Starting phenix.real_space_refine on Mon Jun 16 22:42:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wi4_32521/06_2025/7wi4_32521.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi4_32521/06_2025/7wi4_32521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wi4_32521/06_2025/7wi4_32521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi4_32521/06_2025/7wi4_32521.map" model { file = "/net/cci-nas-00/data/ceres_data/7wi4_32521/06_2025/7wi4_32521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi4_32521/06_2025/7wi4_32521.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.68, per 1000 atoms: 0.97 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: 4.54 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 418 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 414 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 418 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 414 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 414 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 418 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 418 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 414 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 414 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 418 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 418 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 414 " 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 13 sheets defined 56.4% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 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: 4.95 Time building geometry restraints manager: 5.33 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: 0.03 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 6 \ 04 or resid 701 through 703)) 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 6 \ 04 or resid 701 through 703)) 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 6 \ 04 or resid 701 through 703)) 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 6 \ 04 or resid 701 through 703)) 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 6 \ 04 or resid 701 through 703)) 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 6 \ 04 or resid 701 through 703)) } 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 52.770 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.810 ------------------------------------------------------------------------------- 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 : 16.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.004 TRP B 507 HIS 0.010 0.002 HIS A 418 PHE 0.022 0.003 PHE C 214 TYR 0.030 0.004 TYR E 557 ARG 0.008 0.001 ARG E 232 Details of bonding type rmsd hydrogen bonds : bond 0.23927 ( 832) hydrogen bonds : angle 7.43359 ( 2457) metal coordination : bond 0.01387 ( 12) covalent geometry : bond 0.01245 (19572) covalent geometry : angle 1.08599 (26400) 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 : 1.953 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: 0.6396 (pp-130) REVERT: A 398 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7318 (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: 0.6904 (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: 0.7029 (p0) REVERT: D 327 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7630 (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: 0.7249 (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: 0.7375 (tm-30) REVERT: D 456 SER cc_start: 0.8764 (t) cc_final: 0.8521 (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: 0.7733 (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: 0.7353 (ttp-110) REVERT: D 554 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7047 (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: 0.6993 (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: 0.6350 (ttm) REVERT: E 142 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5250 (pp) REVERT: E 163 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7062 (mm-30) REVERT: E 186 LYS cc_start: 0.5389 (OUTLIER) cc_final: 0.3938 (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: 0.1720 (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: 0.7255 (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: 0.7953 (mm-30) REVERT: E 370 LEU cc_start: 0.8383 (mt) cc_final: 0.8110 (mp) REVERT: E 377 LYS cc_start: 0.6257 (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: 0.7172 (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: 0.4418 (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: 0.8052 (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: 0.7033 (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: 0.8029 (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: 0.7446 (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: 0.8289 (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: 0.6442 (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: 0.6923 (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: 0.3595 time to fit residues: 443.0331 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 : 2.217 ------------------------------------------------------------------------------- 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 207 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 329 GLN F 588 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.157677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123925 restraints weight = 105766.180| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 6.23 r_work: 0.3256 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 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 = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 246 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 19587 Z= 0.183 Angle : 0.729 8.962 26400 Z= 0.378 Chirality : 0.046 0.365 2958 Planarity : 0.006 0.072 3432 Dihedral : 15.884 98.700 3386 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 12.56 % Allowed : 23.99 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2400 helix: -0.18 (0.14), residues: 1285 sheet: -0.70 (0.51), residues: 113 loop : -1.87 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 507 HIS 0.007 0.001 HIS C 414 PHE 0.021 0.002 PHE D 213 TYR 0.019 0.002 TYR E 413 ARG 0.009 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.07282 ( 832) hydrogen bonds : angle 5.05411 ( 2457) metal coordination : bond 0.00489 ( 12) covalent geometry : bond 0.00406 (19572) covalent geometry : angle 0.72929 (26400) Misc. bond : bond 0.00489 ( 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 818 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 566 time to evaluate : 2.167 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 153 ASP cc_start: 0.8038 (m-30) cc_final: 0.7629 (m-30) REVERT: A 293 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7432 (p) REVERT: A 332 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8417 (mtpp) REVERT: A 335 MET cc_start: 0.8164 (ttt) cc_final: 0.7854 (tmm) REVERT: A 367 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7957 (mm-30) REVERT: A 382 MET cc_start: 0.7038 (pp-130) cc_final: 0.6648 (pp-130) REVERT: A 398 ARG cc_start: 0.8575 (ttt180) cc_final: 0.8179 (ttp80) REVERT: A 407 GLN cc_start: 0.8638 (mt0) cc_final: 0.8332 (mt0) REVERT: A 491 ASN cc_start: 0.7517 (t0) cc_final: 0.7179 (t0) REVERT: A 554 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: A 566 ASP cc_start: 0.8555 (m-30) cc_final: 0.8229 (m-30) REVERT: A 589 ILE cc_start: 0.8340 (mt) cc_final: 0.8121 (mm) REVERT: A 599 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8446 (ptp-170) REVERT: D 161 LYS cc_start: 0.8299 (mtpp) cc_final: 0.8098 (mmmm) REVERT: D 237 PHE cc_start: 0.7940 (m-80) cc_final: 0.7364 (m-10) REVERT: D 323 ASP cc_start: 0.8073 (p0) cc_final: 0.7471 (p0) REVERT: D 327 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7933 (mtt180) REVERT: D 335 MET cc_start: 0.8171 (tpp) cc_final: 0.7645 (tpp) REVERT: D 367 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: D 382 MET cc_start: 0.6754 (ttp) cc_final: 0.6458 (ttp) REVERT: D 397 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: D 420 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8487 (mt) REVERT: D 443 LEU cc_start: 0.8947 (mm) cc_final: 0.8707 (mt) REVERT: D 451 GLU cc_start: 0.8307 (tt0) cc_final: 0.7794 (tm-30) REVERT: D 456 SER cc_start: 0.8868 (t) cc_final: 0.8569 (p) REVERT: D 483 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: D 537 MET cc_start: 0.8627 (ptt) cc_final: 0.8395 (ptm) REVERT: D 539 ASP cc_start: 0.8331 (t0) cc_final: 0.7906 (t0) REVERT: D 543 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8114 (ttp-110) REVERT: D 554 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7632 (mm-30) REVERT: D 566 ASP cc_start: 0.8622 (m-30) cc_final: 0.8419 (m-30) REVERT: D 579 MET cc_start: 0.8946 (mmm) cc_final: 0.8613 (mtp) REVERT: D 591 ASP cc_start: 0.7730 (m-30) cc_final: 0.7384 (m-30) REVERT: D 604 TRP cc_start: 0.7533 (OUTLIER) cc_final: 0.6552 (t60) REVERT: E 141 MET cc_start: 0.7048 (ttm) cc_final: 0.6816 (ttm) REVERT: E 142 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.5106 (pp) REVERT: E 161 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8297 (mtmm) REVERT: E 186 LYS cc_start: 0.5283 (OUTLIER) cc_final: 0.3977 (mptp) REVERT: E 238 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: E 242 LYS cc_start: 0.2897 (OUTLIER) cc_final: 0.2050 (tptp) REVERT: E 298 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7719 (m-40) REVERT: E 319 VAL cc_start: 0.7520 (t) cc_final: 0.7287 (m) REVERT: E 367 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: E 370 LEU cc_start: 0.8601 (mt) cc_final: 0.8289 (mp) REVERT: E 384 GLU cc_start: 0.8114 (pt0) cc_final: 0.7901 (pt0) REVERT: E 439 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8507 (ptp-110) REVERT: E 491 ASN cc_start: 0.8246 (t0) cc_final: 0.7954 (t0) REVERT: E 498 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8210 (m110) REVERT: E 512 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8742 (ttpp) REVERT: E 589 ILE cc_start: 0.8067 (mt) cc_final: 0.7829 (mm) REVERT: E 591 ASP cc_start: 0.7771 (m-30) cc_final: 0.7498 (m-30) REVERT: F 213 PHE cc_start: 0.5022 (OUTLIER) cc_final: 0.4440 (t80) REVERT: F 237 PHE cc_start: 0.7920 (m-10) cc_final: 0.7293 (m-10) REVERT: F 238 GLU cc_start: 0.8060 (tt0) cc_final: 0.7371 (tp30) REVERT: F 281 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.4039 (pt0) REVERT: F 282 MET cc_start: 0.6230 (ptp) cc_final: 0.5883 (ptp) REVERT: F 292 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7591 (mp) REVERT: F 397 GLU cc_start: 0.8142 (mp0) cc_final: 0.7865 (mp0) REVERT: F 398 ARG cc_start: 0.8356 (ttp-170) cc_final: 0.7891 (ttp80) REVERT: F 407 GLN cc_start: 0.8689 (tt0) cc_final: 0.8394 (tt0) REVERT: F 408 LYS cc_start: 0.8733 (ptpt) cc_final: 0.8507 (ptpp) REVERT: F 433 LYS cc_start: 0.8725 (tttt) cc_final: 0.8432 (ttmt) REVERT: F 451 