0.3238 rms_B_bonded: 5.81 restraints_weight: 2.0000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 260 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 262 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.545 19587 Z= 0.243 Angle : 0.696 10.464 26400 Z= 0.358 Chirality : 0.045 0.207 2958 Planarity : 0.005 0.075 3432 Dihedral : 12.802 84.528 3123 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 10.63 % Allowed : 26.06 % Favored : 63.30 % 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: -0.86 (0.17), residues: 2400 helix: 0.30 (0.14), residues: 1302 sheet: -0.86 (0.50), residues: 113 loop : -1.69 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 596 TYR 0.020 0.002 TYR D 557 PHE 0.038 0.002 PHE A 237 TRP 0.013 0.002 TRP B 507 HIS 0.007 0.001 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00459 (19572) covalent geometry : angle 0.69588 (26400) hydrogen bonds : bond 0.06609 ( 832) hydrogen bonds : angle 4.67126 ( 2457) metal coordination : bond 0.15803 ( 12) Misc. bond : bond 0.00021 ( 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 767 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 554 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8042 (m-30) cc_final: 0.7641 (m-30) REVERT: A 234 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7376 (mtt180) REVERT: A 236 MET cc_start: 0.7674 (mpt) cc_final: 0.7126 (mmt) REVERT: A 237 PHE cc_start: 0.7738 (m-80) cc_final: 0.7531 (m-80) REVERT: A 275 LEU cc_start: 0.3759 (OUTLIER) cc_final: 0.3530 (pp) REVERT: A 293 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7461 (p) REVERT: A 382 MET cc_start: 0.6956 (pp-130) cc_final: 0.6498 (pp-130) REVERT: A 398 ARG cc_start: 0.8515 (ttt180) cc_final: 0.8179 (ttp80) REVERT: A 407 GLN cc_start: 0.8750 (mt0) cc_final: 0.8406 (mt0) REVERT: A 491 ASN cc_start: 0.7682 (t0) cc_final: 0.7328 (t0) REVERT: A 539 ASP cc_start: 0.7938 (t70) cc_final: 0.7532 (t0) REVERT: A 554 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 562 GLN cc_start: 0.8516 (tp40) cc_final: 0.8191 (tp40) REVERT: A 588 GLN cc_start: 0.8231 (mt0) cc_final: 0.7934 (mt0) REVERT: A 589 ILE cc_start: 0.8263 (mt) cc_final: 0.8005 (mm) REVERT: D 237 PHE cc_start: 0.7846 (m-80) cc_final: 0.7487 (m-10) REVERT: D 323 ASP cc_start: 0.8127 (p0) cc_final: 0.7646 (p0) REVERT: D 327 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7772 (mtp85) REVERT: D 382 MET cc_start: 0.6803 (ttp) cc_final: 0.6523 (ttp) REVERT: D 451 GLU cc_start: 0.8188 (tt0) cc_final: 0.7741 (tm-30) REVERT: D 537 MET cc_start: 0.8650 (ptt) cc_final: 0.8424 (ptm) REVERT: D 539 ASP cc_start: 0.8353 (t0) cc_final: 0.7952 (t0) REVERT: D 554 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7868 (mm-30) REVERT: D 591 ASP cc_start: 0.7750 (m-30) cc_final: 0.7439 (m-30) REVERT: D 595 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8150 (mpt90) REVERT: D 604 TRP cc_start: 0.7525 (OUTLIER) cc_final: 0.6470 (t60) REVERT: E 142 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.5127 (pp) REVERT: E 186 LYS cc_start: 0.5392 (OUTLIER) cc_final: 0.4188 (mptp) REVERT: E 242 LYS cc_start: 0.3230 (OUTLIER) cc_final: 0.2285 (tptp) REVERT: E 319 VAL cc_start: 0.7827 (t) cc_final: 0.7465 (m) REVERT: E 331 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8560 (mp) REVERT: E 367 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: E 377 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6064 (mmtm) REVERT: E 491 ASN cc_start: 0.8336 (t0) cc_final: 0.7988 (t0) REVERT: E 562 GLN cc_start: 0.8885 (tp40) cc_final: 0.8080 (tp-100) REVERT: E 591 ASP cc_start: 0.7793 (m-30) cc_final: 0.7550 (m-30) REVERT: F 161 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8224 (mttp) REVERT: F 237 PHE cc_start: 0.7829 (m-10) cc_final: 0.7432 (m-10) REVERT: F 238 GLU cc_start: 0.8033 (tt0) cc_final: 0.7299 (tm-30) REVERT: F 281 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.5066 (pt0) REVERT: F 293 VAL cc_start: 0.8080 (m) cc_final: 0.7728 (p) REVERT: F 331 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8544 (mm) REVERT: F 332 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8475 (mtmm) REVERT: F 398 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.7953 (ttp80) REVERT: F 407 GLN cc_start: 0.8700 (tt0) cc_final: 0.8442 (tt0) REVERT: F 433 LYS cc_start: 0.8660 (tttt) cc_final: 0.8403 (ttmt) REVERT: F 485 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8591 (m) REVERT: F 511 GLU cc_start: 0.8265 (mp0) cc_final: 0.8010 (mp0) REVERT: F 590 ASP cc_start: 0.8458 (t0) cc_final: 0.8232 (t0) REVERT: F 604 TRP cc_start: 0.7195 (OUTLIER) cc_final: 0.6875 (t60) REVERT: B 186 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6329 (pttt) REVERT: B 233 VAL cc_start: 0.8059 (m) cc_final: 0.7370 (p) REVERT: B 236 MET cc_start: 0.7001 (mpt) cc_final: 0.6323 (mpt) REVERT: B 237 PHE cc_start: 0.8034 (m-80) cc_final: 0.7767 (m-80) REVERT: B 238 GLU cc_start: 0.8233 (tp30) cc_final: 0.7962 (tp30) REVERT: B 247 ILE cc_start: 0.1733 (OUTLIER) cc_final: 0.1081 (mp) REVERT: B 367 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8051 (mm-30) REVERT: B 394 MET cc_start: 0.7279 (ptp) cc_final: 0.6747 (ptp) REVERT: B 413 TYR cc_start: 0.8682 (m-80) cc_final: 0.8215 (m-80) REVERT: B 437 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8448 (pt) REVERT: B 455 ILE cc_start: 0.8341 (mm) cc_final: 0.8011 (mp) REVERT: B 547 GLN cc_start: 0.8031 (mt0) cc_final: 0.7802 (mt0) REVERT: B 562 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7531 (tm-30) REVERT: B 579 MET cc_start: 0.8694 (mmm) cc_final: 0.8389 (mmt) REVERT: B 582 GLU cc_start: 0.7915 (tp30) cc_final: 0.7630 (tm-30) REVERT: B 599 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8201 (pmm-80) REVERT: B 604 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.6677 (t60) REVERT: C 161 LYS cc_start: 0.8468 (ttpt) cc_final: 0.7796 (tptp) REVERT: C 200 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6879 (mm) REVERT: C 203 LYS cc_start: 0.6678 (tmmt) cc_final: 0.6386 (tmmt) REVERT: C 236 MET cc_start: 0.7703 (tpp) cc_final: 0.7448 (tpp) REVERT: C 247 ILE cc_start: -0.1122 (OUTLIER) cc_final: -0.1325 (mp) REVERT: C 319 VAL cc_start: 0.7755 (t) cc_final: 0.7466 (m) REVERT: C 324 VAL cc_start: 0.8301 (p) cc_final: 0.8000 (t) REVERT: C 327 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7896 (mtt-85) REVERT: C 329 GLN cc_start: 0.8744 (tp40) cc_final: 0.8197 (mm-40) REVERT: C 367 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8276 (mm-30) REVERT: C 370 LEU cc_start: 0.8527 (mt) cc_final: 0.8279 (mp) REVERT: C 390 ASP cc_start: 0.7871 (m-30) cc_final: 0.7626 (m-30) REVERT: C 397 GLU cc_start: 0.7992 (pm20) cc_final: 0.7298 (pm20) REVERT: C 398 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7876 (mtm110) REVERT: C 433 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8560 (ttpp) REVERT: C 491 ASN cc_start: 0.8671 (t0) cc_final: 0.8356 (t0) REVERT: C 512 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8485 (ttpp) REVERT: C 543 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7695 (ttp80) REVERT: C 547 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: C 562 GLN cc_start: 0.8845 (tp40) cc_final: 0.8076 (tp-100) REVERT: C 566 ASP cc_start: 0.8705 (m-30) cc_final: 0.8002 (m-30) outliers start: 213 outliers final: 157 residues processed: 697 average time/residue: 0.1476 time to fit residues: 148.6959 Evaluate side-chains 722 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 540 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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 420 ILE 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 563 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 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 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 387 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 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 511 GLU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 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 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 389 LYS Chi-restraints excluded: chain E residue 390 ASP 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 559 ARG 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 294 ILE 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 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 421 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 503 MET Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 538 SER 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 200 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 ILE 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 275 LEU Chi-restraints excluded: chain B residue 314 ASP 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 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 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 565 THR Chi-restraints excluded: chain B residue 578 LEU 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 200 LEU 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 293 VAL 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 394 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 512 LYS Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 578 LEU 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: 6.