Starting phenix.real_space_refine on Fri Mar 6 15:55:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mdm_23775/03_2026/7mdm_23775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdm_23775/03_2026/7mdm_23775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mdm_23775/03_2026/7mdm_23775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdm_23775/03_2026/7mdm_23775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mdm_23775/03_2026/7mdm_23775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdm_23775/03_2026/7mdm_23775.map" } resolution = 4.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.075 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 172 5.16 5 C 20123 2.51 5 N 5597 2.21 5 O 6082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31986 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5513 Classifications: {'peptide': 701} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 662} Chain breaks: 2 Chain: "C" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5527 Classifications: {'peptide': 703} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 664} Chain breaks: 2 Chain: "D" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5527 Classifications: {'peptide': 703} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 664} Chain breaks: 2 Chain: "E" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5532 Classifications: {'peptide': 704} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 665} Chain breaks: 2 Chain: "A" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5513 Classifications: {'peptide': 701} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 662} Chain breaks: 2 Chain: "F" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4212 Classifications: {'peptide': 539} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 510} Chain breaks: 2 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.48, per 1000 atoms: 0.23 Number of scatterers: 31986 At special positions: 0 Unit cell: (104.52, 160.68, 171.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 172 16.00 P 12 15.00 O 6082 8.00 N 5597 7.00 C 20123 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=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7616 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 34 sheets defined 44.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 130 through 140 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 209 through 218 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.908A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.139A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 319 through 326 Processing helix chain 'B' and resid 327 through 334 removed outlier: 4.031A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.590A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.744A pdb=" N LYS B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.665A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 525 through 535 removed outlier: 4.160A pdb=" N LYS B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 Processing helix chain 'B' and resid 555 through 568 Processing helix chain 'B' and resid 578 through 582 removed outlier: 4.005A pdb=" N SER B 581 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 582' Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 671 through 676 removed outlier: 3.514A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 704 Processing helix chain 'B' and resid 732 through 741 Processing helix chain 'B' and resid 750 through 763 removed outlier: 3.960A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.787A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.559A pdb=" N ARG C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.998A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 4.466A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 373 through 384 removed outlier: 3.904A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 407 through 424 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 457 Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.762A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.739A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.877A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 568 removed outlier: 3.788A pdb=" N VAL C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 584 removed outlier: 4.350A pdb=" N LYS C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 612 through 616 removed outlier: 3.786A pdb=" N ASN C 616 " --> pdb=" O THR C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 660 Processing helix chain 'C' and resid 673 through 677 removed outlier: 3.858A pdb=" N LYS C 677 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 703 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.536A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 763 removed outlier: 3.972A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 49 removed outlier: 4.461A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 44 through 49' Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.669A pdb=" N ARG D 64 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.657A pdb=" N ARG D 89 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 140 removed outlier: 4.483A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix removed outlier: 3.631A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 removed outlier: 4.156A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.635A pdb=" N HIS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 4.328A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 275 Processing helix chain 'D' and resid 281 through 294 removed outlier: 4.176A pdb=" N GLU D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.800A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 326 Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.574A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.720A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.699A pdb=" N LEU D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 Processing helix chain 'D' and resid 482 through 495 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 523 through 534 Processing helix chain 'D' and resid 544 through 552 removed outlier: 4.496A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 579 through 584 Processing helix chain 'D' and resid 599 through 607 Processing helix chain 'D' and resid 649 through 659 Processing helix chain 'D' and resid 672 through 677 removed outlier: 4.386A pdb=" N ALA D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 704 Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 751 through 763 Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.880A pdb=" N ARG E 89 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.758A pdb=" N TYR E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 228 through 234 removed outlier: 4.090A pdb=" N ALA E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 270 through 275 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.658A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 removed outlier: 4.153A pdb=" N HIS E 317 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 319 No H-bonds generated for 'chain 'E' and resid 318 through 319' Processing helix chain 'E' and resid 320 through 326 Processing helix chain 'E' and resid 327 through 334 Processing helix chain 'E' and resid 373 through 385 removed outlier: 5.259A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 425 removed outlier: 4.037A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 457 Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 500 through 507 Processing helix chain 'E' and resid 523 through 534 removed outlier: 3.664A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 554 removed outlier: 4.180A pdb=" N PHE E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 569 Processing helix chain 'E' and resid 579 through 584 removed outlier: 3.887A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA E 583 " --> pdb=" O ASP E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 608 removed outlier: 3.501A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 615 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 683 through 704 Processing helix chain 'E' and resid 732 through 740 Processing helix chain 'E' and resid 750 through 763 removed outlier: 4.204A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 92 removed outlier: 4.313A pdb=" N ARG A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 130 through 139 removed outlier: 5.067A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 220 through 226 removed outlier: 4.118A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.558A pdb=" N ILE A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.633A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.518A pdb=" N SER A 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.849A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.810A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.540A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'A' and resid 484 through 495 removed outlier: 4.261A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 4.060A pdb=" N LEU A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 554 removed outlier: 4.037A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 removed outlier: 3.599A pdb=" N VAL A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.634A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 630 through 634 removed outlier: 4.033A pdb=" N ILE A 633 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.596A pdb=" N ALA A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 704 removed outlier: 3.687A pdb=" N ILE A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.276A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 226 removed outlier: 5.632A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix removed outlier: 3.506A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 270 through 276 removed outlier: 3.570A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 319 through 326 Processing helix chain 'F' and resid 327 through 332 Processing helix chain 'F' and resid 373 through 385 removed outlier: 3.855A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 403 removed outlier: 3.863A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 398 through 403' Processing helix chain 'F' and resid 407 through 424 Processing helix chain 'F' and resid 438 through 444 removed outlier: 3.780A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 457 Processing helix chain 'F' and resid 459 through 463 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.740A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.626A pdb=" N LYS F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.806A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 