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: F 485 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8598 (m) REVERT: F 504 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8631 (t) REVERT: F 511 GLU cc_start: 0.8234 (mp0) cc_final: 0.7983 (mp0) REVERT: F 548 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: F 566 ASP cc_start: 0.8576 (m-30) cc_final: 0.8368 (m-30) REVERT: B 163 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7281 (mt-10) REVERT: B 233 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7555 (p) REVERT: B 236 MET cc_start: 0.7049 (mpt) cc_final: 0.6683 (mpt) REVERT: B 237 PHE cc_start: 0.8032 (m-80) cc_final: 0.7781 (m-80) REVERT: B 247 ILE cc_start: 0.2123 (OUTLIER) cc_final: 0.1533 (mp) REVERT: B 327 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7805 (mtt-85) REVERT: B 351 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8099 (ttm-80) REVERT: B 367 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 413 TYR cc_start: 0.8668 (m-80) cc_final: 0.8262 (m-80) REVERT: B 455 ILE cc_start: 0.8325 (mm) cc_final: 0.7953 (mp) REVERT: B 543 ARG cc_start: 0.8386 (ttp-170) cc_final: 0.8050 (ttp80) REVERT: B 547 GLN cc_start: 0.8191 (mt0) cc_final: 0.7975 (mt0) REVERT: B 604 TRP cc_start: 0.7845 (OUTLIER) cc_final: 0.6768 (t60) REVERT: C 161 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7653 (tptp) REVERT: C 167 LEU cc_start: 0.7042 (tp) cc_final: 0.6839 (tp) REVERT: C 200 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7115 (mm) REVERT: C 236 MET cc_start: 0.8086 (mmt) cc_final: 0.7661 (mmt) REVERT: C 319 VAL cc_start: 0.7611 (t) cc_final: 0.7300 (m) REVERT: C 324 VAL cc_start: 0.8326 (p) cc_final: 0.8101 (t) REVERT: C 329 GLN cc_start: 0.8751 (tp40) cc_final: 0.8176 (mm-40) REVERT: C 357 SER cc_start: 0.7651 (m) cc_final: 0.7269 (p) REVERT: C 370 LEU cc_start: 0.8526 (mt) cc_final: 0.8265 (mp) REVERT: C 385 PHE cc_start: 0.7948 (m-10) cc_final: 0.7601 (m-80) REVERT: C 390 ASP cc_start: 0.7909 (m-30) cc_final: 0.7599 (m-30) REVERT: C 397 GLU cc_start: 0.7948 (pm20) cc_final: 0.7284 (pm20) REVERT: C 398 ARG cc_start: 0.8201 (mtp180) cc_final: 0.7931 (mtm110) REVERT: C 433 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8494 (ttpp) REVERT: C 491 ASN cc_start: 0.8663 (t0) cc_final: 0.8377 (t0) REVERT: C 543 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7315 (ttp80) REVERT: C 547 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: C 562 GLN cc_start: 0.8748 (tp40) cc_final: 0.7938 (tp-100) REVERT: C 566 ASP cc_start: 0.8695 (m-30) cc_final: 0.7970 (m-30) outliers start: 252 outliers final: 166 residues processed: 750 average time/residue: 0.3582 time to fit residues: 385.2892 Evaluate side-chains 732 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 537 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 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 439 ARG 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 574 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 367 GLU 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 420 ILE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 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 498 ASN Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 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 462 LEU 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 548 GLU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 569 ASP 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 293 VAL 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 436 ILE 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 200 LEU 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 367 GLU 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 6 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 191 optimal weight: 0.0000 chunk 3 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 414 HIS F 572 HIS F 588 GLN B 178 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.159227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125940 restraints weight = 103024.839| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 5.90 r_work: 0.3306 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 246 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 267 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.714 19587 Z= 0.246 Angle : 0.651 8.707 26400 Z= 0.334 Chirality : 0.043 0.225 2958 Planarity : 0.005 0.071 3432 Dihedral : 13.688 89.915 3212 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.04 % Favored : 94.92 % Rotamer: Outliers : 10.14 % Allowed : 25.96 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2400 helix: 0.28 (0.14), residues: 1301 sheet: -0.72 (0.51), residues: 113 loop : -1.67 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 507 HIS 0.004 0.001 HIS E 414 PHE 0.034 0.002 PHE A 237 TYR 0.014 0.001 TYR B 170 ARG 0.011 0.000 ARG E 234 Details of bonding type rmsd hydrogen bonds : bond 0.05585 ( 832) hydrogen bonds : angle 4.59493 ( 2457) metal coordination : bond 0.24675 ( 12) covalent geometry : bond 0.00303 (19572) covalent geometry : angle 0.65124 (26400) Misc. bond : bond 0.00271 ( 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 757 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 554 time to evaluate : 2.808 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: 0.8011 (m-30) cc_final: 0.7627 (m-30) REVERT: A 236 MET cc_start: 0.7573 (mpt) cc_final: 0.7066 (mmt) REVERT: A 275 LEU cc_start: 0.3535 (OUTLIER) cc_final: 0.3323 (pp) REVERT: A 293 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.7394 (p) REVERT: A 367 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 382 MET cc_start: 0.6964 (pp-130) cc_final: 0.6517 (pp-130) REVERT: A 398 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8124 (ttp80) REVERT: A 407 GLN cc_start: 0.8692 (mt0) cc_final: 0.8335 (mt0) REVERT: A 547 GLN cc_start: 0.7910 (mt0) cc_final: 0.7702 (mt0) REVERT: A 554 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 562 GLN cc_start: 0.8319 (tp40) cc_final: 0.7998 (tp40) REVERT: A 566 ASP cc_start: 0.8417 (m-30) cc_final: 0.8145 (m-30) REVERT: A 588 GLN cc_start: 0.8239 (mt0) cc_final: 0.7929 (mt0) REVERT: A 589 ILE cc_start: 0.8251 (mt) cc_final: 0.8010 (mm) REVERT: D 237 PHE cc_start: 0.7844 (m-80) cc_final: 0.7509 (m-10) REVERT: D 323 ASP cc_start: 0.8087 (p0) cc_final: 0.7605 (p0) REVERT: D 327 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7847 (mtt180) REVERT: D 382 MET cc_start: 0.6652 (ttp) cc_final: 0.6377 (ttp) REVERT: D 397 GLU cc_start: 0.7640 (mp0) cc_final: 0.7344 (mp0) REVERT: D 408 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8534 (mtpp) REVERT: D 443 LEU cc_start: 0.8930 (mm) cc_final: 0.8678 (mt) REVERT: D 451 GLU cc_start: 0.8238 (tt0) cc_final: 0.7801 (tm-30) REVERT: D 537 MET cc_start: 0.8629 (ptt) cc_final: 0.8394 (ptm) REVERT: D 539 ASP cc_start: 0.8227 (t0) cc_final: 0.7763 (t0) REVERT: D 543 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7926 (ttp-110) REVERT: D 554 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7702 (mm-30) REVERT: D 562 GLN cc_start: 0.8726 (tp40) cc_final: 0.8504 (tp-100) REVERT: D 566 ASP cc_start: 0.8219 (m-30) cc_final: 0.8011 (m-30) REVERT: D 579 MET cc_start: 0.8747 (mmm) cc_final: 0.8500 (mtp) REVERT: D 604 TRP cc_start: 0.7497 (OUTLIER) cc_final: 0.6479 (t60) REVERT: E 141 MET cc_start: 0.6826 (ttm) cc_final: 0.6624 (ttm) REVERT: E 142 LEU cc_start: 0.5190 (OUTLIER) cc_final: 0.4893 (pp) REVERT: E 158 ASP cc_start: 0.7856 (t0) cc_final: 0.7613 (t0) REVERT: E 161 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8258 (mtmm) REVERT: E 186 LYS cc_start: 0.5182 (OUTLIER) cc_final: 0.4092 (mptp) REVERT: E 203 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7115 (tptp) REVERT: E 242 LYS cc_start: 0.3138 (OUTLIER) cc_final: 0.2355 (tptp) REVERT: E 319 VAL cc_start: 0.7747 (t) cc_final: 0.7426 (m) REVERT: E 329 GLN cc_start: 0.8530 (mm110) cc_final: 0.8293 (mm-40) REVERT: E 330 ILE cc_start: 0.8859 (mt) cc_final: 0.8572 (mp) REVERT: E 331 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8370 (mp) REVERT: E 367 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: E 377 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6269 (mmtm) REVERT: E 398 ARG cc_start: 0.8248 (mtp180) cc_final: 0.8037 (mtp-110) REVERT: E 409 GLU cc_start: 0.8497 (tt0) cc_final: 0.8270 (mt-10) REVERT: E 491 ASN cc_start: 0.8099 (t0) cc_final: 0.7792 (t0) REVERT: E 498 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8155 (m110) REVERT: E 591 ASP cc_start: 0.7694 (m-30) cc_final: 0.7445 (m-30) REVERT: F 161 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8174 (mttt) REVERT: F 237 PHE cc_start: 0.7827 (m-10) cc_final: 0.7291 (m-10) REVERT: F 238 GLU cc_start: 0.7868 (tt0) cc_final: 0.7249 (tp30) REVERT: F 281 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.4850 (pt0) REVERT: F 332 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8490 (mttp) REVERT: F 366 ASN cc_start: 0.8741 (t0) cc_final: 0.8500 (t0) REVERT: F 398 ARG cc_start: 0.8335 (ttp-170) cc_final: 0.7873 (ttp80) REVERT: F 408 LYS cc_start: 0.8680 (ptpt) cc_final: 0.8449 (ptpp) REVERT: F 433 LYS cc_start: 0.8612 (tttt) cc_final: 0.8362 (ttmt) REVERT: F 451 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: F 485 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8579 (m) REVERT: F 511 GLU cc_start: 0.8201 (mp0) cc_final: 0.7991 (mp0) REVERT: B 233 VAL cc_start: 0.7891 (m) cc_final: 0.7357 (p) REVERT: B 236 MET cc_start: 0.7026 (mpt) cc_final: 0.6498 (mpt) REVERT: B 237 PHE cc_start: 0.7930 (m-80) cc_final: 0.7599 (m-80) REVERT: B 238 GLU cc_start: 0.8228 (tp30) cc_final: 0.7720 (pp20) REVERT: B 247 ILE cc_start: 0.1659 (OUTLIER) cc_final: 0.1063 (mp) REVERT: B 351 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8109 (ttm-80) REVERT: B 367 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 370 LEU cc_start: 0.8092 (mm) cc_final: 0.7580 (mp) REVERT: B 413 TYR cc_start: 0.8673 (m-80) cc_final: 0.8144 (m-80) REVERT: B 543 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.8039 (ttp80) REVERT: B 547 GLN cc_start: 0.7925 (mt0) cc_final: 0.7697 (mt0) REVERT: B 562 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7714 (tm-30) REVERT: B 604 TRP cc_start: 0.7850 (OUTLIER) cc_final: 0.6614 (t60) REVERT: C 167 LEU cc_start: 0.7008 (tp) cc_final: 0.6787 (tp) REVERT: C 200 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6810 (mm) REVERT: C 203 LYS cc_start: 0.6466 (tmmt) cc_final: 0.6171 (tmmt) REVERT: C 236 MET cc_start: 0.7735 (mmt) cc_final: 0.7524 (tpp) REVERT: C 237 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.5501 (t80) REVERT: C 319 VAL cc_start: 0.7732 (t) cc_final: 0.7510 (m) REVERT: C 324 VAL cc_start: 0.8264 (p) cc_final: 0.7976 (t) REVERT: C 329 GLN cc_start: 0.8710 (tp40) cc_final: 0.8158 (mm-40) REVERT: C 367 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: C 370 LEU cc_start: 0.8481 (mt) cc_final: 