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 233 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 418 HIS D 562 GLN F 178 GLN F 562 GLN F 588 GLN B 562 GLN B 567 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.158581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123626 restraints weight = 102744.454| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 6.08 r_work: 0.3258 rms_B_bonded: 5.96 restraints_weight: 2.0000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 262 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 270 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.432 19587 Z= 0.171 Angle : 0.650 8.578 26400 Z= 0.334 Chirality : 0.043 0.218 2958 Planarity : 0.005 0.072 3432 Dihedral : 12.289 84.123 3103 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 9.89 % Allowed : 26.71 % Favored : 63.40 % 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: -0.57 (0.17), residues: 2400 helix: 0.53 (0.15), residues: 1306 sheet: -0.90 (0.50), residues: 113 loop : -1.53 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 399 TYR 0.015 0.001 TYR D 557 PHE 0.024 0.001 PHE D 213 TRP 0.011 0.001 TRP D 507 HIS 0.006 0.001 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00304 (19572) covalent geometry : angle 0.64955 (26400) hydrogen bonds : bond 0.05594 ( 832) hydrogen bonds : angle 4.47033 ( 2457) metal coordination : bond 0.12491 ( 12) Misc. bond : bond 0.00025 ( 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 725 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 527 time to evaluate : 0.462 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: 0.6915 (tpp) cc_final: 0.6525 (tpp) REVERT: A 144 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7445 (pp20) REVERT: A 236 MET cc_start: 0.7545 (mpt) cc_final: 0.7337 (mmt) REVERT: A 237 PHE cc_start: 0.7663 (m-80) cc_final: 0.7352 (m-80) REVERT: A 293 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7305 (p) REVERT: A 335 MET cc_start: 0.8336 (tpp) cc_final: 0.8098 (tpp) REVERT: A 382 MET cc_start: 0.7019 (pp-130) cc_final: 0.6522 (pp-130) REVERT: A 398 ARG cc_start: 0.8525 (ttt180) cc_final: 0.8151 (ttp80) REVERT: A 407 GLN cc_start: 0.8781 (mt0) cc_final: 0.8434 (mt0) REVERT: A 554 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 562 GLN cc_start: 0.8229 (tp40) cc_final: 0.8016 (tp40) REVERT: A 589 ILE cc_start: 0.8192 (mt) cc_final: 0.7932 (mm) REVERT: D 190 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.5141 (mmt) REVERT: D 237 PHE cc_start: 0.7782 (m-80) cc_final: 0.7431 (m-10) REVERT: D 323 ASP cc_start: 0.8006 (p0) cc_final: 0.7472 (p0) REVERT: D 327 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7853 (mtt180) REVERT: D 382 MET cc_start: 0.6830 (ttp) cc_final: 0.6529 (ttp) REVERT: D 408 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8552 (mtpp) REVERT: D 451 GLU cc_start: 0.8237 (tt0) cc_final: 0.7740 (tm-30) REVERT: D 470 TYR cc_start: 0.9045 (m-80) cc_final: 0.8805 (m-80) REVERT: D 537 MET cc_start: 0.8666 (ptt) cc_final: 0.8422 (ptm) REVERT: D 539 ASP cc_start: 0.8294 (t0) cc_final: 0.7874 (t0) REVERT: D 543 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8035 (ttp-170) REVERT: D 554 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7664 (mm-30) REVERT: D 566 ASP cc_start: 0.8192 (m-30) cc_final: 0.7974 (m-30) REVERT: D 591 ASP cc_start: 0.7753 (m-30) cc_final: 0.7348 (m-30) REVERT: D 595 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8155 (mpt90) REVERT: D 604 TRP cc_start: 0.7463 (OUTLIER) cc_final: 0.6431 (t60) REVERT: E 142 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.5140 (pp) REVERT: E 161 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8248 (mtmm) REVERT: E 186 LYS cc_start: 0.5006 (OUTLIER) cc_final: 0.3923 (mptp) REVERT: E 242 LYS cc_start: 0.3182 (OUTLIER) cc_final: 0.2291 (tptp) REVERT: E 367 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: E 377 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6056 (mmtm) REVERT: E 491 ASN cc_start: 0.8268 (t0) cc_final: 0.7902 (t0) REVERT: E 537 MET cc_start: 0.8770 (ptt) cc_final: 0.8470 (ptm) REVERT: E 562 GLN cc_start: 0.8786 (tp40) cc_final: 0.7951 (tp-100) REVERT: E 566 ASP cc_start: 0.8309 (m-30) cc_final: 0.7416 (m-30) REVERT: E 591 ASP cc_start: 0.7921 (m-30) cc_final: 0.7660 (m-30) REVERT: F 161 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8178 (mttp) REVERT: F 190 MET cc_start: 0.6502 (mtm) cc_final: 0.6288 (ptp) REVERT: F 237 PHE cc_start: 0.7985 (m-10) cc_final: 0.7367 (m-10) REVERT: F 238 GLU cc_start: 0.8146 (tt0) cc_final: 0.7398 (tp30) REVERT: F 281 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5137 (pt0) REVERT: F 293 VAL cc_start: 0.8004 (m) cc_final: 0.7696 (p) REVERT: F 331 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8517 (mm) REVERT: F 332 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8507 (mtmm) REVERT: F 398 ARG cc_start: 0.8392 (ttp-170) cc_final: 0.7913 (ttp80) REVERT: F 433 LYS cc_start: 0.8710 (tttt) cc_final: 0.8413 (ttmt) REVERT: F 451 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: F 485 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8555 (m) REVERT: F 511 GLU cc_start: 0.8243 (mp0) cc_final: 0.7975 (mp0) REVERT: F 604 TRP cc_start: 0.7117 (OUTLIER) cc_final: 0.6883 (t60) REVERT: B 233 VAL cc_start: 0.8050 (m) cc_final: 0.7353 (p) REVERT: B 236 MET cc_start: 0.7112 (mpt) cc_final: 0.6462 (mpt) REVERT: B 237 PHE cc_start: 0.8046 (m-80) cc_final: 0.7724 (m-80) REVERT: B 238 GLU cc_start: 0.8187 (tp30) cc_final: 0.7882 (pp20) REVERT: B 247 ILE cc_start: 0.1786 (OUTLIER) cc_final: 0.1164 (mp) REVERT: B 329 GLN cc_start: 0.8315 (tp40) cc_final: 0.8029 (mp10) REVERT: B 367 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7986 (mm-30) REVERT: B 394 MET cc_start: 0.7202 (ptp) cc_final: 0.6842 (ptm) REVERT: B 407 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: B 413 TYR cc_start: 0.8586 (m-80) cc_final: 0.8071 (m-80) REVERT: B 437 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8373 (pt) REVERT: B 455 ILE cc_start: 0.8315 (mm) cc_final: 0.8041 (mp) REVERT: B 547 GLN cc_start: 0.8025 (mt0) cc_final: 0.7758 (mt0) REVERT: B 562 GLN cc_start: 0.8214 (tp40) cc_final: 0.7408 (tm-30) REVERT: B 579 MET cc_start: 0.8596 (mmm) cc_final: 0.8320 (mmt) REVERT: B 582 GLU cc_start: 0.7920 (tp30) cc_final: 0.7542 (tm-30) REVERT: B 604 TRP cc_start: 0.7804 (OUTLIER) cc_final: 0.6511 (t60) REVERT: C 161 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7578 (tptp) REVERT: C 200 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6864 (mm) REVERT: C 203 LYS cc_start: 0.6592 (tmmt) cc_final: 0.6327 (tmmt) REVERT: C 216 ILE cc_start: 0.8019 (mm) cc_final: 0.7666 (mm) REVERT: C 236 MET cc_start: 0.7153 (tpp) cc_final: 0.6879 (tpp) REVERT: C 247 ILE cc_start: -0.1518 (OUTLIER) cc_final: -0.2343 (mm) REVERT: C 319 VAL cc_start: 0.7443 (t) cc_final: 0.7185 (m) REVERT: C 327 ARG cc_start: 0.8024 (mtt-85) cc_final: 0.7788 (mtt-85) REVERT: C 329 GLN cc_start: 0.8667 (tp40) cc_final: 0.8086 (mm-40) REVERT: C 367 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: C 370 LEU cc_start: 0.8455 (mt) cc_final: 0.8182 (mp) REVERT: C 390 ASP cc_start: 0.7928 (m-30) cc_final: 0.7673 (m-30) REVERT: C 397 GLU cc_start: 0.7964 (pm20) cc_final: 0.7333 (pm20) REVERT: C 398 ARG cc_start: 0.8275 (mtp180) cc_final: 0.8027 (mtm110) REVERT: C 433 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8525 (ttpp) REVERT: C 547 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7416 (mt0) REVERT: C 562 GLN cc_start: 0.8742 (tp40) cc_final: 0.7978 (tp-100) REVERT: C 566 ASP cc_start: 0.8781 (m-30) cc_final: 0.8069 (m-30) outliers start: 198 outliers final: 144 residues processed: 666 average time/residue: 0.1521 time to fit residues: 145.7999 Evaluate side-chains 706 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 538 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 365 VAL 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 420 ILE Chi-restraints excluded: chain A residue 421 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 563 LEU Chi-restraints excluded: chain A residue 565 THR 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 298 ASN 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 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 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 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 335 MET Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS 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 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 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 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 403 MET 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 437 ILE 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 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 200 LEU Chi-restraints excluded: chain B residue 215 THR 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 325 ARG 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 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 407 GLN 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 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 200 LEU 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 394 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 547 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 244 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 19 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 418 HIS D 562 GLN F 407 GLN F 562 GLN F 588 GLN B 567 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122914 restraints weight = 113684.950| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 6.71 r_work: 0.3237 rms_B_bonded: 6.23 restraints_weight: 2.0000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 270 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 275 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.615 19587 Z= 0.213 Angle : 0.646 8.866 26400 Z= 0.332 Chirality : 0.043 0.240 2958 Planarity : 0.004 0.072 3432 Dihedral : 11.814 82.818 3084 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 9.05 % Allowed : 26.85 % Favored : 64.09 % 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: -0.49 (0.17), residues: 2400 helix: 0.62 (0.15), residues: 1306 sheet: -0.88 (0.50), residues: 113 loop : -1.54 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 172 TYR 0.017 0.002 TYR D 557 PHE 0.022 0.001 PHE D 213 TRP 0.011 0.002 TRP D 507 HIS 0.006 0.001 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00347 (19572) covalent geometry : angle 0.64552 (26400) hydrogen bonds : bond 0.05623 ( 832) hydrogen bonds : angle 4.44908 ( 2457) metal coordination : bond 0.17755 ( 12) Misc. bond : bond 0.00038 ( 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 722 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 541 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.6910 (tpp) cc_final: 0.6577 (tpp) REVERT: A 144 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7473 (pp20) REVERT: A 236 MET cc_start: 0.7558 (mpt) cc_final: 0.7099 (mmt) REVERT: A 237 PHE cc_start: 0.7853 (m-80) cc_final: 0.7419 (m-80) REVERT: A 382 MET cc_start: 0.7028 (pp-130) cc_final: 0.6504 (pp-130) REVERT: A 398 ARG cc_start: 0.8543 (ttt180) cc_final: 0.8174 (ttp80) REVERT: A 407 GLN cc_start: 0.8774 (mt0) cc_final: 0.8400 (mt0) REVERT: A 491 ASN cc_start: 0.7648 (t0) cc_final: 0.7335 (t0) REVERT: A 539 ASP cc_start: 0.7894 (t70) cc_final: 0.7508 (t0) REVERT: A 554 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: A 589 ILE cc_start: 0.8202 (mt) cc_final: 0.7941 (mm) REVERT: D 190 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6021 (mmt) REVERT: D 237 PHE cc_start: 0.7812 (m-80) cc_final: 0.7479 (m-10) REVERT: D 282 MET cc_start: 0.6328 (mmt) cc_final: 0.5930 (mmt) REVERT: D 323 ASP cc_start: 0.8036 (p0) cc_final: 0.7530 (p0) REVERT: D 327 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7744 (mtt180) REVERT: D 382 MET cc_start: 0.6822 (ttp) cc_final: 0.6523 (ttp) REVERT: D 397 GLU cc_start: 0.7970 (mp0) cc_final: 0.7769 (mp0) REVERT: D 408 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8578 (mtpp) REVERT: D 451 GLU cc_start: 0.8236 (tt0) cc_final: 0.7737 (tm-30) REVERT: D 462 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7830 (mp) REVERT: D 470 TYR cc_start: 0.9097 (m-80) cc_final: 0.8878 (m-80) REVERT: D 537 MET cc_start: 0.8708 (ptt) cc_final: 0.8450 (ptm) REVERT: D 539 ASP cc_start: 0.8372 (t0) cc_final: 0.8030 (t0) REVERT: D 543 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7785 (ttp-170) REVERT: D 547 GLN cc_start: 0.7865 (mt0) cc_final: 0.7613 (mt0) REVERT: D 554 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7733 (mm-30) REVERT: D 595 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8117 (mpt90) REVERT: D 604 TRP cc_start: 0.7498 (OUTLIER) cc_final: 0.6429 (t60) REVERT: E 142 LEU cc_start: 0.5436 (OUTLIER) cc_final: 0.5221 (pp) REVERT: E 161 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8214 (mtmm) REVERT: E 186 LYS cc_start: 0.4959 (OUTLIER) cc_final: 0.3969 (mptp) REVERT: E 190 MET cc_start: 0.7070 (mtm) cc_final: 0.6760 (mtm) REVERT: E 242 LYS cc_start: 0.3218 (OUTLIER) cc_final: 0.2288 (tptp) REVERT: E 331 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8529 (mp) REVERT: E 366 ASN cc_start: 0.8854 (t0) cc_final: 0.8597 (t0) REVERT: E 367 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8021 (mm-30) REVERT: E 377 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.5556 (mptt) REVERT: E 398 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.8031 (mtm110) REVERT: E 491 ASN cc_start: 0.8285 (t0) cc_final: 0.7917 (t0) REVERT: E 537 MET cc_start: 0.8795 (ptt) cc_final: 0.8499 (ptm) REVERT: E 562 GLN cc_start: 0.8748 (tp40) cc_final: 0.7892 (tp-100) REVERT: E 591 ASP cc_start: 0.7950 (m-30) cc_final: 0.7684 (m-30) REVERT: F 161 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8196 (mttp) REVERT: F 237 PHE cc_start: 0.7976 (m-10) cc_final: 0.7445 (m-10) REVERT: F 238 GLU cc_start: 0.8072 (tt0) cc_final: 0.7225 (tm-30) REVERT: F 281 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.4935 (pt0) REVERT: F 293 VAL cc_start: 0.8062 (m) cc_final: 0.7769 (p) REVERT: F 327 ARG cc_start: 0.8300 (mtt180) cc_final: 0.8017 (mtp180) REVERT: F 331 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8581 (mm) REVERT: F 332 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8511 (mtmm) REVERT: F 398 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.7948 (ttp80) REVERT: F 407 GLN cc_start: 0.8646 (tt0) cc_final: 0.8403 (tt0) REVERT: F 433 LYS cc_start: 0.8710 (tttt) cc_final: 0.8421 (ttmt) REVERT: F 511 GLU cc_start: 0.8253 (mp0) cc_final: 0.8011 (mp0) REVERT: F 559 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8262 (ttt180) REVERT: F 590 ASP cc_start: 0.8419 (t0) cc_final: 0.8204 (t0) REVERT: F 604 TRP cc_start: 0.7157 (OUTLIER) cc_final: 0.6954 (t60) REVERT: B 233 VAL cc_start: 0.7988 (m) cc_final: 0.7234 (p) REVERT: B 236 MET cc_start: 0.6969 (mpt) cc_final: 0.6328 (mpt) REVERT: B 237 PHE cc_start: 0.8110 (m-80) cc_final: 0.7784 (m-80) REVERT: B 238 GLU cc_start: 0.8213 (tp30) cc_final: 0.7896 (pp20) REVERT: B 247 ILE cc_start: 0.1709 (OUTLIER) cc_final: 0.1127 (mp) REVERT: B 329 GLN cc_start: 0.8325 (tp40) cc_final: 0.8042 (mp10) REVERT: B 367 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7867 (mm-30) REVERT: B 394 MET cc_start: 0.7221 (ptp) cc_final: 0.6804 (ptm) REVERT: B 407 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8481 (mt0) REVERT: B 413 TYR cc_start: 