568 removed outlier: 3.544A pdb=" N VAL F 559 " --> pdb=" O SER F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 582 Processing helix chain 'F' and resid 599 through 608 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.717A pdb=" N ILE F 628 " --> pdb=" O ARG F 625 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 625 through 629' Processing helix chain 'F' and resid 649 through 664 removed outlier: 4.324A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 677 Processing helix chain 'F' and resid 683 through 704 Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 749 through 763 removed outlier: 4.066A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 81 through 84 removed outlier: 6.105A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.600A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 118 removed outlier: 7.031A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 241 through 243 removed outlier: 6.128A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.935A pdb=" N ILE B 540 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 575 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 577 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 84 removed outlier: 5.863A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 38 through 41 removed outlier: 5.532A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.771A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 118 removed outlier: 7.521A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 269 removed outlier: 5.848A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 619 through 623 removed outlier: 4.131A pdb=" N VAL C 514 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR C 517 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.228A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 82 removed outlier: 5.584A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 41 removed outlier: 5.499A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.757A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 114 through 118 removed outlier: 6.627A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.948A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.500A pdb=" N PHE D 267 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D 302 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE D 241 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 539 through 543 removed outlier: 3.661A pdb=" N ILE D 540 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 575 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP D 577 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY D 513 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 81 through 82 removed outlier: 5.618A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 41 removed outlier: 5.572A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 118 removed outlier: 7.859A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AC7, first strand: chain 'E' and resid 300 through 302 removed outlier: 5.790A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 538 through 543 removed outlier: 3.920A pdb=" N ASP E 577 " --> pdb=" O ILE E 542 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 81 through 84 Processing sheet with id=AD1, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.657A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AD3, first strand: chain 'A' and resid 151 through 154 removed outlier: 3.723A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.125A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 342 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.903A pdb=" N GLU A 470 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 514 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A 513 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.395A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.198A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 3153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 3.27 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: 9073 1.33 - 1.46: 5643 1.46 - 1.58: 17504 1.58 - 1.70: 19 1.70 - 1.82: 277 Bond restraints: 32516 Sorted by residual: bond pdb=" C CYS A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.334 1.404 -0.071 8.40e-03 1.42e+04 7.11e+01 bond pdb=" CA GLU E 314 " pdb=" C GLU E 314 " ideal model delta sigma weight residual 1.523 1.589 -0.066 1.80e-02 3.09e+03 1.35e+01 bond pdb=" C ASN B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.334 1.407 -0.074 2.34e-02 1.83e+03 9.87e+00 bond pdb=" C ASN A 460 " pdb=" N PRO A 461 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.54e+00 bond pdb=" C ASN D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.34e+00 ... (remaining 32511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 43104 3.72 - 7.44: 697 7.44 - 11.16: 126 11.16 - 14.88: 14 14.88 - 18.60: 1 Bond angle restraints: 43942 Sorted by residual: angle pdb=" C SER F 326 " pdb=" N GLN F 327 " pdb=" CA GLN F 327 " ideal model delta sigma weight residual 121.54 135.92 -14.38 1.91e+00 2.74e-01 5.67e+01 angle pdb=" N LYS F 211 " pdb=" CA LYS F 211 " pdb=" C LYS F 211 " ideal model delta sigma weight residual 114.56 105.37 9.19 1.27e+00 6.20e-01 5.24e+01 angle pdb=" C SER A 326 " pdb=" N GLN A 327 " pdb=" CA GLN A 327 " ideal model delta sigma weight residual 121.54 134.60 -13.06 1.91e+00 2.74e-01 4.67e+01 angle pdb=" CB MET F 740 " pdb=" CG MET F 740 " pdb=" SD MET F 740 " ideal model delta sigma weight residual 112.70 131.30 -18.60 3.00e+00 1.11e-01 3.84e+01 angle pdb=" N ILE D 369 " pdb=" CA ILE D 369 " pdb=" C ILE D 369 " ideal model delta sigma weight residual 112.96 106.95 6.01 1.00e+00 1.00e+00 3.61e+01 ... (remaining 43937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 19630 32.98 - 65.97: 521 65.97 - 98.95: 35 98.95 - 131.94: 6 131.94 - 164.92: 1 Dihedral angle restraints: 20193 sinusoidal: 8483 harmonic: 11710 Sorted by residual: dihedral pdb=" CA ARG B 95 " pdb=" C ARG B 95 " pdb=" N LEU B 96 " pdb=" CA LEU B 96 " ideal model delta harmonic sigma weight residual 180.00 129.94 50.06 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 104.92 -164.92 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" CA LEU A 331 " pdb=" C LEU A 331 " pdb=" N MET A 332 " pdb=" CA MET A 332 " ideal model delta harmonic sigma weight residual 180.00 147.39 32.61 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 20190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4160 0.089 - 0.179: 712 0.179 - 0.268: 79 0.268 - 0.358: 21 0.358 - 0.447: 6 Chirality restraints: 4978 Sorted by residual: chirality pdb=" CB VAL A 108 " pdb=" CA VAL A 108 " pdb=" CG1 VAL A 108 " pdb=" CG2 VAL A 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CB ILE E 303 " pdb=" CA ILE E 303 " pdb=" CG1 ILE E 303 " pdb=" CG2 ILE E 303 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE E 241 " pdb=" CA ILE E 241 " pdb=" CG1 ILE E 241 " pdb=" CG2 ILE E 241 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 4975 not shown) Planarity restraints: 5767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 495 " 0.057 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 496 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 496 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 496 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C GLN B 327 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN B 327 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 328 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 95 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ARG B 95 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG B 95 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 96 " 0.019 2.00e-02 2.50e+03 ... (remaining 5764 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7556 2.79 - 3.32: 30735 3.32 - 3.84: 57779 3.84 - 4.37: 64881 4.37 - 4.90: 103074 Nonbonded interactions: 264025 Sorted by model distance: nonbonded pdb=" O VAL D 258 " pdb=" OG1 THR D 262 " model vdw 2.261 3.040 nonbonded pdb=" O ILE D 274 " pdb=" OG SER D 282 " model vdw 2.274 3.040 nonbonded pdb=" O MET A 757 " pdb=" OG1 THR A 761 " model vdw 2.280 3.040 nonbonded pdb=" O LEU D 381 " pdb=" OG1 THR D 385 " model vdw 2.293 3.040 nonbonded pdb=" O PRO D 246 " pdb=" OG1 THR D 249 " model vdw 2.296 3.040 ... (remaining 264020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 25 through 582 or resid 598 through 901)) selection = (chain 'D' and (resid 25 through 582 or resid 598 through 901)) selection = (chain 'E' and (resid 25 through 582 or resid 598 through 901)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.380 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.005 0.074 32516 Z= 0.251 Angle : 1.189 18.595 43942 Z= 0.623 Chirality : 0.070 0.447 4978 Planarity : 0.008 0.086 5767 Dihedral : 15.375 164.919 12577 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.03 % Allowed : 0.92 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.11), residues: 4015 helix: -2.92 (0.09), residues: 1644 sheet: -1.61 (0.23), residues: 442 loop : -1.87 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 322 TYR 0.031 0.002 TYR A 495 PHE 0.033 0.002 PHE E 302 TRP 0.014 0.002 TRP B 551 HIS 0.011 0.002 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00509 (32516) covalent geometry : angle 1.18942 (43942) hydrogen bonds : bond 0.18098 ( 1085) hydrogen bonds : angle 7.92218 ( 3153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1035 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9259 (mmm) cc_final: 0.8872 (mmm) REVERT: B 135 LEU cc_start: 0.9184 (tt) cc_final: 0.8697 (mm) REVERT: B 256 ARG cc_start: 0.8772 (tpt90) cc_final: 0.8541 (mmm160) REVERT: B 302 PHE cc_start: 0.8322 (t80) cc_final: 0.7936 (t80) REVERT: B 305 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 363 PHE cc_start: 0.8296 (m-10) cc_final: 0.8085 (m-80) REVERT: B 366 GLU cc_start: 0.8566 (pm20) cc_final: 0.8052 (pm20) REVERT: B 369 ILE cc_start: 0.9093 (tt) cc_final: 0.8834 (tp) REVERT: B 381 LEU cc_start: 0.9479 (mt) cc_final: 0.9119 (mt) REVERT: B 388 MET cc_start: 0.8195 (mmp) cc_final: 0.7385 (mmm) REVERT: B 514 VAL cc_start: 0.9004 (p) cc_final: 0.8731 (p) REVERT: B 516 PHE cc_start: 0.9308 (m-80) cc_final: 0.8717 (m-80) REVERT: B 517 TYR cc_start: 0.8232 (p90) cc_final: 0.7330 (p90) REVERT: B 524 LYS cc_start: 0.8819 (mttt) cc_final: 0.7918 (ttpt) REVERT: B 538 ASN cc_start: 0.9099 (t0) cc_final: 0.8129 (m110) REVERT: B 542 ILE cc_start: 0.8969 (mp) cc_final: 0.8643 (mp) REVERT: B 609 ASP cc_start: 0.9033 (m-30) cc_final: 0.8684 (m-30) REVERT: B 611 MET cc_start: 0.8966 (pmm) cc_final: 0.8682 (pmm) REVERT: B 674 PHE cc_start: 0.8311 (m-80) cc_final: 0.8053 (m-80) REVERT: B 678 MET cc_start: 0.7881 (mtt) cc_final: 