0.8199 (mm) REVERT: C 390 ASP cc_start: 0.7868 (m-30) cc_final: 0.7588 (m-30) REVERT: C 397 GLU cc_start: 0.7860 (pm20) cc_final: 0.7211 (pm20) REVERT: C 398 ARG cc_start: 0.8114 (mtp180) cc_final: 0.7855 (mtm110) REVERT: C 433 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8485 (ttpp) REVERT: C 547 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7091 (mt0) REVERT: C 562 GLN cc_start: 0.8688 (tp40) cc_final: 0.7910 (tp-100) REVERT: C 566 ASP cc_start: 0.8718 (m-30) cc_final: 0.7996 (m-30) outliers start: 203 outliers final: 140 residues processed: 701 average time/residue: 0.4097 time to fit residues: 411.3970 Evaluate side-chains 697 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 536 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 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 405 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 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 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 564 LEU Chi-restraints excluded: chain D residue 565 THR 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 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 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 498 ASN 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 294 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 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 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 200 LEU 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 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 578 LEU Chi-restraints excluded: chain B residue 598 VAL 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 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 367 GLU Chi-restraints excluded: chain C residue 380 VAL 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 189 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN F 407 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN F 572 HIS F 588 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.158315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125417 restraints weight = 115685.644| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 6.70 r_work: 0.3256 rms_B_bonded: 5.88 restraints_weight: 2.0000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 267 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 266 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19587 Z= 0.169 Angle : 0.676 10.005 26400 Z= 0.346 Chirality : 0.044 0.216 2958 Planarity : 0.005 0.072 3432 Dihedral : 12.602 83.624 3116 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 9.50 % Allowed : 26.85 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2400 helix: 0.38 (0.14), residues: 1301 sheet: -0.91 (0.50), residues: 113 loop : -1.62 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 507 HIS 0.008 0.001 HIS E 418 PHE 0.051 0.001 PHE A 237 TYR 0.018 0.002 TYR D 557 ARG 0.006 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.05996 ( 832) hydrogen bonds : angle 4.57752 ( 2457) metal coordination : bond 0.01321 ( 12) covalent geometry : bond 0.00380 (19572) covalent geometry : angle 0.67570 (26400) Misc. bond : bond 0.00010 ( 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 734 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 544 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.7192 (tpp) cc_final: 0.6823 (tpp) REVERT: A 153 ASP cc_start: 0.8056 (m-30) cc_final: 0.7649 (m-30) REVERT: A 236 MET cc_start: 0.7615 (mpt) cc_final: 0.7318 (mmt) REVERT: A 237 PHE cc_start: 0.7585 (m-80) cc_final: 0.7231 (m-80) REVERT: A 275 LEU cc_start: 0.3716 (OUTLIER) cc_final: 0.3512 (pp) REVERT: A 293 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7439 (p) REVERT: A 367 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7987 (mm-30) REVERT: A 382 MET cc_start: 0.6947 (pp-130) cc_final: 0.6479 (pp-130) REVERT: A 398 ARG cc_start: 0.8511 (ttt180) cc_final: 0.8180 (ttp80) REVERT: A 407 GLN cc_start: 0.8738 (mt0) cc_final: 0.8378 (mt0) REVERT: A 539 ASP cc_start: 0.7894 (t70) cc_final: 0.7504 (t0) REVERT: A 547 GLN cc_start: 0.7985 (mt0) cc_final: 0.7751 (mt0) REVERT: A 554 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 562 GLN cc_start: 0.8517 (tp40) cc_final: 0.8157 (tp40) REVERT: A 588 GLN cc_start: 0.8238 (mt0) cc_final: 0.7966 (mt0) REVERT: A 589 ILE cc_start: 0.8256 (mt) cc_final: 0.7999 (mm) REVERT: D 237 PHE cc_start: 0.7847 (m-80) cc_final: 0.7482 (m-10) REVERT: D 323 ASP cc_start: 0.8142 (p0) cc_final: 0.7665 (p0) REVERT: D 327 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7844 (mtt180) REVERT: D 382 MET cc_start: 0.6775 (ttp) cc_final: 0.6503 (ttp) REVERT: D 397 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: D 443 LEU cc_start: 0.8972 (mm) cc_final: 0.8771 (mt) REVERT: D 451 GLU cc_start: 0.8169 (tt0) cc_final: 0.7745 (tm-30) REVERT: D 537 MET cc_start: 0.8633 (ptt) cc_final: 0.8402 (ptm) REVERT: D 539 ASP cc_start: 0.8305 (t0) cc_final: 0.7901 (t0) REVERT: D 554 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7818 (mm-30) REVERT: D 591 ASP cc_start: 0.7716 (m-30) cc_final: 0.7510 (m-30) REVERT: D 595 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8141 (mpt90) REVERT: D 604 TRP cc_start: 0.7542 (OUTLIER) cc_final: 0.6511 (t60) REVERT: E 141 MET cc_start: 0.6895 (ttm) cc_final: 0.6645 (ttm) REVERT: E 142 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.5070 (pp) REVERT: E 158 ASP cc_start: 0.7740 (t0) cc_final: 0.7491 (t70) REVERT: E 161 LYS cc_start: 0.8611 (mmmm) cc_final: 0.8269 (mtmm) REVERT: E 186 LYS cc_start: 0.5325 (OUTLIER) cc_final: 0.4155 (mptp) REVERT: E 242 LYS cc_start: 0.3193 (OUTLIER) cc_final: 0.2359 (tptp) REVERT: E 330 ILE cc_start: 0.8894 (mt) cc_final: 0.8603 (mp) REVERT: E 335 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7383 (tmt) REVERT: E 367 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8055 (mm-30) REVERT: E 377 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6071 (mmtm) REVERT: E 409 GLU cc_start: 0.8541 (tt0) cc_final: 0.8336 (mt-10) REVERT: E 468 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8546 (t) REVERT: E 491 ASN cc_start: 0.8317 (t0) cc_final: 0.7975 (t0) REVERT: E 498 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8228 (m110) REVERT: E 562 GLN cc_start: 0.8922 (tp40) cc_final: 0.8308 (tp-100) REVERT: E 591 ASP cc_start: 0.7763 (m-30) cc_final: 0.7537 (m-30) REVERT: F 161 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8241 (mttt) REVERT: F 190 MET cc_start: 0.6557 (mtm) cc_final: 0.6236 (ptp) REVERT: F 237 PHE cc_start: 0.7938 (m-10) cc_final: 0.7404 (m-10) REVERT: F 238 GLU cc_start: 0.8054 (tt0) cc_final: 0.7417 (tp30) REVERT: F 281 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.4798 (pt0) REVERT: F 293 VAL cc_start: 0.8117 (m) cc_final: 0.7815 (p) REVERT: F 327 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7881 (mtp180) REVERT: F 398 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.7912 (ttp80) REVERT: F 399 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.8258 (ttm110) REVERT: F 407 GLN cc_start: 0.8810 (tt0) cc_final: 0.8567 (tt0) REVERT: F 433 LYS cc_start: 0.8632 (tttt) cc_final: 0.8392 (ttmt) REVERT: F 485 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8554 (m) REVERT: F 511 GLU cc_start: 0.8285 (mp0) cc_final: 0.8040 (mp0) REVERT: F 590 ASP cc_start: 0.8451 (t0) cc_final: 0.8224 (t0) REVERT: F 604 TRP cc_start: 0.7182 (OUTLIER) cc_final: 0.6856 (t60) REVERT: B 233 VAL cc_start: 0.8067 (m) cc_final: 0.7398 (p) REVERT: B 236 MET cc_start: 0.6965 (mpt) cc_final: 0.6319 (mpt) REVERT: B 237 PHE cc_start: 0.8008 (m-80) cc_final: 0.7703 (m-80) REVERT: B 247 ILE cc_start: 0.1813 (OUTLIER) cc_final: 0.1240 (mp) REVERT: B 351 ARG cc_start: 0.8332 (ttp80) cc_final: 0.8132 (ttm-80) REVERT: B 367 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7982 (mm-30) REVERT: B 413 TYR cc_start: 0.8679 (m-80) cc_final: 0.8186 (m-80) REVERT: B 543 ARG cc_start: 0.8363 (ttp-170) cc_final: 0.8159 (ttp80) REVERT: B 547 GLN cc_start: 0.8008 (mt0) cc_final: 0.7777 (mt0) REVERT: B 562 GLN cc_start: 0.8382 (tp-100) cc_final: 0.7659 (tm-30) REVERT: B 599 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8146 (pmm-80) REVERT: B 604 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.6679 (t60) REVERT: C 161 LYS cc_start: 0.8473 (ttpt) cc_final: 0.7809 (tptp) REVERT: C 167 LEU cc_start: 0.7009 (tp) cc_final: 0.6777 (tp) REVERT: C 179 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7421 (mmtm) REVERT: C 200 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6864 (mm) REVERT: C 203 LYS cc_start: 0.6610 (tmmt) cc_final: 0.6353 (tmmt) REVERT: C 236 MET cc_start: 0.7189 (mmt) cc_final: 0.6974 (tpp) REVERT: C 281 GLU cc_start: 0.3869 (OUTLIER) cc_final: 0.3662 (mp0) REVERT: C 319 VAL cc_start: 0.7702 (t) cc_final: 0.7436 (m) REVERT: C 327 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7846 (mtt-85) REVERT: C 329 GLN cc_start: 0.8748 (tp40) cc_final: 0.8216 (mm-40) REVERT: C 367 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8203 (mm-30) REVERT: C 370 LEU cc_start: 0.8505 (mt) cc_final: 0.8220 (mm) REVERT: C 390 ASP cc_start: 0.7932 (m-30) cc_final: 0.7671 (m-30) REVERT: C 397 GLU cc_start: 0.7961 (pm20) cc_final: 0.7311 (pm20) REVERT: C 398 ARG cc_start: 0.8226 (mtp180) cc_final: 0.7957 (mtm110) REVERT: C 433 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8550 (ttpp) REVERT: C 491 ASN cc_start: 0.8599 (t0) cc_final: 0.8252 (t0) REVERT: C 547 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7313 (mt0) REVERT: C 562 GLN cc_start: 0.8826 (tp40) cc_final: 0.8098 (tp-100) REVERT: C 566 ASP cc_start: 0.8752 (m-30) cc_final: 0.8074 (m-30) outliers start: 190 outliers final: 137 residues processed: 675 average time/residue: 0.4020 time to fit residues: 387.7876 Evaluate side-chains 690 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 529 time to evaluate : 1.964 ------------------------------------------------------------------------------- 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 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 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 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain D residue 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 397 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 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 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 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 THR 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 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 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 485 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 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 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 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 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 