0.8576 (m-80) cc_final: 0.8010 (m-80) REVERT: B 437 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8450 (pt) REVERT: B 547 GLN cc_start: 0.8038 (mt0) cc_final: 0.7768 (mt0) REVERT: B 562 GLN cc_start: 0.8236 (tp40) cc_final: 0.7506 (tm-30) REVERT: B 579 MET cc_start: 0.8623 (mmm) cc_final: 0.8371 (mmt) REVERT: B 582 GLU cc_start: 0.7990 (tp30) cc_final: 0.7584 (tm-30) REVERT: B 591 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: B 599 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8274 (pmm-80) REVERT: B 604 TRP cc_start: 0.7787 (OUTLIER) cc_final: 0.6457 (t60) REVERT: C 161 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7639 (tptp) REVERT: C 200 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6867 (mm) REVERT: C 203 LYS cc_start: 0.6617 (tmmt) cc_final: 0.6386 (tmmt) REVERT: C 216 ILE cc_start: 0.8048 (mm) cc_final: 0.7685 (mm) REVERT: C 236 MET cc_start: 0.7033 (tpp) cc_final: 0.6775 (tpp) REVERT: C 237 PHE cc_start: 0.6012 (t80) cc_final: 0.4979 (t80) REVERT: C 247 ILE cc_start: -0.1611 (OUTLIER) cc_final: -0.2425 (mm) REVERT: C 319 VAL cc_start: 0.7363 (t) cc_final: 0.7054 (m) REVERT: C 329 GLN cc_start: 0.8706 (tp40) cc_final: 0.8176 (mm-40) REVERT: C 367 GLU cc_start: 0.8601 (tp30) cc_final: 0.8151 (mm-30) REVERT: C 370 LEU cc_start: 0.8530 (mt) cc_final: 0.8199 (mm) REVERT: C 390 ASP cc_start: 0.7953 (m-30) cc_final: 0.7701 (m-30) REVERT: C 397 GLU cc_start: 0.7999 (pm20) cc_final: 0.7385 (pm20) REVERT: C 398 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7955 (mtm110) REVERT: C 433 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8558 (ttpp) REVERT: C 550 LYS cc_start: 0.8724 (tttm) cc_final: 0.8394 (ttmt) REVERT: C 562 GLN cc_start: 0.8765 (tp40) cc_final: 0.8010 (tp-100) REVERT: C 566 ASP cc_start: 0.8775 (m-30) cc_final: 0.8128 (m-30) outliers start: 181 outliers final: 141 residues processed: 659 average time/residue: 0.1497 time to fit residues: 141.9483 Evaluate side-chains 699 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 534 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 292 ILE 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 365 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 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 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 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 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 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 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 468 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 564 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 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 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 418 HIS 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 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 331 LEU Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR 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 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 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 559 ARG 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 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 348 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 407 GLN 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 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 591 ASP 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 200 LEU 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 340 LEU 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 394 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 547 GLN 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: 0.9980 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 242 optimal weight: 0.0770 chunk 78 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 418 HIS D 562 GLN E 276 ASN E 329 GLN F 407 GLN F 414 HIS F 562 GLN F 588 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.161564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126902 restraints weight = 114154.950| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 6.97 r_work: 0.3285 rms_B_bonded: 6.25 restraints_weight: 2.0000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 275 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 276 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3633 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= 0.195 Angle : 0.626 9.118 26400 Z= 0.321 Chirality : 0.042 0.192 2958 Planarity : 0.004 0.070 3432 Dihedral : 11.131 81.842 3054 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 7.81 % Allowed : 28.64 % Favored : 63.55 % 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: -0.18 (0.17), residues: 2400 helix: 0.98 (0.15), residues: 1272 sheet: -0.80 (0.51), residues: 113 loop : -1.47 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.016 0.001 TYR C 557 PHE 0.024 0.001 PHE D 213 TRP 0.008 0.001 TRP D 507 HIS 0.007 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00271 (19572) covalent geometry : angle 0.62649 (26400) hydrogen bonds : bond 0.04655 ( 832) hydrogen bonds : angle 4.29167 ( 2457) metal coordination : bond 0.18397 ( 12) Misc. bond : bond 0.00026 ( 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 689 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 533 time to evaluate : 0.692 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 141 MET cc_start: 0.6901 (tpp) cc_final: 0.6595 (tpp) REVERT: A 161 LYS cc_start: 0.8291 (mmmm) cc_final: 0.8076 (mmmm) REVERT: A 237 PHE cc_start: 0.7764 (m-80) cc_final: 0.7290 (m-80) REVERT: A 382 MET cc_start: 0.7019 (pp-130) cc_final: 0.6588 (pp-130) REVERT: A 407 GLN cc_start: 0.8724 (mt0) cc_final: 0.8363 (mt0) REVERT: A 498 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8369 (t0) REVERT: A 554 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 562 GLN cc_start: 0.8317 (tp40) cc_final: 0.8012 (tp-100) REVERT: A 589 ILE cc_start: 0.8209 (mt) cc_final: 0.7948 (mm) REVERT: D 179 LYS cc_start: 0.7949 (mmtp) cc_final: 0.7571 (tptt) REVERT: D 323 ASP cc_start: 0.8023 (p0) cc_final: 0.7533 (p0) REVERT: D 327 ARG cc_start: 0.7991 (mtt90) cc_final: 0.7672 (ptp-170) REVERT: D 382 MET cc_start: 0.6779 (ttp) cc_final: 0.6478 (ttp) REVERT: D 408 LYS cc_start: 0.8854 (ttmm) cc_final: 0.8494 (mtpp) REVERT: D 415 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7170 (mp-120) REVERT: D 451 GLU cc_start: 0.8245 (tt0) cc_final: 0.7721 (tm-30) REVERT: D 537 MET cc_start: 0.8675 (ptt) cc_final: 0.8413 (ptm) REVERT: D 539 ASP cc_start: 0.8233 (t0) cc_final: 0.7848 (t0) REVERT: D 595 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8148 (mpt90) REVERT: D 604 TRP cc_start: 0.7353 (OUTLIER) cc_final: 0.6181 (t60) REVERT: E 142 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.5155 (pp) REVERT: E 161 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8198 (mtmm) REVERT: E 186 LYS cc_start: 0.4732 (OUTLIER) cc_final: 0.3891 (mptp) REVERT: E 190 MET cc_start: 0.7019 (mtm) cc_final: 0.6740 (mtm) REVERT: E 242 LYS cc_start: 0.3324 (OUTLIER) cc_final: 0.2431 (tptp) REVERT: E 366 ASN cc_start: 0.8805 (t0) cc_final: 0.8539 (t0) REVERT: E 367 GLU cc_start: 0.8287 (tp30) cc_final: 0.7913 (mm-30) REVERT: E 377 LYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5555 (mptt) REVERT: E 398 ARG cc_start: 0.8348 (mtp-110) cc_final: 0.7942 (ptm-80) REVERT: E 491 ASN cc_start: 0.8192 (t0) cc_final: 0.7813 (t0) REVERT: E 537 MET cc_start: 0.8692 (ptt) cc_final: 0.8422 (ptm) REVERT: F 161 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8195 (mttp) REVERT: F 190 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6410 (ptp) REVERT: F 237 PHE cc_start: 0.8009 (m-10) cc_final: 0.7414 (m-10) REVERT: F 238 GLU cc_start: 0.8157 (tt0) cc_final: 0.7368 (tm-30) REVERT: F 281 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.4483 (pt0) REVERT: F 293 VAL cc_start: 0.8017 (m) cc_final: 0.7738 (p) REVERT: F 327 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7851 (mtp180) REVERT: F 329 GLN cc_start: 0.8531 (mp10) cc_final: 0.8307 (mp10) REVERT: F 331 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8574 (mm) REVERT: F 332 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8538 (mtmm) REVERT: F 398 ARG cc_start: 0.8477 (ttp-170) cc_final: 0.8036 (ttp80) REVERT: F 401 MET cc_start: 0.7257 (mtp) cc_final: 0.6090 (mtp) REVERT: F 433 LYS cc_start: 0.8683 (tttt) cc_final: 0.8394 (ttmt) REVERT: F 451 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: F 483 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: F 511 GLU cc_start: 0.8250 (mp0) cc_final: 0.7996 (mp0) REVERT: F 513 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8653 (mp) REVERT: F 590 ASP cc_start: 0.8419 (t0) cc_final: 0.8208 (t0) REVERT: B 233 VAL cc_start: 0.7918 (m) cc_final: 0.7217 (p) REVERT: B 236 MET cc_start: 0.7048 (mpt) cc_final: 0.6410 (mpt) REVERT: B 237 PHE cc_start: 0.8059 (m-80) cc_final: 0.7838 (m-80) REVERT: B 238 GLU cc_start: 0.8187 (tp30) cc_final: 0.7877 (pp20) REVERT: B 247 ILE cc_start: 0.1774 (OUTLIER) cc_final: 0.1176 (mp) REVERT: B 329 GLN cc_start: 0.8305 (tp40) cc_final: 0.8023 (mp10) REVERT: B 367 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7855 (mm-30) REVERT: B 407 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: B 413 TYR cc_start: 0.8544 (m-80) cc_final: 0.7955 (m-80) REVERT: B 492 ASP cc_start: 0.8073 (m-30) cc_final: 0.7493 (m-30) REVERT: B 547 GLN cc_start: 0.7963 (mt0) cc_final: 0.7753 (mt0) REVERT: B 562 GLN cc_start: 0.8360 (tp40) cc_final: 0.7518 (tm-30) REVERT: B 579 MET cc_start: 0.8557 (mmm) cc_final: 0.8256 (mmt) REVERT: B 591 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: B 599 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8212 (pmm-80) REVERT: B 604 TRP cc_start: 0.7753 (OUTLIER) cc_final: 0.6337 (t60) REVERT: C 161 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7484 (tptp) REVERT: C 200 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6864 (mm) REVERT: C 203 LYS cc_start: 0.6768 (tmmt) cc_final: 0.6547 (tmmt) REVERT: C 216 ILE cc_start: 0.7998 (mm) cc_final: 0.7627 (mm) REVERT: C 236 MET cc_start: 0.6835 (tpp) cc_final: 0.6569 (tpp) REVERT: C 237 PHE cc_start: 0.6024 (t80) cc_final: 0.4600 (t80) REVERT: C 247 ILE cc_start: -0.1208 (OUTLIER) cc_final: -0.2200 (mm) REVERT: C 319 VAL cc_start: 0.7335 (t) cc_final: 0.7035 (m) REVERT: C 329 GLN cc_start: 0.8649 (tp40) cc_final: 0.8091 (mm-40) REVERT: C 367 GLU cc_start: 0.8557 (tp30) cc_final: 0.8106 (mm-30) REVERT: C 370 LEU cc_start: 0.8431 (mt) cc_final: 0.8141 (mp) REVERT: C 397 GLU cc_start: 0.7965 (pm20) cc_final: 0.7326 (pm20) REVERT: C 398 ARG cc_start: 0.8246 (mtp180) cc_final: 0.7894 (mtm110) REVERT: C 433 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8537 (ttpp) REVERT: C 434 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8260 (m) REVERT: C 550 LYS cc_start: 0.8711 (tttm) cc_final: 0.8447 (ttmt) REVERT: C 562 GLN cc_start: 0.8543 (tp40) cc_final: 0.7852 (tp-100) REVERT: C 566 ASP cc_start: 0.8762 (m-30) cc_final: 0.8068 (m-30) outliers start: 156 outliers final: 109 residues processed: 637 average time/residue: 0.1466 time to fit residues: 134.9788 Evaluate side-chains 652 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 520 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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 292 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 338 VAL 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 391 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 435 THR 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 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 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 387 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 464 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 564 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 242 LYS Chi-restraints excluded: chain E residue 275 LEU 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 377 LYS Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 190 MET 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 294 ILE 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 379 VAL 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 483 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 538 SER 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 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 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 348 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 407 GLN 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 591 ASP 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 200 LEU 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 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 436 ILE Chi-restraints excluded: chain C residue 455 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 142 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 208 optimal weight: 0.1980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 418 HIS D 562 GLN E 329 GLN ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 ASN F 558 ASN 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 = 0.3971 r_free = 0.3971 target = 0.159552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125058 restraints weight = 106285.080| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 6.46 r_work: 0.3271 rms_B_bonded: 5.93 restraints_weight: 2.0000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 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 = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 277 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.577 19587 Z= 0.235 Angle : 0.632 8.850 26400 Z= 0.324 Chirality : 0.043 0.212 2958 Planarity : 0.004 0.070 3432 Dihedral : 10.599 79.409 3012 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 7.27 % Allowed : 28.93 % Favored : 63.80 % 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: -0.19 (0.17), residues: 2400 helix: 0.97 (0.15), residues: 1273 sheet: -0.84 (0.51), residues: 113 loop : -1.46 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 596 TYR 0.016 0.002 TYR C 557 PHE 0.023 0.001 PHE D 213 TRP 0.010 0.001 TRP B 507 HIS 0.008 0.001 HIS E 418 Details of bonding type rmsd covalent geometry : bond 0.00331 (19572) covalent geometry : angle 0.63246 (26400) hydrogen bonds : bond 0.05245 ( 832) hydrogen bonds : angle 4.30547 ( 2457) metal coordination : bond 0.22342 ( 12) Misc. bond : bond 0.00022 ( 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 674 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 529 time to evaluate : 0.662 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: 0.6922 (tpp) cc_final: 0.6585 (tpp) REVERT: A 237 PHE cc_start: 0.7846 (m-80) cc_final: 0.7327 (m-80) REVERT: A 327 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.6963 (mtm-85) REVERT: A 377 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.5858 (mmtm) REVERT: A 382 MET cc_start: 0.6960 (pp-130) cc_final: 0.6542 (pp-130) REVERT: A 384 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8140 (tt0) REVERT: A 491 ASN cc_start: 0.7487 (t0) cc_final: 0.7194 (t0) REVERT: A 554 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: A 562 GLN cc_start: 0.8320 (tp40) cc_final: 0.7980 (tp-100) REVERT: A 589 ILE cc_start: 0.8205 (mt) cc_final: 0.7947 (mm) REVERT: D 179 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7550 (tptt) REVERT: D 323 ASP cc_start: 0.7987 (p0) cc_final: 0.7525 (p0) REVERT: D 327 ARG cc_start: 0.8009 (mtt90) cc_final: 0.7695 (ptp-170) REVERT: D 382 MET cc_start: 0.6726 (ttp) cc_final: 0.6438 (ttp) REVERT: D 451 GLU cc_start: 0.8226 (tt0) cc_final: 0.7720 (tm-30) REVERT: D 494 LYS cc_start: 0.8382 (tttt) cc_final: 0.8170 (tttp) REVERT: D 537 MET cc_start: 0.8631 (ptt) cc_final: 0.8385 (ptm) REVERT: D 539 ASP cc_start: 0.8280 (t0) cc_final: 0.7894 (t0) REVERT: D 554 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7762 (mm-30) REVERT: D 591 ASP cc_start: 0.7545 (m-30) cc_final: 0.7040 (m-30) REVERT: D 595 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8145 (mpt90) REVERT: D 604 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.6195 (t60) REVERT: E 161 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8164 (mttm) REVERT: E 186 LYS cc_start: 0.4792 (OUTLIER) cc_final: 0.4030 (mptp) REVERT: E 242 LYS cc_start: 0.3292 (OUTLIER) cc_final: 0.2419 (tptp) REVERT: E 329 GLN cc_start: 0.8558 (mm110) cc_final: 0.8249 (tp40) REVERT: E 331 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8512 (mp) REVERT: E 366 ASN cc_start: 0.8752 (t0) cc_final: 0.8481 (t0) REVERT: E 367 GLU cc_start: 0.8300 (tp30) cc_final: 0.7910 (mm-30) REVERT: E 398 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.7953 (ptm-80) REVERT: E 491 ASN cc_start: 0.8239 (t0) cc_final: 0.7879 (t0) REVERT: E 537 MET cc_start: 0.8777 (ptt) cc_final: 0.8517 (ptm) REVERT: E 562 GLN cc_start: 0.8839 (tp40) cc_final: 0.8499 (tp40) REVERT: E 591 ASP cc_start: 0.8325 (m-30) cc_final: 0.7832 (m-30) REVERT: F 161 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8191 (mttp) REVERT: F 190 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6716 (ptp) REVERT: F 237 PHE cc_start: 0.7966 (m-10) cc_final: 0.7379 (m-10) REVERT: F 238 GLU cc_start: 0.8123 (tt0) cc_final: 0.7202 (tm-30) REVERT: F 281 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.4449 (pt0) REVERT: F 293 VAL cc_start: 0.8035 (m) cc_final: 0.7753 (p) REVERT: F 327 ARG cc_start: 0.8166 (mtt180) cc_final: 0.7939 (mtp180) REVERT: F 329 GLN cc_start: 0.8500 (mp10) cc_final: 0.8280 (mp10) REVERT: F 331 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8653 (mm) REVERT: F 332 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8518 (mtmm) REVERT: F 398 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7989 (ttp80) REVERT: F 401 MET cc_start: 0.7219 (mtp) cc_final: 0.6182 (mtp) REVERT: F 433 LYS cc_start: 0.8686 (tttt) cc_final: 0.8362 (ttmt) REVERT: F 451 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: F 483 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: F 511 GLU cc_start: 0.8219 (mp0) cc_final: 0.7959 (mp0) REVERT: F 590 ASP cc_start: 0.8401 (t0) cc_final: 0.8183 (t0) REVERT: B 233 VAL cc_start: 0.8256 (m) cc_final: 0.7562 (p) REVERT: B 236 MET cc_start: 0.6972 (mpt) cc_final: 0.6285 (mpt) REVERT: B 237 PHE cc_start: 0.8083 (m-80) cc_final: 0.7820 (m-80) REVERT: B 238 GLU cc_start: 0.8200 (tp30) cc_final: 0.7887 (pp20) REVERT: B 247 ILE cc_start: 0.1667 (OUTLIER) cc_final: 0.1128 (mp) REVERT: B 327 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7758 (mtp85) REVERT: B 367 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7975 (mm-30) REVERT: B 397 GLU cc_start: 0.7673 (tp30) cc_final: 0.7457 (tp30) REVERT: B 407 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8232 (mt0) REVERT: B 413 TYR cc_start: 0.8554 (m-80) cc_final: 0.7916 (m-80) REVERT: B 562 GLN cc_start: 0.8358 (tp40) cc_final: 0.7488 (tm-30) REVERT: B 579 MET cc_start: 0.8555 (mmm) cc_final: 0.8269 (mmt) REVERT: B 591 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: B 599 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8224 (pmm-80) REVERT: B 604 TRP cc_start: 0.7744 (OUTLIER) cc_final: 0.6245 (t60) REVERT: C 161 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7493 (tptp) REVERT: C 200 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6830 (mm) REVERT: C 203 LYS cc_start: 0.6772 (tmmt) cc_final: 0.6571 (tmmt) REVERT: C 216 ILE cc_start: 0.8058 (mm) cc_final: 0.7634 (mm) REVERT: C 236 MET cc_start: 0.6857 (tpp) cc_final: 0.6556 (tpp) REVERT: C 237 PHE cc_start: 0.5585 (t80) cc_final: 0.4541 (t80) REVERT: C 247 ILE cc_start: -0.1085 (OUTLIER) cc_final: -0.2134 (mm) REVERT: C 319 VAL cc_start: 0.7268 (t) cc_final: 0.7001 (m) REVERT: C 329 GLN cc_start: 0.8698 (tp40) cc_final: 0.8165 (mm-40) REVERT: C 367 GLU cc_start: 0.8562 (tp30) cc_final: 0.8124 (mm-30) REVERT: C 370 LEU cc_start: 0.8485 (mt) cc_final: 0.8161 (mm) REVERT: C 397 GLU cc_start: 0.7934 (pm20) cc_final: 0.7371 (pm20) REVERT: C 398 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7888 (mtm110) REVERT: C 433 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8510 (ttpp) REVERT: C 550 LYS cc_start: 0.8678 (tttm) cc_final: 0.8407 (ttmt) REVERT: C 562 GLN cc_start: 0.8592 (tp40) cc_final: 0.7918 (tp-100) REVERT: C 566 ASP cc_start: 0.8710 (m-30) cc_final: 0.8079 (m-30) outliers start: 145 outliers final: 111 residues processed: 623 average time/residue: 0.1453 time to fit residues: 130.2403 Evaluate side-chains 659 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 529 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU 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 292 ILE Chi-restraints excluded: chain A residue 338 VAL 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 391 LYS Chi-restraints excluded: chain A residue 421 ILE 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 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 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 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 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 564 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 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 275 LEU Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 190 MET 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 294 ILE 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 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 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 553 ILE Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 583 THR 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 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 325 ARG 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 407 GLN 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 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 591 ASP 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 200 LEU 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 340 LEU 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 394 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 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: 5.9990 chunk 223 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 201 optimal weight: 0.0670 chunk 131 optimal weight: 10.0000 chunk 210 optimal weight: 0.2980 chunk 90 optimal weight: 0.3980 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 overall best weight: 0.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 418 HIS D 547 GLN D 562 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 588 GLN B 547 GLN C 414 HIS C 572 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.163086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128243 restraints weight = 108669.367| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 6.63 r_work: 0.3306 rms_B_bonded: 6.23 restraints_weight: 2.0000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 277 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 283 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.794 19587 Z= 0.248 Angle : 0.624 9.300 26400 Z= 0.318 Chirality : 0.042 0.202 2958 Planarity : 0.004 0.068 3432 Dihedral : 10.312 79.290 2995 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.33 % Allowed : 30.02 % Favored : 63.65 % 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: 0.00 (0.18), residues: 2400 helix: 1.11 (0.15), residues: 1277 sheet: -0.86 (0.51), residues: 113 loop : -1.35 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 596 TYR 0.028 0.001 TYR B 170 PHE 0.023 0.001 PHE D 213 TRP 0.005 0.001 TRP A 507 HIS 0.021 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00265 (19572) covalent geometry : angle 0.62441 (26400) hydrogen bonds : bond 0.04395 ( 832) hydrogen bonds : angle 4.20896 ( 2457) metal coordination : bond 0.26341 ( 12) Misc. bond : bond 0.00027 ( 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 649 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 523 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: symmetry clash REVERT: A 141 MET cc_start: 0.7019 (tpp) cc_final: 0.6783 (tpp) REVERT: A 237 PHE cc_start: 0.7842 (m-80) cc_final: 0.7263 (m-80) REVERT: A 382 MET cc_start: 0.7030 (pp-130) cc_final: 0.6535 (pp-130) REVERT: A 399 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8414 (ttp80) REVERT: A 407 GLN cc_start: 0.8804 (mt0) cc_final: 0.8437 (mt0) REVERT: A 498 ASN cc_start: 0.8637 (m-40) cc_final: 0.8339 (t0) REVERT: A 554 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 562 GLN cc_start: 0.8302 (tp40) cc_final: 0.8015 (tp-100) REVERT: A 589 ILE cc_start: 0.8209 (mt) cc_final: 0.7953 (mm) REVERT: D 179 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7658 (tptt) REVERT: D 323 ASP cc_start: 0.7960 (p0) cc_final: 0.7556 (p0) REVERT: D 327 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7602 (ptp90) REVERT: D 382 MET cc_start: 0.6738 (ttp) cc_final: 0.6435 (ttp) REVERT: D 433 LYS cc_start: 0.8894 (tttt) cc_final: 0.8508 (ttpt) REVERT: D 451 GLU cc_start: 0.8235 (tt0) cc_final: 0.7716 (tm-30) REVERT: D 537 MET cc_start: 0.8631 (ptt) cc_final: 0.8391 (ptm) REVERT: D 591 ASP cc_start: 0.7534 (m-30) cc_final: 0.7021 (m-30) REVERT: D 595 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8299 (mpt90) REVERT: D 604 TRP cc_start: 0.7433 (OUTLIER) cc_final: 0.6162 (t60) REVERT: E 161 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8137 (mttm) REVERT: E 186 LYS cc_start: 0.4876 (OUTLIER) cc_final: 0.4147 (mptp) REVERT: E 238 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7513 (mm-30) REVERT: E 242 LYS cc_start: 0.3185 (OUTLIER) cc_final: 0.2370 (tptp) REVERT: E 324 VAL cc_start: 0.8244 (p) cc_final: 0.7951 (t) REVERT: E 331 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8511 (mp) REVERT: E 367 GLU cc_start: 0.8258 (tp30) cc_final: 0.7884 (mm-30) REVERT: E 398 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7964 (ptm-80) REVERT: E 401 MET cc_start: 0.7709 (mtt) cc_final: 0.7368 (mtp) REVERT: E 491 ASN cc_start: 0.8197 (t0) cc_final: 0.7843 (t0) REVERT: E 537 MET cc_start: 0.8683 (ptt) cc_final: 0.8456 (ptm) REVERT: E 562 GLN cc_start: 0.8775 (tp40) cc_final: 0.8464 (tp-100) REVERT: E 591 ASP cc_start: 0.8339 (m-30) cc_final: 0.7824 (m-30) REVERT: F 161 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8164 (mttp) REVERT: F 190 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6687 (ptp) REVERT: F 237 PHE cc_start: 0.7952 (m-10) cc_final: 0.7392 (m-10) REVERT: F 238 GLU cc_start: 0.8071 (tt0) cc_final: 0.7153 (tm-30) REVERT: F 281 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.3949 (pt0) REVERT: F 293 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7725 (p) REVERT: F 329 GLN cc_start: 0.8498 (mp10) cc_final: 0.8268 (mp10) REVERT: F 331 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8651 (mm) REVERT: F 332 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8537 (mtmm) REVERT: F 397 GLU cc_start: 0.8516 (mp0) cc_final: 0.8291 (mp0) REVERT: F 398 ARG cc_start: 0.8470 (ttp-170) cc_final: 0.8093 (ttp80) REVERT: F 433 LYS cc_start: 0.8714 (tttt) cc_final: 0.8361 (ttmt) REVERT: F 451 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: F 483 GLU cc_start: 0.8582 (pt0) cc_final: 0.7963 (pm20) REVERT: F 511 GLU cc_start: 0.8209 (mp0) cc_final: 0.7985 (mp0) REVERT: F 590 ASP cc_start: 0.8402 (t0) cc_final: 0.8197 (t0) REVERT: B 186 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6195 (pttt) REVERT: B 233 VAL cc_start: 0.8136 (m) cc_final: 0.7389 (p) REVERT: B 236 MET cc_start: 0.7063 (mpt) cc_final: 0.6419 (mpt) REVERT: B 237 PHE cc_start: 0.8040 (m-80) cc_final: 0.7795 (m-80) REVERT: B 238 GLU cc_start: 0.8179 (tp30) cc_final: 0.7869 (pp20) REVERT: B 247 ILE cc_start: 0.1782 (OUTLIER) cc_final: 0.1168 (mp) REVERT: B 329 GLN cc_start: 0.8681 (tp40) cc_final: 0.8086 (mp10) REVERT: B 367 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 407 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: B 409 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8273 (mt-10) REVERT: B 413 TYR cc_start: 0.8535 (m-80) cc_final: 0.7957 (m-80) REVERT: B 485 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8631 (t) REVERT: B 492 ASP cc_start: 0.8064 (m-30) cc_final: 0.7529 (m-30) REVERT: B 562 GLN cc_start: 0.8343 (tp40) cc_final: 0.7484 (tm-30) REVERT: B 579 MET cc_start: 0.8524 (mmm) cc_final: 0.8289 (mmt) REVERT: B 591 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: B 599 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8232 (pmm-80) REVERT: B 604 TRP cc_start: 0.7725 (OUTLIER) cc_final: 0.6161 (t60) REVERT: C 161 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7467 (tptp) REVERT: C 200 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6827 (mm) REVERT: C 203 LYS cc_start: 0.6711 (tmmt) cc_final: 0.6508 (tmmt) REVERT: C 216 ILE cc_start: 0.7985 (mm) cc_final: 0.7391 (mm) REVERT: C 236 MET cc_start: 0.6794 (tpp) cc_final: 0.6385 (tpp) REVERT: C 237 PHE cc_start: 0.5395 (t80) cc_final: 0.4461 (t80) REVERT: C 247 ILE cc_start: -0.1282 (OUTLIER) cc_final: -0.2316 (mm) REVERT: C 319 VAL cc_start: 0.7165 (t) cc_final: 0.6923 (m) REVERT: C 329 GLN cc_start: 0.8702 (tp40) cc_final: 0.8176 (mm-40) REVERT: C 367 GLU cc_start: 0.8532 (tp30) cc_final: 0.8096 (mm-30) REVERT: C 397 GLU cc_start: 0.7968 (pm20) cc_final: 0.7387 (pm20) REVERT: C 398 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7867 (mtm110) REVERT: C 433 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8509 (ttpp) REVERT: C 434 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8100 (m) REVERT: C 547 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7694 (mt0) REVERT: C 562 GLN cc_start: 0.8509 (tp40) cc_final: 0.7853 (tp-100) REVERT: C 566 ASP cc_start: 0.8745 (m-30) cc_final: 0.8084 (m-30) REVERT: C 574 MET cc_start: 0.8202 (ttm) cc_final: 0.7823 (tpp) REVERT: C 591 ASP cc_start: 0.7660 (m-30) cc_final: 0.7448 (m-30) outliers start: 126 outliers final: 92 residues processed: 603 average time/residue: 0.1570 time to fit residues: 135.9923 Evaluate side-chains 627 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 514 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU 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 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 435 THR 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 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 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 564 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 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 331 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 190 MET 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 294 ILE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 574 MET 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 190 MET 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 325 ARG 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 407 GLN 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 537 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 591 ASP 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 200 LEU 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 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 436 ILE Chi-restraints excluded: chain C residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 66 optimal weight: 1.9990 chunk 189 optimal weight: 0.0270 chunk 160 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 298 ASN D 407 GLN D 418 HIS D 547 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 588 GLN B 547 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 = 0.3973 r_free = 0.3973 target = 0.159570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124833 restraints weight = 108890.953| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 6.62 r_work: 0.3265 rms_B_bonded: 6.06 restraints_weight: 2.0000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 283 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 282 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.592 19587 Z= 0.221 Angle : 0.649 10.848 26400 Z= 0.331 Chirality : 0.043 0.224 2958 Planarity : 0.004 0.069 3432 Dihedral : 10.054 78.861 2981 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.71 % Favored : 94.25 % Rotamer: Outliers : 5.98 % Allowed : 30.46 % Favored : 63.55 % 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: -0.16 (0.17), residues: 2400 helix: 0.89 (0.15), residues: 1303 sheet: -1.68 (0.60), residues: 78 loop : -1.27 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 596 TYR 0.017 0.002 TYR D 557 PHE 0.023 0.001 PHE D 213 TRP 0.010 0.002 TRP B 507 HIS 0.008 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00360 (19572) covalent geometry : angle 0.64880 (26400) hydrogen bonds : bond 0.05361 ( 832) hydrogen bonds : angle 4.29101 ( 2457) metal coordination : bond 0.18607 ( 12) Misc. bond : bond 0.00026 ( 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 653 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 534 time to evaluate : 0.643 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: 0.7005 (tpp) cc_final: 0.6644 (tpp) REVERT: A 158 ASP cc_start: 0.7908 (t0) cc_final: 