0.7359 (ptt) REVERT: B 736 PHE cc_start: 0.8628 (m-10) cc_final: 0.8322 (m-10) REVERT: B 756 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8117 (pp20) REVERT: C 148 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8521 (tptp) REVERT: C 162 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7958 (tm-30) REVERT: C 163 PHE cc_start: 0.8891 (m-80) cc_final: 0.8138 (m-80) REVERT: C 200 GLU cc_start: 0.9238 (mm-30) cc_final: 0.9015 (tp30) REVERT: C 203 TYR cc_start: 0.8514 (m-10) cc_final: 0.7212 (m-80) REVERT: C 216 ILE cc_start: 0.9470 (pt) cc_final: 0.9222 (mm) REVERT: C 243 LEU cc_start: 0.9743 (mt) cc_final: 0.8968 (mt) REVERT: C 251 LYS cc_start: 0.9571 (ptpt) cc_final: 0.9338 (mtmm) REVERT: C 260 ASN cc_start: 0.8860 (m110) cc_final: 0.8117 (m110) REVERT: C 269 ILE cc_start: 0.9183 (mp) cc_final: 0.8917 (mp) REVERT: C 285 ASN cc_start: 0.8878 (t160) cc_final: 0.8389 (t0) REVERT: C 288 LYS cc_start: 0.9259 (tmtt) cc_final: 0.8916 (pptt) REVERT: C 291 GLU cc_start: 0.9162 (mp0) cc_final: 0.8633 (pm20) REVERT: C 352 SER cc_start: 0.9306 (m) cc_final: 0.9045 (t) REVERT: C 420 LEU cc_start: 0.9699 (mt) cc_final: 0.9444 (mt) REVERT: C 423 ILE cc_start: 0.9541 (tp) cc_final: 0.9143 (tt) REVERT: C 432 LEU cc_start: 0.8427 (mt) cc_final: 0.7752 (mm) REVERT: C 438 ASP cc_start: 0.8481 (t70) cc_final: 0.8159 (t0) REVERT: C 441 VAL cc_start: 0.8925 (p) cc_final: 0.8663 (p) REVERT: C 442 MET cc_start: 0.8962 (mmp) cc_final: 0.8652 (tpp) REVERT: C 449 MET cc_start: 0.8809 (mmp) cc_final: 0.8101 (mmp) REVERT: C 515 LEU cc_start: 0.8940 (mm) cc_final: 0.8682 (mm) REVERT: C 564 ASP cc_start: 0.8926 (m-30) cc_final: 0.8619 (t0) REVERT: C 609 ASP cc_start: 0.9019 (m-30) cc_final: 0.8614 (m-30) REVERT: C 696 LYS cc_start: 0.9547 (tppt) cc_final: 0.9314 (tttt) REVERT: D 28 VAL cc_start: 0.7316 (t) cc_final: 0.7099 (t) REVERT: D 135 LEU cc_start: 0.8230 (mt) cc_final: 0.7496 (tt) REVERT: D 139 PHE cc_start: 0.8615 (m-80) cc_final: 0.8391 (m-80) REVERT: D 199 ASN cc_start: 0.8533 (p0) cc_final: 0.8023 (p0) REVERT: D 219 MET cc_start: 0.7997 (pmm) cc_final: 0.7425 (pmm) REVERT: D 242 LEU cc_start: 0.9225 (mm) cc_final: 0.8407 (mm) REVERT: D 265 PHE cc_start: 0.7629 (t80) cc_final: 0.6968 (t80) REVERT: D 267 PHE cc_start: 0.8321 (t80) cc_final: 0.8081 (t80) REVERT: D 269 ILE cc_start: 0.9211 (mt) cc_final: 0.8727 (mt) REVERT: D 275 MET cc_start: 0.9439 (ptp) cc_final: 0.9089 (ptp) REVERT: D 302 PHE cc_start: 0.8253 (t80) cc_final: 0.7835 (t80) REVERT: D 315 LYS cc_start: 0.6958 (tptt) cc_final: 0.6242 (tppt) REVERT: D 319 GLU cc_start: 0.9097 (pp20) cc_final: 0.8831 (tm-30) REVERT: D 344 MET cc_start: 0.8732 (ttp) cc_final: 0.8524 (ttp) REVERT: D 388 MET cc_start: 0.8572 (mpp) cc_final: 0.8154 (mpp) REVERT: D 397 GLU cc_start: 0.8992 (mp0) cc_final: 0.8555 (mm-30) REVERT: D 414 LEU cc_start: 0.9112 (tt) cc_final: 0.8806 (tt) REVERT: D 476 TRP cc_start: 0.6295 (m100) cc_final: 0.6031 (m100) REVERT: D 561 GLU cc_start: 0.8169 (pt0) cc_final: 0.7675 (pt0) REVERT: D 562 ILE cc_start: 0.9325 (tp) cc_final: 0.8978 (pt) REVERT: D 575 PHE cc_start: 0.8474 (t80) cc_final: 0.7965 (t80) REVERT: D 656 ILE cc_start: 0.9530 (mt) cc_final: 0.9286 (tp) REVERT: D 700 ARG cc_start: 0.9072 (pmt-80) cc_final: 0.8740 (ptm160) REVERT: E 66 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6377 (mm-30) REVERT: E 86 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7934 (ttp-170) REVERT: E 216 ILE cc_start: 0.9307 (pt) cc_final: 0.8896 (tp) REVERT: E 218 GLU cc_start: 0.9030 (tt0) cc_final: 0.8573 (tm-30) REVERT: E 219 MET cc_start: 0.8894 (ppp) cc_final: 0.8675 (ppp) REVERT: E 269 ILE cc_start: 0.9020 (mp) cc_final: 0.8526 (mp) REVERT: E 291 GLU cc_start: 0.9180 (mp0) cc_final: 0.8859 (mp0) REVERT: E 379 GLU cc_start: 0.9046 (pm20) cc_final: 0.8584 (tp30) REVERT: E 383 ILE cc_start: 0.9571 (mt) cc_final: 0.9286 (mt) REVERT: E 388 MET cc_start: 0.8756 (mmp) cc_final: 0.8545 (mmm) REVERT: E 417 GLU cc_start: 0.9410 (pm20) cc_final: 0.9098 (pm20) REVERT: E 449 MET cc_start: 0.8988 (mmp) cc_final: 0.8524 (mmp) REVERT: E 450 ASP cc_start: 0.8601 (p0) cc_final: 0.8379 (p0) REVERT: E 452 PHE cc_start: 0.8239 (m-10) cc_final: 0.8010 (m-80) REVERT: E 517 TYR cc_start: 0.6672 (p90) cc_final: 0.6399 (p90) REVERT: E 538 ASN cc_start: 0.9126 (t0) cc_final: 0.8607 (m110) REVERT: E 550 MET cc_start: 0.4341 (mmm) cc_final: 0.2849 (tpp) REVERT: E 560 ARG cc_start: 0.9529 (ttt-90) cc_final: 0.9076 (tpp-160) REVERT: E 563 PHE cc_start: 0.9231 (m-10) cc_final: 0.8849 (m-80) REVERT: E 572 CYS cc_start: 0.8156 (p) cc_final: 0.7200 (p) REVERT: E 697 LEU cc_start: 0.8532 (mt) cc_final: 0.8299 (tp) REVERT: E 734 ASP cc_start: 0.9593 (m-30) cc_final: 0.9353 (p0) REVERT: E 736 PHE cc_start: 0.8797 (m-10) cc_final: 0.8310 (m-10) REVERT: E 741 ARG cc_start: 0.8865 (tpm170) cc_final: 0.8476 (mmm-85) REVERT: A 26 LEU cc_start: 0.7949 (mm) cc_final: 0.7614 (mm) REVERT: A 135 LEU cc_start: 0.9192 (tp) cc_final: 0.8903 (tp) REVERT: A 155 ARG cc_start: 0.8346 (mpp-170) cc_final: 0.7697 (ttm-80) REVERT: A 158 MET cc_start: 0.7657 (tmm) cc_final: 0.7189 (tmm) REVERT: A 163 PHE cc_start: 0.8551 (m-10) cc_final: 0.7631 (m-80) REVERT: A 216 ILE cc_start: 0.9431 (pt) cc_final: 0.9053 (mm) REVERT: A 221 GLU cc_start: 0.8435 (pm20) cc_final: 0.8054 (pp20) REVERT: A 237 PRO cc_start: 0.8256 (Cg_endo) cc_final: 0.7444 (Cg_exo) REVERT: A 243 LEU cc_start: 0.9320 (mm) cc_final: 0.9086 (mm) REVERT: A 244 TYR cc_start: 0.7841 (p90) cc_final: 0.7182 (p90) REVERT: A 253 LEU cc_start: 0.8904 (mt) cc_final: 0.8284 (mt) REVERT: A 344 MET cc_start: 0.7858 (mmp) cc_final: 0.7126 (mmp) REVERT: A 349 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8311 (ttm-80) REVERT: A 366 GLU cc_start: 0.7135 (tt0) cc_final: 0.6606 (tt0) REVERT: A 375 THR cc_start: 0.9284 (p) cc_final: 0.9039 (t) REVERT: A 381 LEU cc_start: 0.8967 (tt) cc_final: 0.8472 (tt) REVERT: A 386 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8640 (mmmt) REVERT: A 395 ASP cc_start: 0.8194 (m-30) cc_final: 0.7892 (m-30) REVERT: A 396 LEU cc_start: 0.8490 (mt) cc_final: 0.8253 (mm) REVERT: A 516 PHE cc_start: 0.9018 (m-80) cc_final: 0.8162 (m-80) REVERT: A 541 SER cc_start: 0.9096 (t) cc_final: 0.8634 (t) REVERT: A 549 THR cc_start: 0.8989 (t) cc_final: 0.8769 (t) REVERT: A 564 ASP cc_start: 0.9158 (t0) cc_final: 0.8721 (t0) REVERT: A 644 TYR cc_start: 0.6641 (t80) cc_final: 0.6208 (t80) REVERT: A 651 LYS cc_start: 0.9309 (pttt) cc_final: 0.8949 (tmtt) REVERT: A 752 ILE cc_start: 0.8714 (tt) cc_final: 0.8103 (pt) REVERT: F 204 ASP cc_start: 0.8939 (m-30) cc_final: 0.8262 (p0) REVERT: F 222 LEU cc_start: 0.9265 (tp) cc_final: 0.8402 (tp) REVERT: F 337 GLN cc_start: 0.6674 (mm110) cc_final: 0.4681 (tp40) REVERT: F 351 ASN cc_start: 0.9394 (p0) cc_final: 0.8955 (p0) REVERT: F 357 LEU cc_start: 0.9317 (tp) cc_final: 0.8786 (tp) REVERT: F 364 ASP cc_start: 0.7094 (m-30) cc_final: 0.6750 (m-30) REVERT: F 366 GLU cc_start: 0.7803 (mp0) cc_final: 0.7546 (pm20) REVERT: F 378 LEU cc_start: 0.9749 (tp) cc_final: 0.9500 (tp) REVERT: F 423 ILE cc_start: 0.8429 (pt) cc_final: 0.8166 (mm) REVERT: F 427 MET cc_start: 0.7306 (tpt) cc_final: 0.5653 (tpp) REVERT: F 465 ARG cc_start: 0.6534 (tpt170) cc_final: 0.6076 (ptm160) REVERT: F 470 GLU cc_start: 0.8047 (pp20) cc_final: 0.7411 (pm20) REVERT: F 508 MET cc_start: 0.1107 (ttm) cc_final: 0.0729 (ttm) REVERT: F 609 ASP cc_start: 0.9356 (m-30) cc_final: 0.8755 (m-30) REVERT: F 611 MET cc_start: 0.8384 (pmm) cc_final: 0.8016 (pmm) REVERT: F 678 MET cc_start: 0.7675 (tpt) cc_final: 0.7419 (ttm) REVERT: F 737 GLU cc_start: 0.7097 (tp30) cc_final: 0.6620 (mt-10) REVERT: F 740 MET cc_start: 0.4074 (pmm) cc_final: 0.2914 (pmm) outliers start: 1 outliers final: 0 residues processed: 1036 average time/residue: 0.2366 time to fit residues: 373.5030 Evaluate side-chains 671 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 671 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 760 GLN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 384 HIS C 406 HIS C 458 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 GLN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS E 401 ASN E 692 GLN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS A 499 HIS A 558 ASN F 296 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN F 499 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.097735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.073400 restraints weight = 133967.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.076003 restraints weight = 94931.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.077980 restraints weight = 72488.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.079465 restraints weight = 58447.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.080613 restraints weight = 49197.975| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32516 Z= 0.182 Angle : 0.785 11.896 43942 Z= 0.402 Chirality : 0.048 0.165 4978 Planarity : 0.006 0.080 5767 Dihedral : 8.184 160.376 4446 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.12 % Allowed : 6.46 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.12), residues: 4015 helix: -1.75 (0.11), residues: 1670 sheet: -1.36 (0.23), residues: 472 loop : -1.61 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 638 TYR 0.021 0.002 TYR D 495 PHE 0.031 0.002 PHE A 563 TRP 0.010 0.001 TRP C 476 HIS 0.012 0.002 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00392 (32516) covalent geometry : angle 0.78512 (43942) hydrogen bonds : bond 0.04536 ( 1085) hydrogen bonds : angle 6.18686 ( 3153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 793 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 LYS cc_start: 0.9315 (pttm) cc_final: 0.8868 (pttm) REVERT: B 84 MET cc_start: 0.9197 (mmm) cc_final: 0.8752 (mmm) REVERT: B 100 ILE cc_start: 0.8767 (mt) cc_final: 0.8210 (mt) REVERT: B 134 TYR cc_start: 0.7007 (m-80) cc_final: 0.6522 (m-80) REVERT: B 152 PHE cc_start: 0.7136 (p90) cc_final: 0.6546 (p90) REVERT: B 200 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8278 (mt-10) REVERT: B 209 CYS cc_start: 0.7544 (m) cc_final: 0.7032 (m) REVERT: B 256 ARG cc_start: 0.9257 (tpt90) cc_final: 0.8364 (mmm160) REVERT: B 302 PHE cc_start: 0.8334 (t80) cc_final: 0.7020 (t80) REVERT: B 305 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8010 (mm-30) REVERT: B 330 THR cc_start: 0.9018 (m) cc_final: 0.8808 (m) REVERT: B 344 MET cc_start: 0.9084 (tpt) cc_final: 0.8864 (tpt) REVERT: B 366 GLU cc_start: 0.8931 (pm20) cc_final: 0.8176 (pm20) REVERT: B 379 GLU cc_start: 0.9285 (tp30) cc_final: 0.8716 (pt0) REVERT: B 388 MET cc_start: 0.8393 (mmp) cc_final: 0.7520 (mmm) REVERT: B 514 VAL cc_start: 0.8297 (p) cc_final: 0.7730 (p) REVERT: B 517 TYR cc_start: 0.8458 (p90) cc_final: 