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 253 ILE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 232 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 562 GLN E 329 GLN F 178 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 572 HIS F 588 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.158686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124729 restraints weight = 109524.895| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 6.17 r_work: 0.3271 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 266 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 268 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19587 Z= 0.159 Angle : 0.651 8.944 26400 Z= 0.334 Chirality : 0.044 0.238 2958 Planarity : 0.005 0.073 3432 Dihedral : 12.085 80.500 3097 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 9.10 % Allowed : 27.35 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2400 helix: 0.51 (0.15), residues: 1301 sheet: -0.95 (0.49), residues: 113 loop : -1.58 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 507 HIS 0.008 0.001 HIS E 418 PHE 0.037 0.001 PHE A 237 TYR 0.017 0.002 TYR D 557 ARG 0.006 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.05774 ( 832) hydrogen bonds : angle 4.50617 ( 2457) metal coordination : bond 0.00894 ( 12) covalent geometry : bond 0.00357 (19572) covalent geometry : angle 0.65128 (26400) Misc. bond : bond 0.00020 ( 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 713 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 531 time to evaluate : 2.213 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: 0.7162 (tpp) cc_final: 0.6764 (tpp) REVERT: A 144 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: A 236 MET cc_start: 0.7467 (mpt) cc_final: 0.7245 (mmt) REVERT: A 275 LEU cc_start: 0.3612 (OUTLIER) cc_final: 0.3374 (pp) REVERT: A 293 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7449 (p) REVERT: A 327 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.6989 (mtm-85) REVERT: A 335 MET cc_start: 0.8261 (tpp) cc_final: 0.8044 (tpp) REVERT: A 367 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7993 (mm-30) REVERT: A 382 MET cc_start: 0.6964 (pp-130) cc_final: 0.6524 (pp-130) REVERT: A 398 ARG cc_start: 0.8463 (ttt180) cc_final: 0.8118 (ttp80) REVERT: A 407 GLN cc_start: 0.8724 (mt0) cc_final: 0.8382 (mt0) REVERT: A 491 ASN cc_start: 0.7507 (t0) cc_final: 0.7173 (t0) REVERT: A 554 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: A 589 ILE cc_start: 0.8282 (mt) cc_final: 0.8053 (mm) REVERT: D 190 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.5727 (mmt) REVERT: D 237 PHE cc_start: 0.7775 (m-80) cc_final: 0.7432 (m-10) REVERT: D 323 ASP cc_start: 0.8125 (p0) cc_final: 0.7651 (p0) REVERT: D 327 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7858 (mtt180) REVERT: D 382 MET cc_start: 0.6707 (ttp) cc_final: 0.6434 (ttp) REVERT: D 397 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: D 443 LEU cc_start: 0.8973 (mm) cc_final: 0.8718 (mt) REVERT: D 451 GLU cc_start: 0.8211 (tt0) cc_final: 0.7774 (tm-30) REVERT: D 470 TYR cc_start: 0.9054 (m-80) cc_final: 0.8814 (m-80) REVERT: D 537 MET cc_start: 0.8644 (ptt) cc_final: 0.8419 (ptm) REVERT: D 539 ASP cc_start: 0.8288 (t0) cc_final: 0.7870 (t0) REVERT: D 554 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7787 (mm-30) REVERT: D 595 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8158 (mpt90) REVERT: D 604 TRP cc_start: 0.7518 (OUTLIER) cc_final: 0.6417 (t60) REVERT: E 141 MET cc_start: 0.6991 (ttm) cc_final: 0.6749 (ttm) REVERT: E 142 LEU cc_start: 0.5304 (OUTLIER) cc_final: 0.5081 (pp) REVERT: E 161 LYS cc_start: 0.8635 (mmmm) cc_final: 0.8335 (ttmt) REVERT: E 186 LYS cc_start: 0.5223 (OUTLIER) cc_final: 0.4127 (mptp) REVERT: E 190 MET cc_start: 0.7105 (mtm) cc_final: 0.6853 (mtm) REVERT: E 242 LYS cc_start: 0.3380 (OUTLIER) cc_final: 0.2482 (tptp) REVERT: E 325 ARG cc_start: 0.8728 (tpm-80) cc_final: 0.8504 (tpm-80) REVERT: E 329 GLN cc_start: 0.8641 (mm110) cc_final: 0.8352 (mm-40) REVERT: E 331 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8489 (mp) REVERT: E 367 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: E 377 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6016 (mmtm) REVERT: E 401 MET cc_start: 0.7628 (mtt) cc_final: 0.7417 (mtt) REVERT: E 491 ASN cc_start: 0.8292 (t0) cc_final: 0.7933 (t0) REVERT: E 498 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8205 (m110) REVERT: E 562 GLN cc_start: 0.8921 (tp40) cc_final: 0.8287 (tp-100) REVERT: E 591 ASP cc_start: 0.7731 (m-30) cc_final: 0.7487 (m-30) REVERT: F 161 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8249 (mttt) REVERT: F 190 MET cc_start: 0.6637 (mtm) cc_final: 0.6346 (ptp) REVERT: F 237 PHE cc_start: 0.7840 (m-10) cc_final: 0.7402 (m-10) REVERT: F 238 GLU cc_start: 0.8004 (tt0) cc_final: 0.7203 (tm-30) REVERT: F 281 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5066 (pt0) REVERT: F 293 VAL cc_start: 0.8135 (m) cc_final: 0.7894 (p) REVERT: F 331 LEU cc_start: 0.8814 (mt) cc_final: 0.8441 (mt) REVERT: F 335 MET cc_start: 0.7415 (ptt) cc_final: 0.7211 (ptt) REVERT: F 398 ARG cc_start: 0.8368 (ttp-170) cc_final: 0.7903 (ttp80) REVERT: F 407 GLN cc_start: 0.8750 (tt0) cc_final: 0.8501 (tt0) REVERT: F 433 LYS cc_start: 0.8641 (tttt) cc_final: 0.8393 (ttmt) REVERT: F 451 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: F 511 GLU cc_start: 0.8210 (mp0) cc_final: 0.7968 (mp0) REVERT: F 590 ASP cc_start: 0.8456 (t0) cc_final: 0.8229 (t0) REVERT: F 604 TRP cc_start: 0.7138 (OUTLIER) cc_final: 0.6906 (t60) REVERT: B 233 VAL cc_start: 0.8127 (m) cc_final: 0.7575 (p) REVERT: B 236 MET cc_start: 0.6957 (mpt) cc_final: 0.6306 (mpt) REVERT: B 237 PHE cc_start: 0.7998 (m-80) cc_final: 0.7707 (m-80) REVERT: B 238 GLU cc_start: 0.8184 (tp30) cc_final: 0.7678 (pp20) REVERT: B 247 ILE cc_start: 0.1750 (OUTLIER) cc_final: 0.1138 (mp) REVERT: B 351 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8130 (ttm-80) REVERT: B 370 LEU cc_start: 0.8101 (mm) cc_final: 0.7721 (mp) REVERT: B 401 MET cc_start: 0.7410 (mmm) cc_final: 0.7116 (mtt) REVERT: B 413 TYR cc_start: 0.8636 (m-80) cc_final: 0.8082 (m-80) REVERT: B 543 ARG cc_start: 0.8341 (ttp-170) cc_final: 0.8133 (ttp80) REVERT: B 547 GLN cc_start: 0.7915 (mt0) cc_final: 0.7659 (mt0) REVERT: B 562 GLN cc_start: 0.8366 (tp-100) cc_final: 0.7623 (tm-30) REVERT: B 582 GLU cc_start: 0.7928 (tp30) cc_final: 0.7693 (tp30) REVERT: B 604 TRP cc_start: 0.7843 (OUTLIER) cc_final: 0.6610 (t60) REVERT: C 161 LYS cc_start: 0.8448 (ttpt) cc_final: 0.7654 (tptp) REVERT: C 167 LEU cc_start: 0.6939 (tp) cc_final: 0.6699 (tp) REVERT: C 179 LYS cc_start: 0.7826 (mmtt) cc_final: 0.7477 (mmtm) REVERT: C 200 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6830 (mm) REVERT: C 203 LYS cc_start: 0.6614 (tmmt) cc_final: 0.6369 (tmmt) REVERT: C 237 PHE cc_start: 0.5950 (t80) cc_final: 0.4759 (t80) REVERT: C 319 VAL cc_start: 0.7634 (t) cc_final: 0.7357 (m) REVERT: C 329 GLN cc_start: 0.8705 (tp40) cc_final: 0.8176 (mm-40) REVERT: C 367 GLU cc_start: 0.8532 (tp30) cc_final: 0.8201 (mm-30) REVERT: C 370 LEU cc_start: 0.8484 (mt) cc_final: 0.8222 (mp) REVERT: C 390 ASP cc_start: 0.7934 (m-30) cc_final: 0.7667 (m-30) REVERT: C 397 GLU cc_start: 0.7985 (pm20) cc_final: 0.7357 (pm20) REVERT: C 398 ARG cc_start: 0.8170 (mtp180) cc_final: 0.7895 (mtm110) REVERT: C 433 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8543 (ttpp) REVERT: C 491 ASN cc_start: 0.8598 (t0) cc_final: 0.8242 (t0) REVERT: C 550 LYS cc_start: 0.8729 (tttm) cc_final: 0.8431 (ttmt) REVERT: C 562 GLN cc_start: 0.8774 (tp40) cc_final: 0.8003 (tp-100) REVERT: C 566 ASP cc_start: 0.8717 (m-30) cc_final: 0.8006 (m-30) outliers start: 182 outliers final: 138 residues processed: 655 average time/residue: 0.5005 time to fit residues: 472.1619 Evaluate side-chains 680 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 521 time to evaluate : 2.892 ------------------------------------------------------------------------------- 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 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 391 LYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 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 231 SER 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 397 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 445 VAL 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 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 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 425 VAL Chi-restraints excluded: chain E residue 431 VAL 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 563 LEU Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 179 LYS Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 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 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU 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 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 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 382 MET 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 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 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 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 91 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 572 HIS F 588 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 567 ASN C 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.159387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126240 restraints weight = 110588.455| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 6.51 r_work: 0.3279 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 268 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 270 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19587 Z= 0.142 Angle : 0.633 8.507 26400 Z= 0.325 Chirality : 0.043 0.190 2958 Planarity : 0.004 0.070 3432 Dihedral : 11.567 79.516 3077 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.12 % Favored : 94.83 % Rotamer: Outliers : 8.41 % Allowed : 28.09 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2400 helix: 0.61 (0.15), residues: 1311 sheet: -0.83 (0.50), residues: 113 loop : -1.48 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 507 HIS 0.006 0.001 HIS E 418 PHE 0.041 0.001 PHE A 237 TYR 0.017 0.001 TYR C 557 ARG 0.008 0.000 ARG F 399 Details of bonding type rmsd hydrogen bonds : bond 0.05405 ( 832) hydrogen bonds : angle 4.43023 ( 2457) metal coordination : bond 0.00669 ( 12) covalent geometry : bond 0.00318 (19572) covalent geometry : angle 0.63281 (26400) Misc. bond : bond 0.00011 ( 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 690 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 522 time to evaluate : 2.105 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: 0.7151 (tpp) cc_final: 0.6747 (tpp) REVERT: A 327 