0.7653 (t0) REVERT: A 236 MET cc_start: 0.7147 (mmp) cc_final: 0.6891 (mmp) REVERT: A 237 PHE cc_start: 0.7866 (m-80) cc_final: 0.7277 (m-80) REVERT: A 327 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.6983 (mtm-85) REVERT: A 382 MET cc_start: 0.7045 (pp-130) cc_final: 0.6569 (pp-130) REVERT: A 491 ASN cc_start: 0.7634 (t0) cc_final: 0.7380 (t0) REVERT: A 554 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: A 562 GLN cc_start: 0.8322 (tp40) cc_final: 0.7996 (tp-100) REVERT: A 589 ILE cc_start: 0.8220 (mt) cc_final: 0.7963 (mm) REVERT: D 179 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7606 (tptt) REVERT: D 323 ASP cc_start: 0.7984 (p0) cc_final: 0.7534 (p0) REVERT: D 327 ARG cc_start: 0.8030 (mtt90) cc_final: 0.7729 (ptp-170) REVERT: D 382 MET cc_start: 0.6799 (ttp) cc_final: 0.6510 (ttp) REVERT: D 451 GLU cc_start: 0.8215 (tt0) cc_final: 0.7717 (tm-30) REVERT: D 537 MET cc_start: 0.8649 (ptt) cc_final: 0.8411 (ptm) REVERT: D 539 ASP cc_start: 0.8318 (t0) cc_final: 0.7957 (t0) REVERT: D 554 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7811 (mm-30) REVERT: D 591 ASP cc_start: 0.7587 (m-30) cc_final: 0.7103 (m-30) REVERT: D 595 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8151 (mpt90) REVERT: D 604 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.6096 (t60) REVERT: E 161 LYS cc_start: 0.8512 (mmmm) cc_final: 0.8113 (mtmm) REVERT: E 186 LYS cc_start: 0.4731 (OUTLIER) cc_final: 0.4030 (mptp) REVERT: E 237 PHE cc_start: 0.7978 (m-10) cc_final: 0.7728 (m-10) REVERT: E 242 LYS cc_start: 0.3199 (OUTLIER) cc_final: 0.2357 (tptp) REVERT: E 324 VAL cc_start: 0.8288 (p) cc_final: 0.8012 (t) REVERT: E 331 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8552 (mp) REVERT: E 366 ASN cc_start: 0.8767 (t0) cc_final: 0.8493 (t0) REVERT: E 367 GLU cc_start: 0.8311 (tp30) cc_final: 0.7920 (mm-30) REVERT: E 398 ARG cc_start: 0.8376 (mtp-110) cc_final: 0.7998 (ptm-80) REVERT: E 491 ASN cc_start: 0.8260 (t0) cc_final: 0.7916 (t0) REVERT: E 537 MET cc_start: 0.8779 (ptt) cc_final: 0.8530 (ptm) REVERT: E 562 GLN cc_start: 0.8845 (tp40) cc_final: 0.8234 (tp-100) REVERT: E 591 ASP cc_start: 0.8299 (m-30) cc_final: 0.7778 (m-30) REVERT: F 161 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8181 (mttp) REVERT: F 237 PHE cc_start: 0.8020 (m-10) cc_final: 0.7494 (m-10) REVERT: F 238 GLU cc_start: 0.8068 (tt0) cc_final: 0.7097 (tm-30) REVERT: F 281 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.4291 (pt0) REVERT: F 293 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7781 (p) REVERT: F 329 GLN cc_start: 0.8473 (mp10) cc_final: 0.8233 (mp10) REVERT: F 331 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8680 (mm) REVERT: F 332 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8462 (mtmm) REVERT: F 398 ARG cc_start: 0.8474 (ttp-170) cc_final: 0.8108 (ttp80) REVERT: F 433 LYS cc_start: 0.8698 (tttt) cc_final: 0.8373 (ttmt) REVERT: F 483 GLU cc_start: 0.8620 (pt0) cc_final: 0.7956 (pm20) REVERT: F 511 GLU cc_start: 0.8183 (mp0) cc_final: 0.7936 (mp0) REVERT: F 590 ASP cc_start: 0.8417 (t0) cc_final: 0.8211 (t0) REVERT: B 233 VAL cc_start: 0.8293 (m) cc_final: 0.7589 (p) REVERT: B 236 MET cc_start: 0.6985 (mpt) cc_final: 0.6309 (mpt) REVERT: B 237 PHE cc_start: 0.8090 (m-80) cc_final: 0.7829 (m-80) REVERT: B 238 GLU cc_start: 0.8211 (tp30) cc_final: 0.7896 (pp20) REVERT: B 247 ILE cc_start: 0.1733 (OUTLIER) cc_final: 0.1194 (mp) REVERT: B 329 GLN cc_start: 0.8665 (tp40) cc_final: 0.8082 (mp10) REVERT: B 367 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 407 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: B 413 TYR cc_start: 0.8554 (m-80) cc_final: 0.7941 (m-80) REVERT: B 547 GLN cc_start: 0.7972 (mt0) cc_final: 0.7719 (mt0) REVERT: B 562 GLN cc_start: 0.8388 (tp40) cc_final: 0.7493 (tm-30) REVERT: B 579 MET cc_start: 0.8569 (mmm) cc_final: 0.8271 (mmt) REVERT: B 582 GLU cc_start: 0.7946 (tp30) cc_final: 0.7567 (tm-30) REVERT: B 591 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: B 599 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8218 (pmm-80) REVERT: B 604 TRP cc_start: 0.7721 (OUTLIER) cc_final: 0.6078 (t60) REVERT: C 161 LYS cc_start: 0.8370 (ttpt) cc_final: 0.7504 (tptp) REVERT: C 200 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6877 (mm) REVERT: C 216 ILE cc_start: 0.8072 (mm) cc_final: 0.7490 (mm) REVERT: C 236 MET cc_start: 0.6855 (tpp) cc_final: 0.6427 (tpp) REVERT: C 237 PHE cc_start: 0.5483 (t80) cc_final: 0.4583 (t80) REVERT: C 247 ILE cc_start: -0.0763 (OUTLIER) cc_final: -0.1851 (mm) REVERT: C 329 GLN cc_start: 0.8706 (tp40) cc_final: 0.8182 (mm-40) REVERT: C 367 GLU cc_start: 0.8563 (tp30) cc_final: 0.8151 (mm-30) REVERT: C 370 LEU cc_start: 0.8489 (mt) cc_final: 0.8173 (mp) REVERT: C 397 GLU cc_start: 0.7964 (pm20) cc_final: 0.7398 (pm20) REVERT: C 398 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7896 (mtm110) REVERT: C 433 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8521 (ttpp) REVERT: C 547 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7786 (mt0) REVERT: C 550 LYS cc_start: 0.8674 (tttm) cc_final: 0.8462 (ttmt) REVERT: C 562 GLN cc_start: 0.8563 (tp40) cc_final: 0.7921 (tp-100) REVERT: C 566 ASP cc_start: 0.8725 (m-30) cc_final: 0.8110 (m-30) REVERT: C 591 ASP cc_start: 0.7711 (m-30) cc_final: 0.7482 (m-30) outliers start: 119 outliers final: 100 residues processed: 611 average time/residue: 0.1509 time to fit residues: 133.1415 Evaluate side-chains 650 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 534 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 462 LEU 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 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 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 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 564 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 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 331 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 190 MET 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 294 ILE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 353 THR 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 538 SER Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 574 MET 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 190 MET 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 325 ARG Chi-restraints excluded: chain B residue 338 VAL 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 407 GLN 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 583 THR Chi-restraints excluded: chain B residue 591 ASP 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 200 LEU 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 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 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 227 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 172 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 418 HIS D 547 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 588 GLN ** C 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126297 restraints weight = 101255.889| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 6.26 r_work: 0.3296 rms_B_bonded: 6.08 restraints_weight: 2.0000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 282 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 281 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.518 19587 Z= 0.205 Angle : 0.630 10.919 26400 Z= 0.320 Chirality : 0.042 0.201 2958 Planarity : 0.004 0.068 3432 Dihedral : 9.981 79.479 2981 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 6.08 % Allowed : 30.42 % 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: -0.06 (0.17), residues: 2400 helix: 1.04 (0.15), residues: 1288 sheet: -1.67 (0.60), residues: 78 loop : -1.31 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 327 TYR 0.016 0.001 TYR B 170 PHE 0.022 0.001 PHE D 213 TRP 0.007 0.001 TRP B 507 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00281 (19572) covalent geometry : angle 0.63030 (26400) hydrogen bonds : bond 0.04835 ( 832) hydrogen bonds : angle 4.22815 ( 2457) metal coordination : bond 0.19670 ( 12) Misc. bond : bond 0.00033 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.90 seconds wall clock time: 83 minutes 31.56 seconds (5011.56 seconds total)