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.6991 (mtm-85) REVERT: A 367 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 382 MET cc_start: 0.6937 (pp-130) cc_final: 0.6450 (pp-130) REVERT: A 398 ARG cc_start: 0.8437 (ttt180) cc_final: 0.8226 (mtp180) REVERT: A 539 ASP cc_start: 0.7810 (t70) cc_final: 0.7427 (t0) REVERT: A 554 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: A 562 GLN cc_start: 0.8393 (tp40) cc_final: 0.8136 (tp-100) REVERT: A 589 ILE cc_start: 0.8269 (mt) cc_final: 0.8041 (mm) REVERT: D 179 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7549 (tptt) REVERT: D 190 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6008 (mmt) REVERT: D 323 ASP cc_start: 0.8125 (p0) cc_final: 0.7650 (p0) REVERT: D 327 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7685 (mtt180) REVERT: D 382 MET cc_start: 0.6711 (ttp) cc_final: 0.6441 (ttp) REVERT: D 408 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8545 (mtpp) REVERT: D 451 GLU cc_start: 0.8222 (tt0) cc_final: 0.7799 (tm-30) REVERT: D 462 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7932 (mp) REVERT: D 470 TYR cc_start: 0.9033 (m-80) cc_final: 0.8799 (m-80) REVERT: D 537 MET cc_start: 0.8620 (ptt) cc_final: 0.8383 (ptm) REVERT: D 539 ASP cc_start: 0.8235 (t0) cc_final: 0.7871 (t0) REVERT: D 547 GLN cc_start: 0.7772 (mt0) cc_final: 0.7551 (mt0) REVERT: D 554 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7851 (mm-30) REVERT: D 595 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8189 (mpt90) REVERT: D 604 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.6321 (t60) REVERT: E 141 MET cc_start: 0.6975 (ttm) cc_final: 0.6730 (ttm) REVERT: E 142 LEU cc_start: 0.5251 (OUTLIER) cc_final: 0.5012 (pp) REVERT: E 158 ASP cc_start: 0.7787 (t0) cc_final: 0.7523 (t70) REVERT: E 161 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8319 (ttmt) REVERT: E 186 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4168 (mptp) REVERT: E 242 LYS cc_start: 0.3590 (OUTLIER) cc_final: 0.2736 (tptp) REVERT: E 366 ASN cc_start: 0.8856 (t0) cc_final: 0.8580 (t0) REVERT: E 367 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8005 (mm-30) REVERT: E 377 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6085 (mmtm) REVERT: E 398 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7770 (ptm-80) REVERT: E 401 MET cc_start: 0.7536 (mtt) cc_final: 0.7130 (mtt) REVERT: E 491 ASN cc_start: 0.8238 (t0) cc_final: 0.7861 (t0) REVERT: E 498 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8205 (m110) REVERT: E 562 GLN cc_start: 0.8940 (tp40) cc_final: 0.8341 (tp-100) REVERT: E 591 ASP cc_start: 0.7763 (m-30) cc_final: 0.7512 (m-30) REVERT: F 161 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8241 (mttp) REVERT: F 190 MET cc_start: 0.6662 (mtm) cc_final: 0.6423 (ptp) REVERT: F 237 PHE cc_start: 0.7955 (m-10) cc_final: 0.7395 (m-10) REVERT: F 238 GLU cc_start: 0.7998 (tt0) cc_final: 0.7027 (tm-30) REVERT: F 281 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.4672 (pt0) REVERT: F 293 VAL cc_start: 0.8134 (m) cc_final: 0.7890 (p) REVERT: F 331 LEU cc_start: 0.8809 (mt) cc_final: 0.8413 (mt) REVERT: F 335 MET cc_start: 0.7463 (ptt) cc_final: 0.7254 (ptt) REVERT: F 398 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.7974 (ttp80) REVERT: F 407 GLN cc_start: 0.8692 (tt0) cc_final: 0.8485 (tt0) REVERT: F 433 LYS cc_start: 0.8634 (tttt) cc_final: 0.8386 (ttmt) REVERT: F 451 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: F 511 GLU cc_start: 0.8239 (mp0) cc_final: 0.8001 (mp0) REVERT: B 233 VAL cc_start: 0.8104 (m) cc_final: 0.7539 (p) REVERT: B 236 MET cc_start: 0.6938 (mpt) cc_final: 0.6245 (mpt) REVERT: B 237 PHE cc_start: 0.7961 (m-80) cc_final: 0.7592 (m-80) REVERT: B 247 ILE cc_start: 0.1695 (OUTLIER) cc_final: 0.1082 (mp) REVERT: B 329 GLN cc_start: 0.8745 (tp40) cc_final: 0.8163 (mp10) REVERT: B 351 ARG cc_start: 0.8307 (ttp80) cc_final: 0.8092 (ttm-80) REVERT: B 413 TYR cc_start: 0.8603 (m-80) cc_final: 0.8072 (m-80) REVERT: B 543 ARG cc_start: 0.8297 (ttp-170) cc_final: 0.7916 (ttp80) REVERT: B 547 GLN cc_start: 0.7903 (mt0) cc_final: 0.7644 (mt0) REVERT: B 562 GLN cc_start: 0.8388 (tp40) cc_final: 0.7614 (tm-30) REVERT: B 599 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8155 (pmm-80) REVERT: B 604 TRP cc_start: 0.7753 (OUTLIER) cc_final: 0.6359 (t60) REVERT: C 161 LYS cc_start: 0.8447 (ttpt) cc_final: 0.7668 (tptp) REVERT: C 167 LEU cc_start: 0.6918 (tp) cc_final: 0.6680 (tp) REVERT: C 179 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7667 (mmtm) REVERT: C 200 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6899 (mm) REVERT: C 203 LYS cc_start: 0.6560 (tmmt) cc_final: 0.6349 (tmmt) REVERT: C 216 ILE cc_start: 0.8044 (mm) cc_final: 0.7674 (mm) REVERT: C 236 MET cc_start: 0.7025 (tpp) cc_final: 0.6623 (tpp) REVERT: C 237 PHE cc_start: 0.6009 (t80) cc_final: 0.4835 (t80) REVERT: C 319 VAL cc_start: 0.7602 (t) cc_final: 0.7309 (m) REVERT: C 329 GLN cc_start: 0.8683 (tp40) cc_final: 0.8166 (mm-40) REVERT: C 367 GLU cc_start: 0.8569 (tp30) cc_final: 0.8188 (mm-30) REVERT: C 370 LEU cc_start: 0.8524 (mt) cc_final: 0.8220 (mm) REVERT: C 390 ASP cc_start: 0.7929 (m-30) cc_final: 0.7657 (m-30) REVERT: C 397 GLU cc_start: 0.7991 (pm20) cc_final: 0.7361 (pm20) REVERT: C 398 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7851 (mtm110) REVERT: C 433 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8543 (ttpp) REVERT: C 550 LYS cc_start: 0.8733 (tttm) cc_final: 0.8470 (ttmt) REVERT: C 562 GLN cc_start: 0.8629 (tp40) cc_final: 0.7965 (tp-100) REVERT: C 566 ASP cc_start: 0.8705 (m-30) cc_final: 0.8069 (m-30) REVERT: C 591 ASP cc_start: 0.7662 (m-30) cc_final: 0.7223 (m-30) REVERT: C 599 ARG cc_start: 0.7881 (ptp90) cc_final: 0.7641 (ptp-170) outliers start: 168 outliers final: 130 residues processed: 637 average time/residue: 0.3757 time to fit residues: 343.3169 Evaluate side-chains 660 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 513 time to evaluate : 2.863 ------------------------------------------------------------------------------- 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 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 380 VAL Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 505 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 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 231 SER 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 462 LEU Chi-restraints excluded: chain D residue 464 SER 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 335 MET Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 431 VAL 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 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 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 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 F residue 598 VAL 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 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 382 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 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 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 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 92 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 chunk 129 optimal weight: 0.0170 chunk 215 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 221 optimal weight: 0.0670 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 556 ASN D 562 GLN E 276 ASN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 588 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129284 restraints weight = 104115.256| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 6.13 r_work: 0.3340 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 270 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 270 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19587 Z= 0.119 Angle : 0.627 14.431 26400 Z= 0.316 Chirality : 0.042 0.184 2958 Planarity : 0.004 0.068 3432 Dihedral : 10.932 79.120 3051 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 7.81 % Allowed : 28.88 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2400 helix: 0.98 (0.15), residues: 1282 sheet: -0.80 (0.50), residues: 113 loop : -1.39 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 507 HIS 0.005 0.001 HIS F 418 PHE 0.041 0.001 PHE A 237 TYR 0.013 0.001 TYR C 557 ARG 0.007 0.000 ARG F 327 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 832) hydrogen bonds : angle 4.28069 ( 2457) metal coordination : bond 0.00385 ( 12) covalent geometry : bond 0.00265 (19572) covalent geometry : angle 0.62704 (26400) Misc. bond : bond 0.00012 ( 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 673 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 517 time to evaluate : 2.582 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: 0.7283 (tpp) cc_final: 0.6904 (tpp) REVERT: A 161 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7674 (mttm) REVERT: A 367 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 382 MET cc_start: 0.6905 (pp-130) cc_final: 0.6515 (pp-130) REVERT: A 397 GLU cc_start: 0.8328 (mp0) cc_final: 0.8126 (mm-30) REVERT: A 398 ARG cc_start: 0.8417 (ttt180) cc_final: 0.8082 (ttp80) REVERT: A 407 GLN cc_start: 0.8897 (mt0) cc_final: 0.8524 (mt0) REVERT: A 498 ASN cc_start: 0.8675 (m-40) cc_final: 0.8408 (t0) REVERT: A 554 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: A 562 GLN cc_start: 0.8327 (tp40) cc_final: 0.8094 (tp-100) REVERT: A 574 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8407 (ttp) REVERT: A 589 ILE cc_start: 0.8240 (mt) cc_final: 0.8013 (mm) REVERT: D 179 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7488 (tptt) REVERT: D 323 ASP cc_start: 0.8075 (p0) cc_final: 0.7703 (p0) REVERT: D 327 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7537 (ptp90) REVERT: D 382 MET cc_start: 0.6700 (ttp) cc_final: 0.6414 (ttp) REVERT: D 408 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8487 (mtpp) REVERT: D 443 LEU cc_start: 0.8766 (mm) cc_final: 0.8515 (mt) REVERT: D 451 GLU cc_start: 0.8184 (tt0) cc_final: 0.7791 (tm-30) REVERT: D 470 TYR cc_start: 0.9032 (m-80) cc_final: 0.8826 (m-80) REVERT: D 537 MET cc_start: 0.8574 (ptt) cc_final: 0.8357 (ptm) REVERT: D 591 ASP cc_start: 0.7472 (m-30) cc_final: 0.6917 (m-30) REVERT: D 595 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8209 (mpt90) REVERT: D 604 TRP cc_start: 0.7462 (OUTLIER) cc_final: 0.6213 (t60) REVERT: E 141 MET cc_start: 0.6935 (ttm) cc_final: 0.6690 (ttm) REVERT: E 142 LEU cc_start: 0.5112 (OUTLIER) cc_final: 0.4871 (pp) REVERT: E 158 ASP cc_start: 0.7795 (t0) cc_final: 0.7542 (t70) REVERT: E 161 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8279 (ttmt) REVERT: E 186 LYS cc_start: 0.4866 (OUTLIER) cc_final: 0.4060 (mptp) REVERT: E 242 LYS cc_start: 0.3802 (OUTLIER) cc_final: 0.2866 (tptp) REVERT: E 324 VAL cc_start: 0.8046 (p) cc_final: 0.7627 (t) REVERT: E 329 GLN cc_start: 0.8604 (mm110) cc_final: 0.8228 (mm-40) REVERT: E 331 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8480 (mp) REVERT: E 366 ASN cc_start: 0.8798 (t0) cc_final: 0.8525 (t0) REVERT: E 367 GLU cc_start: 0.8249 (tp30) cc_final: 0.7925 (mm-30) REVERT: E 398 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7881 (ptm-80) REVERT: E 401 MET cc_start: 0.7482 (mtt) cc_final: 0.7161 (mtp) REVERT: E 415 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8223 (mp10) REVERT: E 491 ASN cc_start: 0.8108 (t0) cc_final: 0.7790 (t0) REVERT: E 498 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8250 (m110) REVERT: E 546 ASP cc_start: 0.7806 (m-30) cc_final: 0.7499 (m-30) REVERT: E 562 GLN cc_start: 0.8860 (tp40) cc_final: 0.8419 (tp-100) REVERT: E 591 ASP cc_start: 0.7827 (m-30) cc_final: 0.7562 (m-30) REVERT: F 161 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8241 (mttp) REVERT: F 179 LYS cc_start: 0.5872 (OUTLIER) cc_final: 0.5511 (mttm) REVERT: F 237 PHE cc_start: 0.7835 (m-10) cc_final: 0.7327 (m-10) REVERT: F 238 GLU cc_start: 0.8013 (tt0) cc_final: 0.7072 (tm-30) REVERT: F 281 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.4313 (pt0) REVERT: F 335 MET cc_start: 0.7466 (ptt) cc_final: 0.7257 (ptt) REVERT: F 398 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.7925 (ttp80) REVERT: F 401 MET cc_start: 0.6938 (mtp) cc_final: 0.5970 (mtp) REVERT: F 407 GLN cc_start: 0.8621 (tt0) cc_final: 0.8369 (tt0) REVERT: F 433 LYS cc_start: 0.8643 (tttt) cc_final: 0.8384 (ttmt) REVERT: F 451 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: F 483 GLU cc_start: 0.8410 (pt0) cc_final: 0.7853 (pm20) REVERT: F 511 GLU cc_start: 0.8212 (mp0) cc_final: 0.7974 (mp0) REVERT: F 513 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8761 (mp) REVERT: B 233 VAL cc_start: 0.8222 (m) cc_final: 0.7600 (p) REVERT: B 236 MET cc_start: 0.6888 (mpt) cc_final: 0.6250 (mpt) REVERT: B 237 PHE cc_start: 0.7898 (m-80) cc_final: 0.7629 (m-80) REVERT: B 247 ILE cc_start: 0.1718 (OUTLIER) cc_final: 0.1133 (mp) REVERT: B 329 GLN cc_start: 0.8742 (tp40) cc_final: 0.8145 (mp10) REVERT: B 401 MET cc_start: 0.7441 (mmm) cc_final: 0.7091 (mtt) REVERT: B 409 GLU cc_start: 0.8576 (tt0) cc_final: 0.8331 (mt-10) REVERT: B 413 TYR cc_start: 0.8570 (m-80) cc_final: 0.7971 (m-80) REVERT: B 485 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8646 (t) REVERT: B 543 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7871 (ttp80) REVERT: B 547 GLN cc_start: 0.7768 (mt0) cc_final: 0.7561 (mt0) REVERT: B 562 GLN cc_start: 0.8415 (tp40) cc_final: 0.7582 (tm-30) REVERT: B 591 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: B 599 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8099 (pmm-80) REVERT: B 604 TRP cc_start: 0.7722 (OUTLIER) cc_final: 0.6221 (t60) REVERT: C 161 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7552 (tptp) REVERT: C 167 LEU cc_start: 0.6921 (tp) cc_final: 0.6699 (tp) REVERT: C 200 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6803 (mm) REVERT: C 216 ILE cc_start: 0.7944 (mm) cc_final: 0.7412 (mm) REVERT: C 236 MET cc_start: 0.6838 (tpp) cc_final: 0.6519 (tpp) REVERT: C 237 PHE cc_start: 0.5863 (t80) cc_final: 0.4767 (t80) REVERT: C 247 ILE cc_start: -0.1174 (OUTLIER) cc_final: -0.2007 (mm) REVERT: C 319 VAL cc_start: 0.7514 (t) cc_final: 0.7227 (m) REVERT: C 329 GLN cc_start: 0.8660 (tp40) cc_final: 0.8146 (mm-40) REVERT: C 367 GLU cc_start: 0.8522 (tp30) cc_final: 0.8152 (mm-30) REVERT: C 397 GLU cc_start: 0.7936 (pm20) cc_final: 0.7298 (pm20) REVERT: C 398 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7749 (mtm110) REVERT: C 433 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8516 (ttpp) REVERT: C 434 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8177 (m) REVERT: C 550 LYS cc_start: 0.8717 (tttm) cc_final: 0.8462 (ttmt) REVERT: C 562 GLN cc_start: 0.8525 (tp40) cc_final: 0.7892 (tp-100) REVERT: C 566 ASP cc_start: 0.8642 (m-30) cc_final: 0.8022 (m-30) REVERT: C 591 ASP cc_start: 0.7586 (m-30) cc_final: 0.7224 (m-30) outliers start: 156 outliers final: 104 residues processed: 625 average time/residue: 0.4068 time to fit residues: 369.7071 Evaluate side-chains 635 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 510 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 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 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 461 LYS 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 167 LEU Chi-restraints excluded: chain D residue 180 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 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 445 VAL Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 511 GLU 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 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 331 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 179 LYS 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 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 402 VAL 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 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 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 318 VAL 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 418 HIS Chi-restraints excluded: chain B residue 434 VAL 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 150 THR 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 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 173 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 240 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 187 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 F 366 ASN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 ASN F 558 ASN F 562 GLN F 588 GLN ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.161957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128973 restraints weight = 113752.248| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 6.82 r_work: 0.3315 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 270 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 276 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.591 19587 Z= 0.186 Angle : 0.614 8.523 26400 Z= 0.314 Chirality : 0.042 0.189 2958 Planarity : 0.004 0.068 3432 Dihedral : 10.313 78.444 2998 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 6.92 % Allowed : 29.67 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2400 helix: 1.06 (0.15), residues: 1282 sheet: -0.71 (0.50), residues: 113 loop : -1.35 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 507 HIS 0.005 0.001 HIS F 418 PHE 0.045 0.001 PHE A 237 TYR 0.024 0.001 TYR B 170 ARG 0.006 0.000 ARG F 327 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 832) hydrogen bonds : angle 4.22948 ( 2457) metal coordination : bond 0.17073 ( 12) covalent geometry : bond 0.00274 (19572) covalent geometry : angle 0.61428 (26400) Misc. bond : bond 0.00003 ( 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 652 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 514 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8272 (mmmm) cc_final: 0.7681 (mttm) REVERT: A 236 MET cc_start: 0.7010 (mmt) cc_final: 0.6638 (mmp) REVERT: A 367 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 382 MET cc_start: 0.6978 (pp-130) cc_final: 0.6530 (pp-130) REVERT: A 399 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8453 (ttp80) REVERT: A 407 GLN cc_start: 0.8890 (mt0) cc_final: 0.8525 (mt0) REVERT: A 498 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8421 (t0) REVERT: A 554 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: A 562 GLN cc_start: 0.8371 (tp40) cc_final: 0.8078 (tp-100) REVERT: A 574 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8409 (ttp) REVERT: A 589 ILE cc_start: 0.8247 (mt) cc_final: 0.8023 (mm) REVERT: D 179 LYS cc_start: 0.7965 (mmtp) cc_final: 0.7509 (tptt) REVERT: D 323 ASP cc_start: 0.8059 (p0) cc_final: 0.7703 (p0) REVERT: D 327 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7582 (ptp90) REVERT: D 382 MET cc_start: 0.6762 (ttp) cc_final: 0.6487 (ttp) REVERT: D 443 LEU cc_start: 0.8791 (mm) cc_final: 0.8539 (mt) REVERT: D 451 GLU cc_start: 0.8214 (tt0) cc_final: 0.7775 (tm-30) REVERT: D 537 MET cc_start: 0.8596 (ptt) cc_final: 0.8385 (ptm) REVERT: D 539 ASP cc_start: 0.8131 (t0) cc_final: 0.7751 (t0) REVERT: D 591 ASP cc_start: 0.7530 (m-30) cc_final: 0.7028 (m-30) REVERT: D 595 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8193 (mpt90) REVERT: D 604 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.6096 (t60) REVERT: E 141 MET cc_start: 0.6957 (ttm) cc_final: 0.6711 (ttm) REVERT: E 142 LEU cc_start: 0.5112 (OUTLIER) cc_final: 0.4858 (pp) REVERT: E 161 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8240 (ttmt) REVERT: E 186 LYS cc_start: 0.4949 (OUTLIER) cc_final: 0.4186 (mptp) REVERT: E 242 LYS cc_start: 0.3830 (OUTLIER) cc_final: 0.3028 (tppt) REVERT: E 329 GLN cc_start: 0.8672 (mm110) cc_final: 0.8304 (mm-40) REVERT: E 366 ASN cc_start: 0.8781 (t0) cc_final: 0.8496 (t0) REVERT: E 367 GLU cc_start: 0.8314 (tp30) cc_final: 0.7956 (mm-30) REVERT: E 398 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7792 (ptm-80) REVERT: E 401 MET cc_start: 0.7561 (mtt) cc_final: 0.7188 (mtt) REVERT: E 409 GLU cc_start: 0.8480 (tt0) cc_final: 0.8187 (mt-10) REVERT: E 415 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8369 (mp10) REVERT: E 491 ASN cc_start: 0.8187 (t0) cc_final: 0.7830 (t0) REVERT: E 498 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8262 (m110) REVERT: E 546 ASP cc_start: 0.7841 (m-30) cc_final: 0.7558 (m-30) REVERT: E 562 GLN cc_start: 0.8881 (tp40) cc_final: 0.8435 (tp-100) REVERT: E 591 ASP cc_start: 0.7870 (m-30) cc_final: 0.7611 (m-30) REVERT: F 161 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8249 (mttp) REVERT: F 190 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6824 (ptp) REVERT: F 237 PHE cc_start: 0.7885 (m-10) cc_final: 0.7383 (m-10) REVERT: F 238 GLU cc_start: 0.8013 (tt0) cc_final: 0.7228 (tm-30) REVERT: F 281 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.4298 (pt0) REVERT: F 335 MET cc_start: 0.7582 (ptt) cc_final: 0.7341 (ptt) REVERT: F 398 ARG cc_start: 0.8518 (ttp-170) cc_final: 0.7989 (ttp80) REVERT: F 401 MET cc_start: 0.7061 (mtp) cc_final: 0.6127 (mtp) REVERT: F 407 GLN cc_start: 0.8655 (tt0) cc_final: 0.8400 (tt0) REVERT: F 433 LYS cc_start: 0.8661 (tttt) cc_final: 0.8385 (ttmt) REVERT: F 451 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: F 483 GLU cc_start: 0.8499 (pt0) cc_final: 0.7922 (pm20) REVERT: F 511 GLU cc_start: 0.8232 (mp0) cc_final: 0.8003 (mp0) REVERT: F 590 ASP cc_start: 0.8470 (t0) cc_final: 0.8257 (t0) REVERT: B 186 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6260 (pttt) REVERT: B 233 VAL cc_start: 0.8247 (m) cc_final: 0.7547 (p) REVERT: B 236 MET cc_start: 0.6922 (mpt) cc_final: 0.6244 (mpt) REVERT: B 237 PHE cc_start: 0.7939 (m-80) cc_final: 0.7664 (m-80) REVERT: B 247 ILE cc_start: 0.1637 (OUTLIER) cc_final: 0.1076 (mp) REVERT: B 329 GLN cc_start: 0.8765 (tp40) cc_final: 0.8173 (mp10) REVERT: B 370 LEU cc_start: 0.8073 (mm) cc_final: 0.7518 (mp) REVERT: B 401 MET cc_start: 0.7488 (mmm) cc_final: 0.7083 (mtt) REVERT: B 409 GLU cc_start: 0.8598 (tt0) cc_final: 0.8292 (mt-10) REVERT: B 413 TYR cc_start: 0.8588 (m-80) cc_final: 0.7997 (m-80) REVERT: B 485 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8681 (t) REVERT: B 562 GLN cc_start: 0.8467 (tp40) cc_final: 0.7616 (tm-30) REVERT: B 582 GLU cc_start: 0.7763 (tp30) cc_final: 0.7523 (tp30) REVERT: B 591 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: B 599 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8070 (pmm-80) REVERT: B 604 TRP cc_start: 0.7663 (OUTLIER) cc_final: 0.6053 (t60) REVERT: C 161 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7604 (tptp) REVERT: C 167 LEU cc_start: 0.6927 (tp) cc_final: 0.6699 (tp) REVERT: C 200 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6922 (mm) REVERT: C 216 ILE cc_start: 0.7970 (mm) cc_final: 0.7436 (mm) REVERT: C 236 MET cc_start: 0.6805 (tpp) cc_final: 0.6467 (tpp) REVERT: C 247 ILE cc_start: -0.0983 (OUTLIER) cc_final: -0.1848 (mm) REVERT: C 319 VAL cc_start: 0.7476 (t) cc_final: 0.7229 (m) REVERT: C 329 GLN cc_start: 0.8712 (tp40) cc_final: 0.8232 (mm-40) REVERT: C 367 GLU cc_start: 0.8586 (tp30) cc_final: 0.8211 (mm-30) REVERT: C 397 GLU cc_start: 0.7989 (pm20) cc_final: 0.7360 (pm20) REVERT: C 398 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7788 (mtm110) REVERT: C 433 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8523 (ttpp) REVERT: C 550 LYS cc_start: 0.8659 (tttm) cc_final: 0.8423 (ttmt) REVERT: C 562 GLN cc_start: 0.8551 (tp40) cc_final: 0.7935 (tp-100) REVERT: C 566 ASP cc_start: 0.8658 (m-30) cc_final: 0.8066 (m-30) REVERT: C 591 ASP cc_start: 0.7641 (m-30) cc_final: 0.7218 (m-30) outliers start: 138 outliers final: 104 residues processed: 606 average time/residue: 0.3506 time to fit residues: 306.2094 Evaluate side-chains 629 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 505 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU 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 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 433 LYS Chi-restraints excluded: chain A residue 435 THR 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 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 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 474 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 511 GLU 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 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 335 MET Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 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 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 402 VAL 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 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 F residue 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 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 318 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 ILE 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 599 ARG 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 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 281 GLU 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 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 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 195 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 179 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 130 optimal weight: 0.0170 chunk 93 optimal weight: 0.0980 chunk 212 optimal weight: 1.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 366 ASN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 562 GLN F 588 GLN B 407 GLN B 547 GLN ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.162927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130848 restraints weight = 110004.185| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 6.23 r_work: 0.3355 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 276 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 276 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.402 19587 Z= 0.153 Angle : 0.610 8.819 26400 Z= 0.312 Chirality : 0.042 0.191 2958 Planarity : 0.004 0.068 3432 Dihedral : 10.032 78.373 2990 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 6.18 % Allowed : 30.42 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2400 helix: 1.16 (0.15), residues: 1282 sheet: -0.62 (0.50), residues: 113 loop : -1.29 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.005 0.001 HIS F 418 PHE 0.043 0.001 PHE A 237 TYR 0.017 0.001 TYR B 170 ARG 0.006 0.000 ARG F 327 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 832) hydrogen bonds : angle 4.17929 ( 2457) metal coordination : bond 0.11624 ( 12) covalent geometry : bond 0.00266 (19572) covalent geometry : angle 0.61024 (26400) Misc. bond : bond 0.00013 ( 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 631 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 508 time to evaluate : 2.121 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 161 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7667 (mttm) REVERT: A 190 MET cc_start: 0.6561 (mpp) cc_final: 0.5907 (mtp) REVERT: A 236 MET cc_start: 0.6967 (mmt) cc_final: 0.6661 (mmp) REVERT: A 367 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 382 MET cc_start: 0.7017 (pp-130) cc_final: 0.6554 (pp-130) REVERT: A 399 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8377 (ttp80) REVERT: A 407 GLN cc_start: 0.8769 (mt0) cc_final: 0.8373 (mt0) REVERT: A 498 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8398 (t0) REVERT: A 554 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: A 562 GLN cc_start: 0.8320 (tp40) cc_final: 0.8011 (tp-100) REVERT: A 574 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8396 (ttp) REVERT: A 589 ILE cc_start: 0.8214 (mt) cc_final: 0.7986 (mm) REVERT: D 179 LYS cc_start: 0.7969 (mmtp) cc_final: 0.7627 (tptt) REVERT: D 323 ASP cc_start: 0.7962 (p0) cc_final: 0.7646 (p0) REVERT: D 327 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7578 (ptp90) REVERT: D 382 MET cc_start: 0.6718 (ttp) cc_final: 0.6443 (ttp) REVERT: D 451 GLU cc_start: 0.8178 (tt0) cc_final: 0.7794 (tm-30) REVERT: D 537 MET cc_start: 0.8564 (ptt) cc_final: 0.8350 (ptm) REVERT: D 595 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8348 (mpt90) REVERT: D 604 TRP cc_start: 0.7377 (OUTLIER) cc_final: 0.6020 (t60) REVERT: E 141 MET cc_start: 0.6955 (ttm) cc_final: 0.6715 (ttm) REVERT: E 142 LEU cc_start: 0.5075 (OUTLIER) cc_final: 0.4825 (pp) REVERT: E 161 LYS cc_start: 0.8479 (mmmm) cc_final: 0.8163 (ttmt) REVERT: E 186 LYS cc_start: 0.4921 (OUTLIER) cc_final: 0.4199 (mptp) REVERT: E 242 LYS cc_start: 0.3649 (OUTLIER) cc_final: 0.2805 (tptp) REVERT: E 324 VAL cc_start: 0.8235 (p) cc_final: 0.7936 (t) REVERT: E 353 THR cc_start: 0.7567 (p) cc_final: 0.6645 (t) REVERT: E 366 ASN cc_start: 0.8739 (t0) cc_final: 0.8450 (t0) REVERT: E 367 GLU cc_start: 0.8263 (tp30) cc_final: 0.7894 (mm-30) REVERT: E 398 ARG cc_start: 0.8156 (mtp-110) cc_final: 0.7817 (ptm-80) REVERT: E 401 MET cc_start: 0.7567 (mtt) cc_final: 0.7172 (mtt) REVERT: E 409 GLU cc_start: 0.8387 (tt0) cc_final: 0.8117 (mt-10) REVERT: E 415 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8329 (mp10) REVERT: E 491 ASN cc_start: 0.8123 (t0) cc_final: 0.7765 (t0) REVERT: E 498 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8262 (m110) REVERT: E 546 ASP cc_start: 0.7771 (m-30) cc_final: 0.7482 (m-30) REVERT: E 562 GLN cc_start: 0.8833 (tp40) cc_final: 0.8338 (tp-100) REVERT: F 161 LYS cc_start: 0.8477 (mmmm) cc_final: 0.8239 (mttp) REVERT: F 237 PHE cc_start: 0.7856 (m-10) cc_final: 0.7417 (m-10) REVERT: F 238 GLU cc_start: 0.7970 (tt0) cc_final: 0.7258 (tp30) REVERT: F 281 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.4198 (pt0) REVERT: F 366 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8414 (t0) REVERT: F 398 ARG cc_start: 0.8467 (ttp-170) cc_final: 0.7935 (ttp80) REVERT: F 401 MET cc_start: 0.7061 (mtp) cc_final: 0.6121 (mtp) REVERT: F 407 GLN cc_start: 0.8634 (tt0) cc_final: 0.8353 (tt0) REVERT: F 433 LYS cc_start: 0.8675 (tttt) cc_final: 0.8391 (ttmt) REVERT: F 451 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: F 483 GLU cc_start: 0.8506 (pt0) cc_final: 0.7901 (pm20) REVERT: F 562 GLN cc_start: 0.8511 (tp40) cc_final: 0.8271 (tp-100) REVERT: F 590 ASP cc_start: 0.8434 (t0) cc_final: 0.8231 (t0) REVERT: B 233 VAL cc_start: 0.8250 (m) cc_final: 0.7561 (p) REVERT: B 236 MET cc_start: 0.6848 (mpt) cc_final: 0.6237 (mpt) REVERT: B 237 PHE cc_start: 0.7856 (m-80) cc_final: 0.7576 (m-80) REVERT: B 247 ILE cc_start: 0.1558 (OUTLIER) cc_final: 0.1006 (mp) REVERT: B 329 GLN cc_start: 0.8715 (tp40) cc_final: 0.8127 (mp10) REVERT: B 401 MET cc_start: 0.7321 (mmm) cc_final: 0.6986 (mtt) REVERT: B 409 GLU cc_start: 0.8480 (tt0) cc_final: 0.8184 (mt-10) REVERT: B 413 TYR cc_start: 0.8563 (m-80) cc_final: 0.7976 (m-80) REVERT: B 485 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8661 (t) REVERT: B 562 GLN cc_start: 0.8463 (tp40) cc_final: 0.8129 (tm-30) REVERT: B 582 GLU cc_start: 0.7659 (tp30) cc_final: 0.7435 (tp30) REVERT: B 591 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: B 599 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8160 (pmm-80) REVERT: B 604 TRP cc_start: 0.7665 (OUTLIER) cc_final: 0.6012 (t60) REVERT: C 161 LYS cc_start: 0.8279 (ttpt) cc_final: 0.8058 (ttmt) REVERT: C 167 LEU cc_start: 0.6859 (tp) cc_final: 0.6635 (tp) REVERT: C 200 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6858 (mm) REVERT: C 216 ILE cc_start: 0.7961 (mm) cc_final: 0.7398 (mm) REVERT: C 236 MET cc_start: 0.6675 (tpp) cc_final: 0.6352 (tpp) REVERT: C 237 PHE cc_start: 0.5394 (t80) cc_final: 0.4558 (t80) REVERT: C 247 ILE cc_start: -0.0964 (OUTLIER) cc_final: -0.1802 (mm) REVERT: C 329 GLN cc_start: 0.8682 (tp40) cc_final: 0.8207 (mm-40) REVERT: C 367 GLU cc_start: 0.8575 (tp30) cc_final: 0.8188 (mm-30) REVERT: C 397 GLU cc_start: 0.7915 (pm20) cc_final: 0.7335 (pm20) REVERT: C 398 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7776 (mtm110) REVERT: C 433 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8500 (ttpp) REVERT: C 547 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7636 (mt0) REVERT: C 562 GLN cc_start: 0.8431 (tp40) cc_final: 0.8029 (tp40) REVERT: C 566 ASP cc_start: 0.8686 (m-30) cc_final: 0.8143 (m-30) REVERT: C 591 ASP cc_start: 0.7592 (m-30) cc_final: 0.7168 (m-30) outliers start: 123 outliers final: 101 residues processed: 590 average time/residue: 0.3495 time to fit residues: 297.3772 Evaluate side-chains 624 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 504 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU 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 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 404 THR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 435 THR 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 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 474 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 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 498 ASN 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 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 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 366 ASN Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL 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 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 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 ARG 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 318 VAL 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 418 HIS Chi-restraints excluded: chain B residue 434 VAL 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 599 ARG 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 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 281 GLU 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 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 455 ILE Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 236 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 212 optimal weight: 0.0970 chunk 43 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 588 GLN B 547 GLN ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128925 restraints weight = 126510.818| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 7.19 r_work: 0.3292 rms_B_bonded: 6.54 restraints_weight: 2.0000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 276 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 276 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 19587 Z= 0.188 Angle : 0.773 59.199 26400 Z= 0.446 Chirality : 0.044 0.605 2958 Planarity : 0.004 0.069 3432 Dihedral : 9.938 78.371 2983 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 6.43 % Allowed : 30.56 % Favored : 63.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2400 helix: 1.15 (0.15), residues: 1282 sheet: -1.49 (0.58), residues: 78 loop : -1.20 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.027 0.001 HIS D 418 PHE 0.076 0.002 PHE E 237 TYR 0.017 0.001 TYR B 170 ARG 0.023 0.000 ARG E 596 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 832) hydrogen bonds : angle 4.18298 ( 2457) metal coordination : bond 0.05151 ( 12) covalent geometry : bond 0.00388 (19572) covalent geometry : angle 0.77342 (26400) Misc. bond : bond 0.00007 ( 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 633 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 505 time to evaluate : 2.799 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 161 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7690 (mttm) REVERT: A 190 MET cc_start: 0.6671 (mpp) cc_final: 0.6022 (mtp) REVERT: A 327 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.6918 (mtm-85) REVERT: A 367 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8020 (mm-30) REVERT: A 382 MET cc_start: 0.7124 (pp-130) cc_final: 0.6646 (pp-130) REVERT: A 399 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8450 (ttp80) REVERT: A 407 GLN cc_start: 0.8843 (mt0) cc_final: 0.8452 (mt0) REVERT: A 498 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8462 (t0) REVERT: A 554 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: A 562 GLN cc_start: 0.8351 (tp40) cc_final: 0.8034 (tp-100) REVERT: A 589 ILE cc_start: 0.8255 (mt) cc_final: 0.8028 (mm) REVERT: D 179 LYS cc_start: 0.8031 (mmtp) cc_final: 0.7662 (tptt) REVERT: D 323 ASP cc_start: 0.8073 (p0) cc_final: 0.7754 (p0) REVERT: D 327 ARG cc_start: 0.8035 (mtt90) cc_final: 0.7671 (ptp90) REVERT: D 382 MET cc_start: 0.6805 (ttp) cc_final: 0.6531 (ttp) REVERT: D 451 GLU cc_start: 0.8225 (tt0) cc_final: 0.7781 (tm-30) REVERT: D 537 MET cc_start: 0.8632 (ptt) cc_final: 0.8419 (ptm) REVERT: D 595 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8324 (mpt90) REVERT: D 604 TRP cc_start: 0.7437 (OUTLIER) cc_final: 0.6093 (t60) REVERT: E 141 MET cc_start: 0.7059 (ttm) cc_final: 0.6813 (ttm) REVERT: E 142 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4891 (pp) REVERT: E 161 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8177 (ttmt) REVERT: E 186 LYS cc_start: 0.5072 (OUTLIER) cc_final: 0.4335 (mptp) REVERT: E 238 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7634 (mm-30) REVERT: E 242 LYS cc_start: 0.3814 (OUTLIER) cc_final: 0.2844 (tptp) REVERT: E 324 VAL cc_start: 0.8269 (p) cc_final: 0.7965 (t) REVERT: E 331 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8607 (mp) REVERT: E 353 THR cc_start: 0.7629 (p) cc_final: 0.6621 (t) REVERT: E 366 ASN cc_start: 0.8793 (t0) cc_final: 0.8507 (t0) REVERT: E 367 GLU cc_start: 0.8338 (tp30) cc_final: 0.7965 (mm-30) REVERT: E 398 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.7906 (ptm-80) REVERT: E 401 MET cc_start: 0.7793 (mtt) cc_final: 0.7406 (mtt) REVERT: E 409 GLU cc_start: 0.8482 (tt0) cc_final: 0.8206 (mt-10) REVERT: E 415 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8363 (mp10) REVERT: E 491 ASN cc_start: 0.8233 (t0) cc_final: 0.7894 (t0) REVERT: E 498 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8304 (m110) REVERT: E 562 GLN cc_start: 0.8876 (tp40) cc_final: 0.8382 (tp-100) REVERT: F 161 LYS cc_start: 0.8518 (mmmm) cc_final: 0.8268 (mttp) REVERT: F 237 PHE cc_start: 0.7949 (m-10) cc_final: 0.7510 (m-10) REVERT: F 238 GLU cc_start: 0.8003 (tt0) cc_final: 0.7289 (tp30) REVERT: F 281 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.4186 (pt0) REVERT: F 398 ARG cc_start: 0.8560 (ttp-170) cc_final: 0.8034 (ttp80) REVERT: F 401 MET cc_start: 0.7217 (mtp) cc_final: 0.6309 (mtp) REVERT: F 407 GLN cc_start: 0.8691 (tt0) cc_final: 0.8422 (tt0) REVERT: F 433 LYS cc_start: 0.8726 (tttt) cc_final: 0.8448 (ttmt) REVERT: F 451 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: F 483 GLU cc_start: 0.8619 (pt0) cc_final: 0.8005 (pm20) REVERT: F 562 GLN cc_start: 0.8527 (tp40) cc_final: 0.8298 (tp-100) REVERT: B 233 VAL cc_start: 0.8266 (m) cc_final: 0.7591 (p) REVERT: B 236 MET cc_start: 0.6969 (mpt) cc_final: 0.6349 (mpt) REVERT: B 237 PHE cc_start: 0.7947 (m-80) cc_final: 0.7670 (m-80) REVERT: B 247 ILE cc_start: 0.1690 (OUTLIER) cc_final: 0.1116 (mp) REVERT: B 401 MET cc_start: 0.7500 (mmm) cc_final: 0.7081 (mtt) REVERT: B 409 GLU cc_start: 0.8598 (tt0) cc_final: 0.8305 (mt-10) REVERT: B 413 TYR cc_start: 0.8597 (m-80) cc_final: 0.8010 (m-80) REVERT: B 485 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8677 (t) REVERT: B 582 GLU cc_start: 0.7788 (tp30) cc_final: 0.7583 (tp30) REVERT: B 591 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: B 599 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8189 (pmm-80) REVERT: B 604 TRP cc_start: 0.7705 (OUTLIER) cc_final: 0.6069 (t60) REVERT: C 161 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8105 (ttmt) REVERT: C 167 LEU cc_start: 0.6884 (tp) cc_final: 0.6657 (tp) REVERT: C 200 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6917 (mm) REVERT: C 216 ILE cc_start: 0.7997 (mm) cc_final: 0.7450 (mm) REVERT: C 236 MET cc_start: 0.6720 (tpp) cc_final: 0.6392 (tpp) REVERT: C 237 PHE cc_start: 0.5417 (t80) cc_final: 0.4507 (t80) REVERT: C 247 ILE cc_start: -0.0794 (OUTLIER) cc_final: -0.1679 (mm) REVERT: C 329 GLN cc_start: 0.8767 (tp40) cc_final: 0.8292 (mm-40) REVERT: C 367 GLU cc_start: 0.8635 (tp30) cc_final: 0.8256 (mm-30) REVERT: C 397 GLU cc_start: 0.8030 (pm20) cc_final: 0.7435 (pm20) REVERT: C 398 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7896 (mtm110) REVERT: C 433 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8556 (ttpp) REVERT: C 547 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7722 (mt0) REVERT: C 562 GLN cc_start: 0.8485 (tp40) cc_final: 0.8094 (tp40) REVERT: C 566 ASP cc_start: 0.8734 (m-30) cc_final: 0.8207 (m-30) REVERT: C 591 ASP cc_start: 0.7677 (m-30) cc_final: 0.7249 (m-30) outliers start: 128 outliers final: 106 residues processed: 590 average time/residue: 0.3500 time to fit residues: 297.7367 Evaluate side-chains 622 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 498 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 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 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 404 THR Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR 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 474 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 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 331 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 498 ASN 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 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 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL 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 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 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 ARG 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 318 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL 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 599 ARG 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 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 281 GLU 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 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 455 ILE Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 160 optimal weight: 0.0670 chunk 69 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 588 GLN ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.162447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127911 restraints weight = 105014.073| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 6.33 r_work: 0.3320 rms_B_bonded: 6.06 restraints_weight: 2.0000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 276 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 279 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 19587 Z= 0.188 Angle : 0.773 59.199 26400 Z= 0.446 Chirality : 0.044 0.605 2958 Planarity : 0.004 0.069 3432 Dihedral : 9.938 78.371 2983 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 6.23 % Allowed : 30.81 % Favored : 62.96 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2400 helix: 1.15 (0.15), residues: 1282 sheet: -1.49 (0.58), residues: 78 loop : -1.20 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.027 0.001 HIS D 418 PHE 0.076 0.002 PHE E 237 TYR 0.017 0.001 TYR B 170 ARG 0.023 0.000 ARG E 596 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 832) hydrogen bonds : angle 4.18298 ( 2457) metal coordination : bond 0.05151 ( 12) covalent geometry : bond 0.00388 (19572) covalent geometry : angle 0.77338 (26400) Misc. bond : bond 0.00007 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11786.66 seconds wall clock time: 207 minutes 22.53 seconds (12442.53 seconds total)