0.7813 (p90) REVERT: B 538 ASN cc_start: 0.9281 (t0) cc_final: 0.8935 (t0) REVERT: B 576 PHE cc_start: 0.8479 (t80) cc_final: 0.8254 (t80) REVERT: B 608 MET cc_start: 0.8860 (ptp) cc_final: 0.8342 (ptp) REVERT: B 611 MET cc_start: 0.9160 (pmm) cc_final: 0.8700 (pmm) REVERT: B 649 ASP cc_start: 0.8172 (p0) cc_final: 0.7967 (p0) REVERT: B 678 MET cc_start: 0.7973 (mtt) cc_final: 0.6970 (ptt) REVERT: B 736 PHE cc_start: 0.8610 (m-10) cc_final: 0.8338 (m-10) REVERT: C 131 PHE cc_start: 0.8114 (m-10) cc_final: 0.7796 (m-10) REVERT: C 148 LYS cc_start: 0.8906 (tmtt) cc_final: 0.8620 (tptp) REVERT: C 154 VAL cc_start: 0.8444 (t) cc_final: 0.8241 (t) REVERT: C 163 PHE cc_start: 0.8744 (m-80) cc_final: 0.8016 (m-80) REVERT: C 190 LYS cc_start: 0.9597 (pptt) cc_final: 0.9310 (pptt) REVERT: C 200 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9145 (tp30) REVERT: C 221 GLU cc_start: 0.8001 (pt0) cc_final: 0.7552 (pt0) REVERT: C 244 TYR cc_start: 0.7646 (p90) cc_final: 0.7409 (p90) REVERT: C 260 ASN cc_start: 0.8902 (m110) cc_final: 0.8478 (m110) REVERT: C 265 PHE cc_start: 0.8537 (t80) cc_final: 0.8297 (t80) REVERT: C 268 LEU cc_start: 0.9069 (tp) cc_final: 0.8716 (tt) REVERT: C 269 ILE cc_start: 0.9215 (mp) cc_final: 0.8836 (mp) REVERT: C 288 LYS cc_start: 0.9241 (tmtt) cc_final: 0.8923 (pptt) REVERT: C 306 LEU cc_start: 0.9041 (mm) cc_final: 0.8724 (mm) REVERT: C 362 ARG cc_start: 0.7594 (mpp-170) cc_final: 0.7268 (mmt90) REVERT: C 378 LEU cc_start: 0.9269 (mt) cc_final: 0.8890 (pp) REVERT: C 432 LEU cc_start: 0.7940 (mt) cc_final: 0.7738 (mm) REVERT: C 449 MET cc_start: 0.8847 (mmp) cc_final: 0.8010 (mmp) REVERT: C 515 LEU cc_start: 0.8934 (mm) cc_final: 0.8703 (mm) REVERT: C 542 ILE cc_start: 0.9092 (tp) cc_final: 0.8878 (tp) REVERT: C 609 ASP cc_start: 0.9106 (m-30) cc_final: 0.8494 (m-30) REVERT: C 673 GLU cc_start: 0.9263 (tp30) cc_final: 0.8602 (mp0) REVERT: C 696 LYS cc_start: 0.9698 (tppt) cc_final: 0.9403 (mptt) REVERT: D 99 VAL cc_start: 0.8803 (t) cc_final: 0.8596 (p) REVERT: D 135 LEU cc_start: 0.8513 (mt) cc_final: 0.8019 (mt) REVERT: D 139 PHE cc_start: 0.8898 (m-80) cc_final: 0.8589 (m-80) REVERT: D 158 MET cc_start: 0.7479 (ppp) cc_final: 0.7086 (ppp) REVERT: D 162 GLU cc_start: 0.8264 (pp20) cc_final: 0.7952 (pp20) REVERT: D 199 ASN cc_start: 0.8872 (p0) cc_final: 0.8569 (p0) REVERT: D 219 MET cc_start: 0.8187 (pmm) cc_final: 0.7463 (pmm) REVERT: D 241 ILE cc_start: 0.8470 (tp) cc_final: 0.8210 (tp) REVERT: D 265 PHE cc_start: 0.8005 (t80) cc_final: 0.7394 (t80) REVERT: D 269 ILE cc_start: 0.9200 (mt) cc_final: 0.8926 (mt) REVERT: D 301 ILE cc_start: 0.9161 (mp) cc_final: 0.8857 (mp) REVERT: D 313 ARG cc_start: 0.7557 (tmm160) cc_final: 0.7212 (ptm-80) REVERT: D 315 LYS cc_start: 0.6750 (tptt) cc_final: 0.6515 (tppt) REVERT: D 319 GLU cc_start: 0.9472 (pp20) cc_final: 0.9181 (pp20) REVERT: D 366 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8113 (mp0) REVERT: D 385 THR cc_start: 0.9316 (p) cc_final: 0.9041 (p) REVERT: D 388 MET cc_start: 0.8818 (mpp) cc_final: 0.8109 (mpp) REVERT: D 404 HIS cc_start: 0.8315 (p-80) cc_final: 0.7842 (p-80) REVERT: D 414 LEU cc_start: 0.8932 (tt) cc_final: 0.8684 (tt) REVERT: D 476 TRP cc_start: 0.6756 (m100) cc_final: 0.6064 (m100) REVERT: D 508 MET cc_start: 0.1658 (ptt) cc_final: 0.0595 (ptt) REVERT: D 515 LEU cc_start: 0.9277 (mm) cc_final: 0.8986 (mm) REVERT: D 516 PHE cc_start: 0.8754 (m-80) cc_final: 0.8368 (m-80) REVERT: D 550 MET cc_start: 0.6101 (pmm) cc_final: 0.5691 (pmm) REVERT: D 575 PHE cc_start: 0.8910 (t80) cc_final: 0.8675 (t80) REVERT: D 609 ASP cc_start: 0.9024 (p0) cc_final: 0.8736 (p0) REVERT: D 656 ILE cc_start: 0.9500 (mt) cc_final: 0.9288 (tp) REVERT: D 678 MET cc_start: 0.3838 (ptt) cc_final: 0.3356 (ptt) REVERT: D 700 ARG cc_start: 0.9043 (pmt-80) cc_final: 0.8607 (ptm160) REVERT: E 28 VAL cc_start: 0.8143 (m) cc_final: 0.7766 (m) REVERT: E 66 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6252 (mm-30) REVERT: E 218 GLU cc_start: 0.9219 (tt0) cc_final: 0.8861 (tm-30) REVERT: E 219 MET cc_start: 0.9065 (ppp) cc_final: 0.8292 (ptm) REVERT: E 275 MET cc_start: 0.9198 (mpp) cc_final: 0.8971 (mpp) REVERT: E 291 GLU cc_start: 0.9180 (mp0) cc_final: 0.8600 (tp30) REVERT: E 305 GLU cc_start: 0.7850 (mp0) cc_final: 0.7552 (mp0) REVERT: E 388 MET cc_start: 0.8641 (mmp) cc_final: 0.8430 (mmm) REVERT: E 449 MET cc_start: 0.9139 (mmp) cc_final: 0.8509 (mmp) REVERT: E 451 ASP cc_start: 0.8574 (m-30) cc_final: 0.8296 (m-30) REVERT: E 452 PHE cc_start: 0.7856 (m-10) cc_final: 0.7504 (m-80) REVERT: E 470 GLU cc_start: 0.8524 (tt0) cc_final: 0.7834 (tm-30) REVERT: E 515 LEU cc_start: 0.9065 (mm) cc_final: 0.8852 (mm) REVERT: E 538 ASN cc_start: 0.8700 (t0) cc_final: 0.8281 (m110) REVERT: E 550 MET cc_start: 0.3904 (mmm) cc_final: 0.2500 (tpp) REVERT: E 560 ARG cc_start: 0.9515 (ttt-90) cc_final: 0.9041 (tpp-160) REVERT: E 563 PHE cc_start: 0.9224 (m-10) cc_final: 0.8826 (m-80) REVERT: E 564 ASP cc_start: 0.9245 (m-30) cc_final: 0.8765 (m-30) REVERT: E 579 LEU cc_start: 0.8838 (pt) cc_final: 0.8617 (mm) REVERT: E 615 LYS cc_start: 0.8677 (mmtm) cc_final: 0.7832 (mptt) REVERT: E 734 ASP cc_start: 0.9504 (m-30) cc_final: 0.9286 (p0) REVERT: E 736 PHE cc_start: 0.8744 (m-10) cc_final: 0.8437 (m-10) REVERT: A 64 ARG cc_start: 0.8648 (tpt90) cc_final: 0.8076 (tpm170) REVERT: A 80 GLU cc_start: 0.9053 (pm20) cc_final: 0.8826 (pm20) REVERT: A 158 MET cc_start: 0.8193 (tmm) cc_final: 0.7965 (tmm) REVERT: A 163 PHE cc_start: 0.8661 (m-10) cc_final: 0.7891 (m-80) REVERT: A 237 PRO cc_start: 0.8001 (Cg_endo) cc_final: 0.7495 (Cg_exo) REVERT: A 241 ILE cc_start: 0.8725 (tp) cc_final: 0.8126 (tp) REVERT: A 243 LEU cc_start: 0.9259 (mm) cc_final: 0.8957 (mm) REVERT: A 244 TYR cc_start: 0.8172 (p90) cc_final: 0.7525 (p90) REVERT: A 253 LEU cc_start: 0.9395 (mt) cc_final: 0.8981 (mt) REVERT: A 269 ILE cc_start: 0.9659 (mt) cc_final: 0.9384 (mt) REVERT: A 286 LEU cc_start: 0.9050 (mt) cc_final: 0.8845 (mt) REVERT: A 287 ARG cc_start: 0.9274 (mmp80) cc_final: 0.9056 (mmp80) REVERT: A 304 ASP cc_start: 0.7920 (p0) cc_final: 0.7327 (p0) REVERT: A 344 MET cc_start: 0.8685 (mmp) cc_final: 0.7788 (mmp) REVERT: A 349 ARG cc_start: 0.8937 (ttm110) cc_final: 0.8362 (ttm-80) REVERT: A 366 GLU cc_start: 0.7515 (tt0) cc_final: 0.6905 (tt0) REVERT: A 375 THR cc_start: 0.9044 (p) cc_final: 0.8235 (t) REVERT: A 388 MET cc_start: 0.7962 (mpp) cc_final: 0.7628 (mpp) REVERT: A 417 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8919 (tp30) REVERT: A 459 SER cc_start: 0.9442 (t) cc_final: 0.9091 (m) REVERT: A 516 PHE cc_start: 0.9244 (m-80) cc_final: 0.8422 (m-80) REVERT: A 644 TYR cc_start: 0.6750 (t80) cc_final: 0.6486 (t80) REVERT: A 651 LYS cc_start: 0.9361 (pttt) cc_final: 0.8911 (tmtt) REVERT: A 752 ILE cc_start: 0.8185 (tt) cc_final: 0.7944 (pt) REVERT: F 204 ASP cc_start: 0.8740 (m-30) cc_final: 0.8023 (p0) REVERT: F 222 LEU cc_start: 0.9504 (tp) cc_final: 0.8534 (tp) REVERT: F 242 LEU cc_start: 0.9296 (mt) cc_final: 0.8945 (mt) REVERT: F 251 LYS cc_start: 0.9611 (mtmt) cc_final: 0.9364 (mtpt) REVERT: F 253 LEU cc_start: 0.9736 (mm) cc_final: 0.9509 (mm) REVERT: F 269 ILE cc_start: 0.9627 (mt) cc_final: 0.8844 (mt) REVERT: F 337 GLN cc_start: 0.7132 (mm110) cc_final: 0.4910 (tp40) REVERT: F 338 ARG cc_start: 0.8490 (tpp80) cc_final: 0.8244 (tpp80) REVERT: F 351 ASN cc_start: 0.9289 (p0) cc_final: 0.8995 (p0) REVERT: F 368 ASP cc_start: 0.8815 (t0) cc_final: 0.8582 (t0) REVERT: F 442 MET cc_start: 0.8174 (mmp) cc_final: 0.7082 (ptt) REVERT: F 465 ARG cc_start: 0.6705 (tpt170) cc_final: 0.5531 (mtm180) REVERT: F 470 GLU cc_start: 0.8038 (pp20) cc_final: 0.7327 (pm20) REVERT: F 495 TYR cc_start: 0.8771 (m-80) cc_final: 0.8267 (m-80) REVERT: F 517 TYR cc_start: 0.9224 (p90) cc_final: 0.8958 (p90) REVERT: F 609 ASP cc_start: 0.9005 (m-30) cc_final: 0.8610 (m-30) REVERT: F 611 MET cc_start: 0.8468 (pmm) cc_final: 0.8079 (pmm) REVERT: F 644 TYR cc_start: 0.8757 (t80) cc_final: 0.8281 (t80) REVERT: F 678 MET cc_start: 0.8413 (tpt) cc_final: 0.8087 (mtp) REVERT: F 740 MET cc_start: 0.4354 (pmm) cc_final: 0.3186 (pmm) outliers start: 4 outliers final: 0 residues processed: 795 average time/residue: 0.2198 time to fit residues: 271.4843 Evaluate side-chains 593 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 346 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 365 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 203 optimal weight: 20.0000 chunk 164 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 568 GLN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 406 HIS C 568 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 499 HIS F 199 ASN F 260 ASN F 499 HIS F 624 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.094980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070658 restraints weight = 136691.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073247 restraints weight = 95505.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.075194 restraints weight = 72243.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.076667 restraints weight = 58013.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.077776 restraints weight = 48806.570| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32516 Z= 0.191 Angle : 0.772 11.697 43942 Z= 0.393 Chirality : 0.049 0.192 4978 Planarity : 0.006 0.070 5767 Dihedral : 7.989 168.893 4446 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.06 % Allowed : 6.63 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.13), residues: 4015 helix: -1.36 (0.12), residues: 1682 sheet: -1.41 (0.22), residues: 504 loop : -1.43 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 424 TYR 0.018 0.002 TYR C 755 PHE 0.018 0.002 PHE F 360 TRP 0.028 0.002 TRP B 551 HIS 0.024 0.002 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00399 (32516) covalent geometry : angle 0.77225 (43942) hydrogen bonds : bond 0.04126 ( 1085) hydrogen bonds : angle 6.01272 ( 3153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 744 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8155 (mmp) cc_final: 0.7853 (mmm) REVERT: B 63 LYS cc_start: 0.9287 (pttm) cc_final: 0.8958 (pttm) REVERT: B 84 MET cc_start: 0.9183 (mmm) cc_final: 0.8725 (mmm) REVERT: B 200 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 239 ARG cc_start: 0.8521 (mmm160) cc_final: 0.8090 (tpp-160) REVERT: B 302 PHE cc_start: 0.8359 (t80) cc_final: 0.7101 (t80) REVERT: B 305 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 330 THR cc_start: 0.9104 (m) cc_final: 0.8885 (m) REVERT: B 366 GLU cc_start: 0.8978 (pm20) cc_final: 0.8310 (pm20) REVERT: B 379 GLU cc_start: 0.9318 (tp30) cc_final: 0.8749 (pt0) REVERT: B 388 MET cc_start: 0.8445 (mmp) cc_final: 0.7813 (mmm) REVERT: B 426 LYS cc_start: 0.9625 (mptt) cc_final: 0.9402 (mmtt) REVERT: B 451 ASP cc_start: 0.8633 (m-30) cc_final: 0.8360 (m-30) REVERT: B 514 VAL cc_start: 0.8052 (p) cc_final: 0.7796 (p) REVERT: B 517 TYR cc_start: 0.8453 (p90) cc_final: 0.7710 (p90) REVERT: B 538 ASN cc_start: 0.9335 (t0) cc_final: 0.8953 (t0) REVERT: B 608 MET cc_start: 0.8976 (ptp) cc_final: 0.8518 (ptp) REVERT: B 609 ASP cc_start: 0.9118 (m-30) cc_final: 0.8856 (m-30) REVERT: B 611 MET cc_start: 0.9245 (pmm) cc_final: 0.8772 (pmm) REVERT: B 678 MET cc_start: 0.7605 (mtt) cc_final: 0.6809 (ptt) REVERT: B 736 PHE cc_start: 0.8632 (m-10) cc_final: 0.8356 (m-10) REVERT: B 757 MET cc_start: 0.8297 (ttt) cc_final: 0.7882 (tmm) REVERT: C 131 PHE cc_start: 0.8127 (m-10) cc_final: 0.7822 (m-10) REVERT: C 139 PHE cc_start: 0.8712 (m-10) cc_final: 0.8488 (m-10) REVERT: C 154 VAL cc_start: 0.8392 (t) cc_final: 0.8115 (t) REVERT: C 163 PHE cc_start: 0.8801 (m-80) cc_final: 0.8162 (m-80) REVERT: C 190 LYS cc_start: 0.9582 (pptt) cc_final: 0.9257 (pptt) REVERT: C 200 GLU cc_start: 0.9422 (mm-30) cc_final: 0.9158 (tp30) REVERT: C 203 TYR cc_start: 0.8636 (m-10) cc_final: 0.7763 (m-10) REVERT: C 221 GLU cc_start: 0.8110 (pt0) cc_final: 0.7781 (pt0) REVERT: C 244 TYR cc_start: 0.7578 (p90) cc_final: 0.7170 (p90) REVERT: C 260 ASN cc_start: 0.8510 (m110) cc_final: 0.8164 (m110) REVERT: C 269 ILE cc_start: 0.9232 (mp) cc_final: 0.9022 (mp) REVERT: C 291 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9111 (pt0) REVERT: C 306 LEU cc_start: 0.9039 (mm) cc_final: 0.8666 (mm) REVERT: C 340 HIS cc_start: 0.7219 (m90) cc_final: 0.7018 (m90) REVERT: C 362 ARG cc_start: 0.7591 (mpp-170) cc_final: 0.7367 (mpt180) REVERT: C 449 MET cc_start: 0.8735 (mmp) cc_final: 0.8093 (mmp) REVERT: C 467 THR cc_start: 0.8391 (t) cc_final: 0.8055 (p) REVERT: C 515 LEU cc_start: 0.9056 (mm) cc_final: 0.8803 (mm) REVERT: C 609 ASP cc_start: 0.9111 (m-30) cc_final: 0.8460 (m-30) REVERT: C 639 LEU cc_start: 0.6674 (mm) cc_final: 0.6365 (mm) REVERT: C 662 ARG cc_start: 0.9070 (tmm160) cc_final: 0.8825 (ttp80) REVERT: C 696 LYS cc_start: 0.9723 (tppt) cc_final: 0.9217 (mttt) REVERT: D 114 ILE cc_start: 0.5981 (tp) cc_final: 0.5457 (mm) REVERT: D 135 LEU cc_start: 0.8498 (mt) cc_final: 0.7970 (mt) REVERT: D 139 PHE cc_start: 0.8859 (m-80) cc_final: 0.8527 (m-80) REVERT: D 158 MET cc_start: 0.6811 (ppp) cc_final: 0.6344 (ppp) REVERT: D 199 ASN cc_start: 0.8906 (p0) cc_final: 0.8568 (p0) REVERT: D 219 MET cc_start: 0.8516 (pmm) cc_final: 0.7663 (pmm) REVERT: D 265 PHE cc_start: 0.8084 (t80) cc_final: 0.7550 (t80) REVERT: D 268 LEU cc_start: 0.9591 (tt) cc_final: 0.9382 (tt) REVERT: D 291 GLU cc_start: 0.8876 (pm20) cc_final: 0.8644 (pp20) REVERT: D 301 ILE cc_start: 0.9214 (mp) cc_final: 0.8888 (mp) REVERT: D 302 PHE cc_start: 0.8806 (t80) cc_final: 0.8488 (t80) REVERT: D 304 ASP cc_start: 0.7572 (p0) cc_final: 0.7254 (p0) REVERT: D 315 LYS cc_start: 0.7097 (tptt) cc_final: 0.6772 (tppt) REVERT: D 319 GLU cc_start: 0.9536 (pp20) cc_final: 0.9302 (pp20) REVERT: D 366 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8175 (mp0) REVERT: D 386 LYS cc_start: 0.9356 (ttpt) cc_final: 0.8933 (ptmm) REVERT: D 388 MET cc_start: 0.8980 (mpp) cc_final: 0.8362 (mpp) REVERT: D 404 HIS cc_start: 0.8456 (p-80) cc_final: 0.8006 (p-80) REVERT: D 449 MET cc_start: 0.8953 (mmp) cc_final: 0.8679 (mmp) REVERT: D 476 TRP cc_start: 0.6866 (m100) cc_final: 0.6661 (m100) REVERT: D 508 MET cc_start: 0.2361 (ptt) cc_final: 0.1372 (ptt) REVERT: D 516 PHE cc_start: 0.8675 (m-80) cc_final: 0.8456 (m-10) REVERT: D 550 MET cc_start: 0.5973 (pmm) cc_final: 0.5574 (pmm) REVERT: D 565 LYS cc_start: 0.9235 (ptmt) cc_final: 0.8928 (tptt) REVERT: D 575 PHE cc_start: 0.8853 (t80) cc_final: 0.8165 (t80) REVERT: D 609 ASP cc_start: 0.9002 (p0) cc_final: 0.8719 (p0) REVERT: D 678 MET cc_start: 0.3069 (ptt) cc_final: 0.2827 (ptt) REVERT: D 687 LEU cc_start: 0.9578 (mt) cc_final: 0.9298 (mt) REVERT: D 700 ARG cc_start: 0.9094 (pmt-80) cc_final: 0.8375 (tmm160) REVERT: E 218 GLU cc_start: 0.9372 (tt0) cc_final: 0.9031 (tm-30) REVERT: E 219 MET cc_start: 0.9191 (ppp) cc_final: 0.8628 (ppp) REVERT: E 275 MET cc_start: 0.9213 (mpp) cc_final: 0.8962 (mpp) REVERT: E 291 GLU cc_start: 0.9345 (mp0) cc_final: 0.8665 (tp30) REVERT: E 388 MET cc_start: 0.8951 (mmp) cc_final: 0.8705 (mmm) REVERT: E 449 MET cc_start: 0.9236 (mmp) cc_final: 0.8609 (mmp) REVERT: E 451 ASP cc_start: 0.8497 (m-30) cc_final: 0.8249 (m-30) REVERT: E 452 PHE cc_start: 0.7553 (m-80) cc_final: 0.7207 (m-80) REVERT: E 470 GLU cc_start: 0.8559 (tt0) cc_final: 0.7770 (tm-30) REVERT: E 538 ASN cc_start: 0.8807 (t0) cc_final: 0.8284 (m-40) REVERT: E 550 MET cc_start: 0.3978 (mmm) cc_final: 0.2567 (tpp) REVERT: E 560 ARG cc_start: 0.9517 (ttt-90) cc_final: 0.9073 (tpp-160) REVERT: E 563 PHE cc_start: 0.9193 (m-10) cc_final: 0.8798 (m-80) REVERT: E 564 ASP cc_start: 0.9267 (m-30) cc_final: 0.8776 (m-30) REVERT: E 579 LEU cc_start: 0.8901 (pt) cc_final: 0.8653 (mm) REVERT: E 736 PHE cc_start: 0.8671 (m-10) cc_final: 0.8351 (m-10) REVERT: A 64 ARG cc_start: 0.8604 (tpt90) cc_final: 0.7994 (tpm170) REVERT: A 80 GLU cc_start: 0.9086 (pm20) cc_final: 0.8860 (pm20) REVERT: A 135 LEU cc_start: 0.9122 (tp) cc_final: 0.8876 (tp) REVERT: A 163 PHE cc_start: 0.8794 (m-10) cc_final: 0.7970 (m-80) REVERT: A 221 GLU cc_start: 0.8480 (pm20) cc_final: 0.8267 (pm20) REVERT: A 243 LEU cc_start: 0.9339 (mm) cc_final: 0.9063 (mm) REVERT: A 253 LEU cc_start: 0.9364 (mt) cc_final: 0.8721 (mt) REVERT: A 256 ARG cc_start: 0.9086 (mtm-85) cc_final: 0.8392 (mtm-85) REVERT: A 344 MET cc_start: 0.8800 (mmp) cc_final: 0.7959 (mmp) REVERT: A 349 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8791 (mmm-85) REVERT: A 369 ILE cc_start: 0.9363 (tp) cc_final: 0.9142 (tp) REVERT: A 388 MET cc_start: 0.8091 (mpp) cc_final: 0.7575 (mpp) REVERT: A 417 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8855 (tp30) REVERT: A 459 SER cc_start: 0.9483 (t) cc_final: 0.9081 (m) REVERT: A 516 PHE cc_start: 0.9181 (m-80) cc_final: 0.8242 (m-80) REVERT: A 635 ARG cc_start: 0.9083 (mpp-170) cc_final: 0.8674 (mtt90) REVERT: A 651 LYS cc_start: 0.9398 (pttt) cc_final: 0.9009 (tmtt) REVERT: F 204 ASP cc_start: 0.8823 (m-30) cc_final: 0.8083 (p0) REVERT: F 231 LYS cc_start: 0.8295 (ptpt) cc_final: 0.7987 (ptpt) REVERT: F 242 LEU cc_start: 0.9281 (mt) cc_final: 0.8890 (mt) REVERT: F 251 LYS cc_start: 0.9563 (mtmt) cc_final: 0.9330 (mtpt) REVERT: F 253 LEU cc_start: 0.9766 (mm) cc_final: 0.9546 (mm) REVERT: F 329 LEU cc_start: 0.9489 (mt) cc_final: 0.9188 (mm) REVERT: F 337 GLN cc_start: 0.6904 (mm110) cc_final: 0.4543 (tp40) REVERT: F 338 ARG cc_start: 0.8589 (tpp80) cc_final: 0.8369 (tpp80) REVERT: F 417 GLU cc_start: 0.9590 (mp0) cc_final: 0.9297 (mp0) REVERT: F 442 MET cc_start: 0.8563 (mmp) cc_final: 0.7452 (ptt) REVERT: F 470 GLU cc_start: 0.8134 (pp20) cc_final: 0.7479 (pm20) REVERT: F 495 TYR cc_start: 0.8945 (m-80) cc_final: 0.8522 (m-80) REVERT: F 508 MET cc_start: -0.0343 (ttt) cc_final: -0.1527 (tmm) REVERT: F 608 MET cc_start: 0.7799 (ptp) cc_final: 0.7594 (ptm) REVERT: F 609 ASP cc_start: 0.9018 (m-30) cc_final: 0.8652 (m-30) REVERT: F 611 MET cc_start: 0.8428 (pmm) cc_final: 0.8042 (pmm) REVERT: F 740 MET cc_start: 0.4229 (pmm) cc_final: 0.3435 (pmm) outliers start: 2 outliers final: 0 residues processed: 745 average time/residue: 0.2218 time to fit residues: 256.8197 Evaluate side-chains 568 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 245 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 201 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 222 optimal weight: 30.0000 chunk 199 optimal weight: 0.0000 chunk 4 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 406 HIS ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.095066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071197 restraints weight = 133403.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.073618 restraints weight = 94450.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.075536 restraints weight = 72470.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.076948 restraints weight = 58714.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.078017 restraints weight = 49720.666| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32516 Z= 0.162 Angle : 0.755 12.084 43942 Z= 0.381 Chirality : 0.049 0.217 4978 Planarity : 0.006 0.125 5767 Dihedral : 7.907 172.410 4446 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.13), residues: 4015 helix: -1.11 (0.12), residues: 1672 sheet: -1.37 (0.23), residues: 501 loop : -1.40 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 53 TYR 0.034 0.002 TYR A 495 PHE 0.050 0.002 PHE B 563 TRP 0.010 0.001 TRP B 551 HIS 0.008 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00350 (32516) covalent geometry : angle 0.75491 (43942) hydrogen bonds : bond 0.03827 ( 1085) hydrogen bonds : angle 5.91375 ( 3153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 732 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8307 (mmp) cc_final: 0.7985 (mmm) REVERT: B 63 LYS cc_start: 0.9297 (pttm) cc_final: 0.8947 (pttm) REVERT: B 200 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 302 PHE cc_start: 0.8446 (t80) cc_final: 0.7329 (t80) REVERT: B 305 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 344 MET cc_start: 0.9074 (tpt) cc_final: 0.8743 (tpt) REVERT: B 351 ASN cc_start: 0.9158 (p0) cc_final: 0.8893 (p0) REVERT: B 363 PHE cc_start: 0.8105 (m-10) cc_final: 0.7868 (m-80) REVERT: B 366 GLU cc_start: 0.9058 (pm20) cc_final: 0.8424 (pm20) REVERT: B 379 GLU cc_start: 0.9305 (tp30) cc_final: 0.8743 (pt0) REVERT: B 388 MET cc_start: 0.8504 (mmp) cc_final: 0.7392 (mmm) REVERT: B 426 LYS cc_start: 0.9650 (mptt) cc_final: 0.9374 (mmtt) REVERT: B 517 TYR cc_start: 0.8619 (p90) cc_final: 0.8025 (p90) REVERT: B 538 ASN cc_start: 0.9270 (t0) cc_final: 0.8925 (t0) REVERT: B 620 ILE cc_start: 0.9115 (mp) cc_final: 0.8796 (mp) REVERT: B 678 MET cc_start: 0.7441 (mtt) cc_final: 0.6773 (ptt) REVERT: B 689 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8752 (tm-30) REVERT: B 736 PHE cc_start: 0.8552 (m-10) cc_final: 0.8120 (m-10) REVERT: B 757 MET cc_start: 0.8293 (ttt) cc_final: 0.7887 (tmm) REVERT: C 131 PHE cc_start: 0.8094 (m-10) cc_final: 0.7743 (m-10) REVERT: C 154 VAL cc_start: 0.8355 (t) cc_final: 0.8145 (t) REVERT: C 163 PHE cc_start: 0.8783 (m-80) cc_final: 0.8122 (m-80) REVERT: C 190 LYS cc_start: 0.9615 (pptt) cc_final: 0.9321 (pptt) REVERT: C 200 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9156 (tp30) REVERT: C 221 GLU cc_start: 0.7926 (pt0) cc_final: 0.7571 (pt0) REVERT: C 244 TYR cc_start: 0.7611 (p90) cc_final: 0.7158 (p90) REVERT: C 251 LYS cc_start: 0.9305 (ptpp) cc_final: 0.9089 (mtmm) REVERT: C 260 ASN cc_start: 0.8526 (m110) cc_final: 0.8159 (m110) REVERT: C 269 ILE cc_start: 0.9271 (mp) cc_final: 0.9034 (mp) REVERT: C 306 LEU cc_start: 0.9136 (mm) cc_final: 0.8790 (mm) REVERT: C 322 ARG cc_start: 0.8977 (mpt180) cc_final: 0.7878 (mpt180) REVERT: C 362 ARG cc_start: 0.7624 (mpp-170) cc_final: 0.7378 (mpt180) REVERT: C 449 MET cc_start: 0.8726 (mmp) cc_final: 0.8080 (mmp) REVERT: C 563 PHE cc_start: 0.9332 (m-80) cc_final: 0.9087 (m-80) REVERT: C 609 ASP cc_start: 0.9115 (m-30) cc_final: 0.8505 (m-30) REVERT: C 639 LEU cc_start: 0.6561 (mm) cc_final: 0.6302 (mm) REVERT: C 678 MET cc_start: 0.4107 (ptt) cc_final: 0.3763 (ptt) REVERT: C 696 LYS cc_start: 0.9685 (tppt) cc_final: 0.9128 (mttt) REVERT: D 135 LEU cc_start: 0.8462 (mt) cc_final: 0.7937 (mt) REVERT: D 139 PHE cc_start: 0.8932 (m-80) cc_final: 0.8479 (m-80) REVERT: D 158 MET cc_start: 0.7011 (ppp) cc_final: 0.6377 (ppp) REVERT: D 199 ASN cc_start: 0.8778 (p0) cc_final: 0.8444 (p0) REVERT: D 219 MET cc_start: 0.8288 (pmm) cc_final: 0.7485 (pmm) REVERT: D 253 LEU cc_start: 0.9661 (mp) cc_final: 0.9457 (mp) REVERT: D 256 ARG cc_start: 0.9483 (mmt90) cc_final: 0.9116 (mmm-85) REVERT: D 265 PHE cc_start: 0.8034 (t80) cc_final: 0.7504 (t80) REVERT: D 268 LEU cc_start: 0.9475 (tt) cc_final: 0.9074 (tt) REVERT: D 291 GLU cc_start: 0.8826 (pm20) cc_final: 0.8623 (pp20) REVERT: D 295 LYS cc_start: 0.9486 (mtmt) cc_final: 0.9275 (mtmt) REVERT: D 301 ILE cc_start: 0.9178 (mp) cc_final: 0.8908 (mp) REVERT: D 302 PHE cc_start: 0.8759 (t80) cc_final: 0.8535 (t80) REVERT: D 315 LYS cc_start: 0.7194 (tptt) cc_final: 0.6377 (tppt) REVERT: D 319 GLU cc_start: 0.9514 (pp20) cc_final: 0.9240 (pp20) REVERT: D 329 LEU cc_start: 0.9462 (mt) cc_final: 0.9204 (mp) REVERT: D 366 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8306 (mp0) REVERT: D 388 MET cc_start: 0.8974 (mpp) cc_final: 0.8399 (mpp) REVERT: D 404 HIS cc_start: 0.8414 (p-80) cc_final: 0.7945 (p-80) REVERT: D 449 MET cc_start: 0.9055 (mmp) cc_final: 0.8787 (mmp) REVERT: D 516 PHE cc_start: 0.8591 (m-80) cc_final: 0.8369 (m-10) REVERT: D 550 MET cc_start: 0.6150 (pmm) cc_final: 0.5778 (pmm) REVERT: D 565 LYS cc_start: 0.9233 (ptmt) cc_final: 0.8891 (tptt) REVERT: D 575 PHE cc_start: 0.8844 (t80) cc_final: 0.8147 (t80) REVERT: D 609 ASP cc_start: 0.8893 (p0) cc_final: 0.8609 (p0) REVERT: D 700 ARG cc_start: 0.8919 (pmt-80) cc_final: 0.8232 (tmm160) REVERT: E 66 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6246 (mm-30) REVERT: E 218 GLU cc_start: 0.9428 (tt0) cc_final: 0.9107 (tm-30) REVERT: E 219 MET cc_start: 0.9165 (ppp) cc_final: 0.8725 (ppp) REVERT: E 243 LEU cc_start: 0.8214 (mt) cc_final: 0.7982 (mt) REVERT: E 274 ILE cc_start: 0.9618 (mp) cc_final: 0.9398 (mp) REVERT: E 275 MET cc_start: 0.9259 (mpp) cc_final: 0.9031 (mpp) REVERT: E 291 GLU cc_start: 0.9399 (mp0) cc_final: 0.8612 (tp30) REVERT: E 348 ASN cc_start: 0.8428 (t0) cc_final: 0.7884 (t0) REVERT: E 379 GLU cc_start: 0.9023 (tp30) cc_final: 0.8790 (tp30) REVERT: E 388 MET cc_start: 0.8979 (mmp) cc_final: 0.8696 (mmm) REVERT: E 449 MET cc_start: 0.9035 (mmp) cc_final: 0.8614 (mmp) REVERT: E 451 ASP cc_start: 0.8442 (m-30) cc_final: 0.8213 (m-30) REVERT: E 452 PHE cc_start: 0.7499 (m-80) cc_final: 0.7247 (m-80) REVERT: E 470 GLU cc_start: 0.8645 (tt0) cc_final: 0.7791 (tm-30) REVERT: E 515 LEU cc_start: 0.9106 (mm) cc_final: 0.8886 (mm) REVERT: E 516 PHE cc_start: 0.8505 (m-80) cc_final: 0.8057 (m-80) REVERT: E 538 ASN cc_start: 0.8721 (t0) cc_final: 0.8173 (m-40) REVERT: E 542 ILE cc_start: 0.9043 (tp) cc_final: 0.8795 (tp) REVERT: E 550 MET cc_start: 0.3876 (mmm) cc_final: 0.3441 (mmm) REVERT: E 560 ARG cc_start: 0.9589 (ttt-90) cc_final: 0.9145 (tpp-160) REVERT: E 563 PHE cc_start: 0.9196 (m-10) cc_final: 0.8768 (m-80) REVERT: E 564 ASP cc_start: 0.9273 (m-30) cc_final: 0.8790 (m-30) REVERT: E 579 LEU cc_start: 0.8875 (pt) cc_final: 0.8643 (mm) REVERT: E 615 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8618 (mmtt) REVERT: E 736 PHE cc_start: 0.8639 (m-10) cc_final: 0.8290 (m-10) REVERT: E 740 MET cc_start: 0.8022 (mmp) cc_final: 0.7597 (mmp) REVERT: A 50 GLN cc_start: 0.9184 (pp30) cc_final: 0.8881 (pp30) REVERT: A 64 ARG cc_start: 0.8611 (tpt90) cc_final: 0.8065 (tpm170) REVERT: A 135 LEU cc_start: 0.9084 (tp) cc_final: 0.8844 (tp) REVERT: A 163 PHE cc_start: 0.8775 (m-10) cc_final: 0.7875 (m-80) REVERT: A 241 ILE cc_start: 0.8868 (tp) cc_final: 0.8398 (tp) REVERT: A 243 LEU cc_start: 0.9349 (mm) cc_final: 0.9048 (mm) REVERT: A 253 LEU cc_start: 0.9370 (mt) cc_final: 0.8875 (mp) REVERT: A 256 ARG cc_start: 0.9111 (mtm-85) cc_final: 0.8671 (mtm110) REVERT: A 344 MET cc_start: 0.8943 (mmp) cc_final: 0.8118 (mmp) REVERT: A 349 ARG cc_start: 0.9041 (ttm110) cc_final: 0.8777 (mmm-85) REVERT: A 366 GLU cc_start: 0.7668 (tt0) cc_final: 0.7354 (tt0) REVERT: A 375 THR cc_start: 0.9169 (p) cc_final: 0.8813 (t) REVERT: A 388 MET cc_start: 0.8196 (mpp) cc_final: 0.7615 (mpp) REVERT: A 417 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8667 (tp30) REVERT: A 459 SER cc_start: 0.9442 (t) cc_final: 0.9012 (m) REVERT: A 516 PHE cc_start: 0.9155 (m-80) cc_final: 0.8168 (m-80) REVERT: A 651 LYS cc_start: 0.9393 (pttt) cc_final: 0.9010 (tmtt) REVERT: F 204 ASP cc_start: 0.8870 (m-30) cc_final: 0.8107 (p0) REVERT: F 222 LEU cc_start: 0.9494 (tp) cc_final: 0.9021 (tp) REVERT: F 231 LYS cc_start: 0.8449 (ptpt) cc_final: 0.8090 (ptpt) REVERT: F 251 LYS cc_start: 0.9429 (mtmt) cc_final: 0.9163 (mtpt) REVERT: F 253 LEU cc_start: 0.9769 (mm) cc_final: 0.9539 (mm) REVERT: F 269 ILE cc_start: 0.9568 (tp) cc_final: 0.9195 (tp) REVERT: F 329 LEU cc_start: 0.9404 (mt) cc_final: 0.9165 (mp) REVERT: F 337 GLN cc_start: 0.7047 (mm110) cc_final: 0.4732 (tp40) REVERT: F 338 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8357 (tpp80) REVERT: F 359 ARG cc_start: 0.8641 (tpt170) cc_final: 0.8414 (tpt170) REVERT: F 417 GLU cc_start: 0.9584 (mp0) cc_final: 0.9158 (mp0) REVERT: F 442 MET cc_start: 0.8588 (mmp) cc_final: 0.7414 (ptt) REVERT: F 470 GLU cc_start: 0.8197 (pp20) cc_final: 0.7471 (pm20) REVERT: F 495 TYR cc_start: 0.8975 (m-80) cc_final: 0.8381 (m-10) REVERT: F 508 MET cc_start: 0.0249 (ttt) cc_final: -0.0178 (tpp) REVERT: F 608 MET cc_start: 0.8051 (ptp) cc_final: 0.7650 (ptm) REVERT: F 609 ASP cc_start: 0.9063 (m-30) cc_final: 0.8694 (m-30) REVERT: F 611 MET cc_start: 0.8677 (pmm) cc_final: 0.8255 (pmm) REVERT: F 644 TYR cc_start: 0.8728 (t80) cc_final: 0.8364 (t80) REVERT: F 678 MET cc_start: 0.8288 (mtp) cc_final: 0.8008 (mmm) outliers start: 2 outliers final: 1 residues processed: 734 average time/residue: 0.2096 time to fit residues: 240.1492 Evaluate side-chains 571 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 570 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 339 optimal weight: 3.9990 chunk 367 optimal weight: 5.9990 chunk 368 optimal weight: 7.9990 chunk 103 optimal weight: 0.0270 chunk 168 optimal weight: 4.9990 chunk 225 optimal weight: 40.0000 chunk 19 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 3.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 568 GLN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 406 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN E 660 ASN A 499 HIS ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.091390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.067845 restraints weight = 135831.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070256 restraints weight = 95038.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.072122 restraints weight = 72367.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073527 restraints weight = 58400.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.074548 restraints weight = 49231.883| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32516 Z= 0.218 Angle : 0.799 12.108 43942 Z= 0.408 Chirality : 0.050 0.223 4978 Planarity : 0.006 0.085 5767 Dihedral : 7.954 171.963 4446 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.13), residues: 4015 helix: -1.23 (0.12), residues: 1689 sheet: -1.58 (0.22), residues: 493 loop : -1.41 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 365 TYR 0.032 0.002 TYR B 495 PHE 0.033 0.002 PHE A 563 TRP 0.023 0.002 TRP E 551 HIS 0.007 0.002 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00456 (32516) covalent geometry : angle 0.79852 (43942) hydrogen bonds : bond 0.04096 ( 1085) hydrogen bonds : angle 6.06381 ( 3153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 701 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8280 (mmp) cc_final: 0.7922 (mmm) REVERT: B 63 LYS cc_start: 0.9372 (pttm) cc_final: 0.8945 (pttm) REVERT: B 130 LEU cc_start: 0.9017 (tt) cc_final: 0.8494 (mp) REVERT: B 239 ARG cc_start: 0.8363 (mmm160) cc_final: 0.7827 (tpp-160) REVERT: B 302 PHE cc_start: 0.8567 (t80) cc_final: 0.7782 (t80) REVERT: B 305 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8069 (mm-30) REVERT: B 344 MET cc_start: 0.9226 (tpt) cc_final: 0.8856 (tmm) REVERT: B 351 ASN cc_start: 0.9356 (p0) cc_final: 0.9067 (p0) REVERT: B 363 PHE cc_start: 0.8078 (m-10) cc_final: 0.7819 (m-80) REVERT: B 366 GLU cc_start: 0.9075 (pm20) cc_final: 0.8467 (pm20) REVERT: B 388 MET cc_start: 0.8677 (mmp) cc_final: 0.7474 (mmm) REVERT: B 426 LYS cc_start: 0.9703 (mptt) cc_final: 0.9434 (mmtt) REVERT: B 538 ASN cc_start: 0.9371 (t0) cc_final: 0.8967 (t0) REVERT: B 565 LYS cc_start: 0.9595 (pptt) cc_final: 0.9301 (pptt) REVERT: B 678 MET cc_start: 0.7741 (mtt) cc_final: 0.7000 (ptt) REVERT: B 757 MET cc_start: 0.8298 (ttt) cc_final: 0.7943 (tmm) REVERT: C 59 LEU cc_start: 0.8432 (tt) cc_final: 0.8230 (tt) REVERT: C 117 LEU cc_start: 0.8313 (mt) cc_final: 0.8064 (mt) REVERT: C 131 PHE cc_start: 0.8229 (m-10) cc_final: 0.7951 (m-10) REVERT: C 163 PHE cc_start: 0.8949 (m-80) cc_final: 0.8379 (m-80) REVERT: C 190 LYS cc_start: 0.9660 (pptt) cc_final: 0.9378 (pptt) REVERT: C 203 TYR cc_start: 0.8634 (m-10) cc_final: 0.7891 (m-80) REVERT: C 221 GLU cc_start: 0.8024 (pt0) cc_final: 0.7680 (pt0) REVERT: C 244 TYR cc_start: 0.7780 (p90) cc_final: 0.7344 (p90) REVERT: C 251 LYS cc_start: 0.9270 (ptpp) cc_final: 0.9047 (mtmm) REVERT: C 260 ASN cc_start: 0.8850 (m110) cc_final: 0.8622 (m-40) REVERT: C 265 PHE cc_start: 0.8339 (t80) cc_final: 0.8110 (t80) REVERT: C 268 LEU cc_start: 0.9303 (tp) cc_final: 0.9075 (tt) REVERT: C 269 ILE cc_start: 0.9427 (mp) cc_final: 0.9023 (mp) REVERT: C 306 LEU cc_start: 0.9013 (mm) cc_final: 0.8636 (mm) REVERT: C 322 ARG cc_start: 0.8922 (mpt180) cc_final: 0.8054 (mpt180) REVERT: C 362 ARG cc_start: 0.8165 (mpp-170) cc_final: 0.7952 (mpt180) REVERT: C 449 MET cc_start: 0.8871 (mmp) cc_final: 0.8232 (mmp) REVERT: C 515 LEU cc_start: 0.9182 (mm) cc_final: 0.8964 (mm) REVERT: C 609 ASP cc_start: 0.9058 (m-30) cc_final: 0.8382 (m-30) REVERT: C 639 LEU cc_start: 0.6773 (mm) cc_final: 0.6478 (mm) REVERT: C 696 LYS cc_start: 0.9756 (tppt) cc_final: 0.9257 (mttt) REVERT: D 135 LEU cc_start: 0.8589 (mt) cc_final: 0.8143 (mt) REVERT: D 139 PHE cc_start: 0.9008 (m-80) cc_final: 0.8553 (m-80) REVERT: D 158 MET cc_start: 0.7620 (ppp) cc_final: 0.6513 (ppp) REVERT: D 199 ASN cc_start: 0.8823 (p0) cc_final: 0.8510 (p0) REVERT: D 219 MET cc_start: 0.8678 (pmm) cc_final: 0.8253 (pmm) REVERT: D 265 PHE cc_start: 0.8190 (t80) cc_final: 0.7834 (t80) REVERT: D 268 LEU cc_start: 0.9473 (tt) cc_final: 0.8999 (tt) REVERT: D 301 ILE cc_start: 0.9352 (mp) cc_final: 0.9067 (mp) REVERT: D 302 PHE cc_start: 0.8660 (t80) cc_final: 0.8362 (t80) REVERT: D 315 LYS cc_start: 0.6891 (tptt) cc_final: 0.6166 (tppt) REVERT: D 319 GLU cc_start: 0.9606 (pp20) cc_final: 0.9303 (pp20) REVERT: D 329 LEU cc_start: 0.9567 (mt) cc_final: 0.9279 (mp) REVERT: D 349 ARG cc_start: 0.8768 (tpm170) cc_final: 0.8416 (tpp80) REVERT: D 366 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8499 (mp0) REVERT: D 382 GLN cc_start: 0.8808 (mp10) cc_final: 0.8452 (mp10) REVERT: D 388 MET cc_start: 0.9001 (mpp) cc_final: 0.8402 (mpp) REVERT: D 516 PHE cc_start: 0.8647 (m-80) cc_final: 0.8426 (m-80) REVERT: D 565 LYS cc_start: 0.9230 (ptmt) cc_final: 0.8919 (tptt) REVERT: D 575 PHE cc_start: 0.8892 (t80) cc_final: 0.8267 (t80) REVERT: D 578 GLU cc_start: 0.8763 (tp30) cc_final: 0.8538 (tp30) REVERT: D 609 ASP cc_start: 0.8837 (p0) cc_final: 0.8586 (p0) REVERT: D 678 MET cc_start: 0.2930 (ptt) cc_final: 0.2502 (ptt) REVERT: D 740 MET cc_start: 0.4343 (ptt) cc_final: 0.4083 (ptt) REVERT: E 89 ARG cc_start: 0.8650 (mtt180) cc_final: 0.8424 (mtt180) REVERT: E 218 GLU cc_start: 0.9446 (tt0) cc_final: 0.9031 (tm-30) REVERT: E 219 MET cc_start: 0.9245 (ppp) cc_final: 0.8492 (ptm) REVERT: E 274 ILE cc_start: 0.9624 (mp) cc_final: 0.9398 (mp) REVERT: E 275 MET cc_start: 0.9227 (mpp) cc_final: 0.8885 (mpp) REVERT: E 379 GLU cc_start: 0.9111 (tp30) cc_final: 0.8900 (tp30) REVERT: E 388 MET cc_start: 0.8896 (mmp) cc_final: 0.8559 (mmm) REVERT: E 449 MET cc_start: 0.9078 (mmp) cc_final: 0.8577 (mmp) REVERT: E 451 ASP cc_start: 0.8415 (m-30) cc_final: 0.8163 (m-30) REVERT: E 452 PHE cc_start: 0.7536 (m-80) cc_final: 0.7232 (m-80) REVERT: E 470 GLU cc_start: 0.8548 (tt0) cc_final: 0.7661 (tm-30) REVERT: E 515 LEU cc_start: 0.9113 (mm) cc_final: 0.8809 (mm) REVERT: E 516 PHE cc_start: 0.8573 (m-80) cc_final: 0.8228 (m-80) REVERT: E 538 ASN cc_start: 0.8805 (t0) cc_final: 0.8259 (m-40) REVERT: E 542 ILE cc_start: 0.9050 (tp) cc_final: 0.8801 (tp) REVERT: E 550 MET cc_start: 0.4189 (mmm) cc_final: 0.3378 (tpp) REVERT: E 560 ARG cc_start: 0.9636 (ttt-90) cc_final: 0.9201 (tpp-160) REVERT: E 563 PHE cc_start: 0.9313 (m-10) cc_final: 0.8894 (m-80) REVERT: E 564 ASP cc_start: 0.9302 (m-30) cc_final: 0.8670 (m-30) REVERT: E 579 LEU cc_start: 0.9088 (pt) cc_final: 0.8868 (mm) REVERT: E 678 MET cc_start: 0.4132 (mtp) cc_final: 0.3646 (ttm) REVERT: E 736 PHE cc_start: 0.8730 (m-10) cc_final: 0.8476 (m-10) REVERT: E 740 MET cc_start: 0.7949 (mmp) cc_final: 0.6197 (mmp) REVERT: E 741 ARG cc_start: 0.8963 (tpm170) cc_final: 0.8467 (mmt-90) REVERT: A 50 GLN cc_start: 0.9225 (pp30) cc_final: 0.8914 (pp30) REVERT: A 64 ARG cc_start: 0.8673 (tpt90) cc_final: 0.8335 (tpt170) REVERT: A 135 LEU cc_start: 0.9009 (tp) cc_final: 0.8747 (tp) REVERT: A 163 PHE cc_start: 0.8779 (m-80) cc_final: 0.7982 (m-80) REVERT: A 221 GLU cc_start: 0.8487 (pm20) cc_final: 0.7896 (pm20) REVERT: A 243 LEU cc_start: 0.9414 (mm) cc_final: 0.9172 (mm) REVERT: A 253 LEU cc_start: 0.9404 (mt) cc_final: 0.8817 (mp) REVERT: A 256 ARG cc_start: 0.9210 (mtm-85) cc_final: 0.8669 (mtm-85) REVERT: A 344 MET cc_start: 0.9009 (mmp) cc_final: 0.8150 (mmp) REVERT: A 349 ARG cc_start: 0.9111 (ttm110) cc_final: 0.8898 (mmm-85) REVERT: A 362 ARG cc_start: 0.7776 (mpt90) cc_final: 0.7464 (mmt180) REVERT: A 388 MET cc_start: 0.8513 (mpp) cc_final: 0.8276 (mpp) REVERT: A 417 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8707 (tp30) REVERT: A 516 PHE cc_start: 0.9190 (m-80) cc_final: 0.8286 (m-80) REVERT: A 651 LYS cc_start: 0.9386 (pttt) cc_final: 0.9039 (tmtt) REVERT: F 204 ASP cc_start: 0.9044 (m-30) cc_final: 0.8196 (p0) REVERT: F 251 LYS cc_start: 0.9472 (mtmt) cc_final: 0.9230 (mtpt) REVERT: F 253 LEU cc_start: 0.9774 (mm) cc_final: 0.9555 (mm) REVERT: F 269 ILE cc_start: 0.9697 (tp) cc_final: 0.9289 (tp) REVERT: F 332 MET cc_start: 0.8264 (ppp) cc_final: 0.7317 (ppp) REVERT: F 338 ARG cc_start: 0.8021 (tpp80) cc_final: 0.7793 (tpp80) REVERT: F 417 GLU cc_start: 0.9630 (mp0) cc_final: 0.9245 (mp0) REVERT: F 495 TYR cc_start: 0.9006 (m-80) cc_final: 0.8289 (m-10) REVERT: F 508 MET cc_start: 0.1215 (ttt) cc_final: 0.0570 (tpp) REVERT: F 565 LYS cc_start: 0.9313 (pttp) cc_final: 0.8934 (pttp) REVERT: F 608 MET cc_start: 0.8393 (ptp) cc_final: 0.8052 (ptm) REVERT: F 609 ASP cc_start: 0.8921 (m-30) cc_final: 0.8510 (m-30) REVERT: F 611 MET cc_start: 0.8732 (pmm) cc_final: 0.8220 (pmm) outliers start: 2 outliers final: 0 residues processed: 702 average time/residue: 0.2223 time to fit residues: 244.0710 Evaluate side-chains 535 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 250 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 226 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 31 optimal weight: 0.4980 chunk 213 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 341 optimal weight: 1.9990 chunk 383 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 285 ASN C 337 GLN C 406 HIS D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 660 ASN A 499 HIS ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.094804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071006 restraints weight = 131967.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073592 restraints weight = 93088.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075524 restraints weight = 70667.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076932 restraints weight = 56742.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.078027 restraints weight = 47799.672| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32516 Z= 0.137 Angle : 0.759 10.835 43942 Z= 0.376 Chirality : 0.050 0.265 4978 Planarity : 0.005 0.085 5767 Dihedral : 7.784 175.244 4446 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 4015 helix: -1.04 (0.12), residues: 1698 sheet: -1.44 (0.22), residues: 483 loop : -1.31 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 377 TYR 0.018 0.002 TYR A 495 PHE 0.028 0.002 PHE B 563 TRP 0.017 0.001 TRP D 476 HIS 0.017 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00309 (32516) covalent geometry : angle 0.75857 (43942) hydrogen bonds : bond 0.03548 ( 1085) hydrogen bonds : angle 5.79986 ( 3153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 731 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8376 (mmp) cc_final: 0.8018 (mmm) REVERT: B 63 LYS cc_start: 0.9297 (pttm) cc_final: 0.9013 (pttm) REVERT: B 84 MET cc_start: 0.8810 (mmp) cc_final: 0.8516 (mmm) REVERT: B 130 LEU cc_start: 0.8985 (tt) cc_final: 0.8583 (mt) REVERT: B 244 TYR cc_start: 0.8735 (p90) cc_final: 0.8436 (p90) REVERT: B 302 PHE cc_start: 0.8531 (t80) cc_final: 0.7470 (t80) REVERT: B 305 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 332 MET cc_start: 0.8660 (tmm) cc_final: 0.8313 (tmm) REVERT: B 344 MET cc_start: 0.9194 (tpt) cc_final: 0.8618 (tpt) REVERT: B 351 ASN cc_start: 0.9317 (p0) cc_final: 0.9002 (p0) REVERT: B 366 GLU cc_start: 0.8792 (pm20) cc_final: 0.8231 (pm20) REVERT: B 379 GLU cc_start: 0.9235 (tp30) cc_final: 0.8761 (pt0) REVERT: B 388 MET cc_start: 0.8580 (mmp) cc_final: 0.7403 (mmm) REVERT: B 426 LYS cc_start: 0.9602 (mptt) cc_final: 0.9321 (mmtt) REVERT: B 538 ASN cc_start: 0.9256 (t0) cc_final: 0.8926 (t0) REVERT: B 565 LYS cc_start: 0.9574 (pptt) cc_final: 0.9243 (pptt) REVERT: B 620 ILE cc_start: 0.9050 (mp) cc_final: 0.8656 (mp) REVERT: B 678 MET cc_start: 0.7439 (mtt) cc_final: 0.6728 (ptt) REVERT: B 757 MET cc_start: 0.8371 (ttt) cc_final: 0.8049 (tmm) REVERT: C 117 LEU cc_start: 0.7998 (mt) cc_final: 0.7728 (tp) REVERT: C 131 PHE cc_start: 0.7972 (m-10) cc_final: 0.7684 (m-10) REVERT: C 163 PHE cc_start: 0.8939 (m-80) cc_final: 0.8295 (m-80) REVERT: C 190 LYS cc_start: 0.9619 (pptt) cc_final: 0.9368 (pptt) REVERT: C 201 VAL cc_start: 0.8814 (m) cc_final: 0.8087 (p) REVERT: C 221 GLU cc_start: 0.8002 (pt0) cc_final: 0.7660 (pt0) REVERT: C 244 TYR cc_start: 0.7696 (p90) cc_final: 0.7140 (p90) REVERT: C 260 ASN cc_start: 0.8624 (m-40) cc_final: 0.8238 (m110) REVERT: C 261 GLU cc_start: 0.7984 (pt0) cc_final: 0.7467 (mp0) REVERT: C 265 PHE cc_start: 0.8215 (t80) cc_final: 0.8004 (t80) REVERT: C 268 LEU cc_start: 0.9252 (tp) cc_final: 0.9035 (tt) REVERT: C 269 ILE cc_start: 0.9374 (mp) cc_final: 0.9038 (mp) REVERT: C 322 ARG cc_start: 0.9051 (mpt180) cc_final: 0.8351 (mpt180) REVERT: C 337 GLN cc_start: 0.5501 (OUTLIER) cc_final: 0.5255 (mm-40) REVERT: C 396 LEU cc_start: 0.9515 (mt) cc_final: 0.9277 (mt) REVERT: C 449 MET cc_start: 0.8705 (mmp) cc_final: 0.8018 (mmp) REVERT: C 609 ASP cc_start: 0.9175 (m-30) cc_final: 0.8626 (m-30) REVERT: C 639 LEU cc_start: 0.6585 (mm) cc_final: 0.6300 (mm) REVERT: C 678 MET cc_start: 0.4732 (ptt) cc_final: 0.4487 (ptt) REVERT: C 696 LYS cc_start: 0.9727 (tppt) cc_final: 0.9232 (mttt) REVERT: D 135 LEU cc_start: 0.8535 (mt) cc_final: 0.7996 (mt) REVERT: D 139 PHE cc_start: 0.8917 (m-80) cc_final: 0.8421 (m-80) REVERT: D 158 MET cc_start: 0.7065 (ppp) cc_final: 0.6156 (ppp) REVERT: D 199 ASN cc_start: 0.8795 (p0) cc_final: 0.8384 (p0) REVERT: D 219 MET cc_start: 0.8266 (pmm) cc_final: 0.7663 (pmm) REVERT: D 251 LYS cc_start: 0.9566 (mppt) cc_final: 0.9241 (mtmt) REVERT: D 256 ARG cc_start: 0.9375 (mmt90) cc_final: 0.9104 (mmm-85) REVERT: D 265 PHE cc_start: 0.7994 (t80) cc_final: 0.7594 (t80) REVERT: D 268 LEU cc_start: 0.9454 (tt) cc_final: 0.7874 (tt) REVERT: D 288 LYS cc_start: 0.9329 (pptt) cc_final: 0.9089 (pptt) REVERT: D 301 ILE cc_start: 0.9239 (mp) cc_final: 0.8876 (mp) REVERT: D 302 PHE cc_start: 0.8737 (t80) cc_final: 0.7991 (t80) REVERT: D 303 ILE cc_start: 0.9622 (mp) cc_final: 0.9399 (tp) REVERT: D 315 LYS cc_start: 0.6527 (tptt) cc_final: 0.5881 (tppt) REVERT: D 319 GLU cc_start: 0.9481 (pp20) cc_final: 0.9095 (pp20) REVERT: D 329 LEU cc_start: 0.9396 (mt) cc_final: 0.9131 (mp) REVERT: D 349 ARG cc_start: 0.8525 (tpm170) cc_final: 0.8117 (tpp80) REVERT: D 366 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8355 (mp0) REVERT: D 382 GLN cc_start: 0.8727 (mp10) cc_final: 0.8409 (pt0) REVERT: D 386 LYS cc_start: 0.9421 (ptmt) cc_final: 0.9034 (ptmt) REVERT: D 388 MET cc_start: 0.8920 (mpp) cc_final: 0.8377 (mpp) REVERT: D 449 MET cc_start: 0.8916 (mmp) cc_final: 0.8685 (mmp) REVERT: D 543 LYS cc_start: 0.9181 (mppt) cc_final: 0.8980 (mmtm) REVERT: D 565 LYS cc_start: 0.9091 (ptmt) cc_final: 0.8784 (tptt) REVERT: D 575 PHE cc_start: 0.8769 (t80) cc_final: 0.8158 (t80) REVERT: D 578 GLU cc_start: 0.8586 (tp30) cc_final: 0.8164 (tm-30) REVERT: D 609 ASP cc_start: 0.8939 (p0) cc_final: 0.8674 (p0) REVERT: D 700 ARG cc_start: 0.9229 (ppt170) cc_final: 0.8956 (ptm-80) REVERT: E 89 ARG cc_start: 0.8656 (mtt180) cc_final: 0.8450 (mtt180) REVERT: E 218 GLU cc_start: 0.9406 (tt0) cc_final: 0.9014 (tm-30) REVERT: E 219 MET cc_start: 0.9180 (ppp) cc_final: 0.8432 (ptm) REVERT: E 267 PHE cc_start: 0.8788 (t80) cc_final: 0.8349 (t80) REVERT: E 274 ILE cc_start: 0.9661 (mp) cc_final: 0.9442 (mp) REVERT: E 275 MET cc_start: 0.9353 (mpp) cc_final: 0.9058 (mpp) REVERT: E 291 GLU cc_start: 0.9398 (mp0) cc_final: 0.8598 (tp30) REVERT: E 379 GLU cc_start: 0.9151 (tp30) cc_final: 0.8841 (tp30) REVERT: E 388 MET cc_start: 0.9055 (mmp) cc_final: 0.8358 (mmm) REVERT: E 449 MET cc_start: 0.8960 (mmp) cc_final: 0.8436 (mmp) REVERT: E 451 ASP cc_start: 0.8363 (m-30) cc_final: 0.8131 (m-30) REVERT: E 452 PHE cc_start: 0.7401 (m-80) cc_final: 0.6892 (m-80) REVERT: E 470 GLU cc_start: 0.8459 (tt0) cc_final: 0.7524 (tm-30) REVERT: E 515 LEU cc_start: 0.9034 (mm) cc_final: 0.8780 (mm) REVERT: E 516 PHE cc_start: 0.8665 (m-80) cc_final: 0.8288 (m-10) REVERT: E 517 TYR cc_start: 0.6678 (p90) cc_final: 0.6443 (p90) REVERT: E 538 ASN cc_start: 0.8695 (t0) cc_final: 0.8151 (m-40) REVERT: E 550 MET cc_start: 0.4051 (mmm) cc_final: 0.3344 (tpp) REVERT: E 560 ARG cc_start: 0.9619 (ttt-90) cc_final: 0.9178 (tpp-160) REVERT: E 563 PHE cc_start: 0.9239 (m-10) cc_final: 0.8870 (m-80) REVERT: E 564 ASP cc_start: 0.9322 (m-30) cc_final: 0.8605 (m-30) REVERT: E 579 LEU cc_start: 0.8912 (pt) cc_final: 0.8708 (mm) REVERT: E 635 ARG cc_start: 0.8504 (ptt-90) cc_final: 0.7427 (mmt180) REVERT: E 678 MET cc_start: 0.4801 (mtp) cc_final: 0.4078 (ttm) REVERT: E 736 PHE cc_start: 0.8707 (m-10) cc_final: 0.8312 (m-10) REVERT: E 740 MET cc_start: 0.7872 (mmp) cc_final: 0.7499 (mmp) REVERT: A 50 GLN cc_start: 0.9268 (pp30) cc_final: 0.8981 (pp30) REVERT: A 64 ARG cc_start: 0.8545 (tpt90) cc_final: 0.8186 (tpt170) REVERT: A 84 MET cc_start: 0.8879 (mpp) cc_final: 0.8655 (mpp) REVERT: A 163 PHE cc_start: 0.8687 (m-80) cc_final: 0.7835 (m-80) REVERT: A 241 ILE cc_start: 0.8795 (tp) cc_final: 0.8390 (tp) REVERT: A 243 LEU cc_start: 0.9302 (mm) cc_final: 0.8985 (mm) REVERT: A 253 LEU cc_start: 0.9350 (mt) cc_final: 0.8855 (mp) REVERT: A 256 ARG cc_start: 0.9085 (mtm-85) cc_final: 0.8722 (mtm-85) REVERT: A 287 ARG cc_start: 0.9060 (mmp80) cc_final: 0.8803 (mmp80) REVERT: A 319 GLU cc_start: 0.9194 (pm20) cc_final: 0.8942 (pm20) REVERT: A 344 MET cc_start: 0.8980 (mmp) cc_final: 0.8177 (mmp) REVERT: A 349 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8774 (mmm-85) REVERT: A 366 GLU cc_start: 0.7682 (tt0) cc_final: 0.7041 (tt0) REVERT: A 417 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8390 (tp30) REVERT: A 459 SER cc_start: 0.9405 (t) cc_final: 0.9128 (m) REVERT: A 516 PHE cc_start: 0.9177 (m-80) cc_final: 0.8250 (m-80) REVERT: A 651 LYS cc_start: 0.9385 (pttt) cc_final: 0.9009 (tmtt) REVERT: F 204 ASP cc_start: 0.8873 (m-30) cc_final: 0.8057 (p0) REVERT: F 222 LEU cc_start: 0.9454 (tp) cc_final: 0.9250 (tp) REVERT: F 251 LYS cc_start: 0.9371 (mtmt) cc_final: 0.9058 (mtpt) REVERT: F 253 LEU cc_start: 0.9762 (mm) cc_final: 0.9545 (mm) REVERT: F 269 ILE cc_start: 0.9560 (tp) cc_final: 0.9193 (tp) REVERT: F 304 ASP cc_start: 0.7819 (p0) cc_final: 0.7260 (p0) REVERT: F 305 GLU cc_start: 0.7322 (pm20) cc_final: 0.6990 (pm20) REVERT: F 337 GLN cc_start: 0.6922 (mm110) cc_final: 0.4561 (tp40) REVERT: F 338 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7617 (tpp80) REVERT: F 417 GLU cc_start: 0.9658 (mp0) cc_final: 0.9217 (mp0) REVERT: F 442 MET cc_start: 0.8689 (mmp) cc_final: 0.7475 (ptt) REVERT: F 452 PHE cc_start: 0.8094 (m-80) cc_final: 0.7522 (m-80) REVERT: F 458 GLN cc_start: 0.8930 (mp10) cc_final: 0.8590 (mp10) REVERT: F 465 ARG cc_start: 0.6870 (mmm160) cc_final: 0.6011 (mtt180) REVERT: F 470 GLU cc_start: 0.8134 (pp20) cc_final: 0.7387 (pm20) REVERT: F 495 TYR cc_start: 0.8895 (m-80) cc_final: 0.8402 (m-80) REVERT: F 508 MET cc_start: 0.0756 (ttt) cc_final: -0.0177 (tpp) REVERT: F 608 MET cc_start: 0.8659 (ptp) cc_final: 0.8339 (ptp) REVERT: F 609 ASP cc_start: 0.8938 (m-30) cc_final: 0.8546 (m-30) REVERT: F 611 MET cc_start: 0.8442 (pmm) cc_final: 0.8074 (pmm) REVERT: F 644 TYR cc_start: 0.8808 (t80) cc_final: 0.8503 (t80) REVERT: F 678 MET cc_start: 0.7861 (mtp) cc_final: 0.7496 (mtt) outliers start: 2 outliers final: 1 residues processed: 733 average time/residue: 0.2284 time to fit residues: 260.0728 Evaluate side-chains 555 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 553 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 330 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 390 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 384 HIS C 406 HIS D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** 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 = 0.3693 r_free = 0.3693 target = 0.091398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.067725 restraints weight = 138368.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070204 restraints weight = 96131.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.072100 restraints weight = 72816.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.073505 restraints weight = 58497.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074531 restraints weight = 49274.825| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32516 Z= 0.200 Angle : 0.801 14.326 43942 Z= 0.407 Chirality : 0.051 0.268 4978 Planarity : 0.006 0.071 5767 Dihedral : 7.831 171.627 4446 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 4015 helix: -1.17 (0.12), residues: 1731 sheet: -1.72 (0.22), residues: 497 loop : -1.28 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 377 TYR 0.026 0.002 TYR C 203 PHE 0.034 0.002 PHE E 302 TRP 0.041 0.002 TRP D 476 HIS 0.015 0.002 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00424 (32516) covalent geometry : angle 0.80102 (43942) hydrogen bonds : bond 0.03941 ( 1085) hydrogen bonds : angle 5.95898 ( 3153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8325 (mmp) cc_final: 0.8052 (mmm) REVERT: B 84 MET cc_start: 0.8749 (mmp) cc_final: 0.8251 (mmm) REVERT: B 130 LEU cc_start: 0.8959 (tt) cc_final: 0.8674 (mp) REVERT: B 218 GLU cc_start: 0.8967 (pm20) cc_final: 0.8702 (mp0) REVERT: B 302 PHE cc_start: 0.8635 (t80) cc_final: 0.7986 (t80) REVERT: B 305 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8225 (mm-30) REVERT: B 351 ASN cc_start: 0.9393 (p0) cc_final: 0.9082 (p0) REVERT: B 366 GLU cc_start: 0.8932 (pm20) cc_final: 0.8404 (pm20) REVERT: B 379 GLU cc_start: 0.9267 (tp30) cc_final: 0.8630 (tt0) REVERT: B 388 MET cc_start: 0.8604 (mmp) cc_final: 0.7344 (mmm) REVERT: B 426 LYS cc_start: 0.9673 (mptt) cc_final: 0.9422 (mmtt) REVERT: B 515 LEU cc_start: 0.9338 (mm) cc_final: 0.9132 (mm) REVERT: B 524 LYS cc_start: 0.9006 (mttt) cc_final: 0.7893 (pttt) REVERT: B 538 ASN cc_start: 0.9361 (t0) cc_final: 0.8938 (t0) REVERT: B 620 ILE cc_start: 0.9064 (mp) cc_final: 0.8717 (mp) REVERT: B 639 LEU cc_start: 0.9466 (mp) cc_final: 0.9231 (mp) REVERT: B 678 MET cc_start: 0.7585 (mtt) cc_final: 0.6964 (ptt) REVERT: B 736 PHE cc_start: 0.8797 (m-10) cc_final: 0.8566 (m-10) REVERT: B 757 MET cc_start: 0.8372 (ttt) cc_final: 0.8085 (tmm) REVERT: C 117 LEU cc_start: 0.8270 (mt) cc_final: 0.7892 (mt) REVERT: C 131 PHE cc_start: 0.8185 (m-10) cc_final: 0.7941 (m-10) REVERT: C 163 PHE cc_start: 0.8902 (m-80) cc_final: 0.8315 (m-80) REVERT: C 190 LYS cc_start: 0.9642 (pptt) cc_final: 0.9380 (pptt) REVERT: C 203 TYR cc_start: 0.8798 (m-80) cc_final: 0.7969 (m-80) REVERT: C 221 GLU cc_start: 0.7876 (pt0) cc_final: 0.7504 (pp20) REVERT: C 244 TYR cc_start: 0.7919 (p90) cc_final: 0.6862 (p90) REVERT: C 260 ASN cc_start: 0.8814 (m-40) cc_final: 0.8594 (m110) REVERT: C 265 PHE cc_start: 0.8255 (t80) cc_final: 0.8028 (t80) REVERT: C 268 LEU cc_start: 0.9313 (tp) cc_final: 0.9093 (tt) REVERT: C 269 ILE cc_start: 0.9496 (mp) cc_final: 0.9064 (mp) REVERT: C 352 SER cc_start: 0.9058 (t) cc_final: 0.8858 (t) REVERT: C 449 MET cc_start: 0.8878 (mmp) cc_final: 0.8165 (mmm) REVERT: C 609 ASP cc_start: 0.9049 (m-30) cc_final: 0.8382 (m-30) REVERT: C 639 LEU cc_start: 0.6784 (mm) cc_final: 0.6513 (mm) REVERT: D 135 LEU cc_start: 0.8530 (mt) cc_final: 0.8040 (mt) REVERT: D 139 PHE cc_start: 0.9043 (m-80) cc_final: 0.8569 (m-80) REVERT: D 158 MET cc_start: 0.7629 (ppp) cc_final: 0.6613 (ppp) REVERT: D 199 ASN cc_start: 0.8828 (p0) cc_final: 0.8487 (p0) REVERT: D 219 MET cc_start: 0.8713 (pmm) cc_final: 0.8109 (pmm) REVERT: D 243 LEU cc_start: 0.9477 (mm) cc_final: 0.9234 (mm) REVERT: D 265 PHE cc_start: 0.8277 (t80) cc_final: 0.8028 (t80) REVERT: D 302 PHE cc_start: 0.8777 (t80) cc_final: 0.8136 (t80) REVERT: D 319 GLU cc_start: 0.9601 (pp20) cc_final: 0.9257 (pp20) REVERT: D 344 MET cc_start: 0.8947 (ppp) cc_final: 0.8481 (ppp) REVERT: D 366 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8317 (mp0) REVERT: D 382 GLN cc_start: 0.8720 (mp10) cc_final: 0.8299 (pt0) REVERT: D 386 LYS cc_start: 0.9388 (ptmt) cc_final: 0.9046 (ptmt) REVERT: D 388 MET cc_start: 0.9024 (mpp) cc_final: 0.8500 (mpp) REVERT: D 410 ASP cc_start: 0.9137 (p0) cc_final: 0.8912 (p0) REVERT: D 414 LEU cc_start: 0.9139 (tt) cc_final: 0.8858 (tt) REVERT: D 449 MET cc_start: 0.8960 (mmp) cc_final: 0.8678 (mmp) REVERT: D 516 PHE cc_start: 0.8554 (m-80) cc_final: 0.8336 (m-10) REVERT: D 543 LYS cc_start: 0.9143 (mppt) cc_final: 0.8838 (mmmt) REVERT: D 565 LYS cc_start: 0.9207 (ptmt) cc_final: 0.8942 (tptt) REVERT: D 575 PHE cc_start: 0.8799 (t80) cc_final: 0.7890 (t80) REVERT: D 609 ASP cc_start: 0.8920 (p0) cc_final: 0.8672 (p0) REVERT: D 678 MET cc_start: 0.2763 (ptt) cc_final: 0.2511 (ptt) REVERT: D 700 ARG cc_start: 0.9200 (ppt170) cc_final: 0.8849 (ptm-80) REVERT: E 158 MET cc_start: 0.8449 (tpp) cc_final: 0.8223 (tpp) REVERT: E 218 GLU cc_start: 0.9394 (tt0) cc_final: 0.8935 (tm-30) REVERT: E 219 MET cc_start: 0.9230 (ppp) cc_final: 0.8600 (ptm) REVERT: E 379 GLU cc_start: 0.9221 (tp30) cc_final: 0.8863 (tp30) REVERT: E 383 ILE cc_start: 0.9722 (mt) cc_final: 0.9518 (mt) REVERT: E 384 HIS cc_start: 0.8750 (t-90) cc_final: 0.8294 (t-170) REVERT: E 388 MET cc_start: 0.8897 (mmp) cc_final: 0.8483 (mmm) REVERT: E 449 MET cc_start: 0.8939 (mmp) cc_final: 0.8537 (mmp) REVERT: E 451 ASP cc_start: 0.8410 (m-30) cc_final: 0.8203 (m-30) REVERT: E 452 PHE cc_start: 0.7380 (m-80) cc_final: 0.7045 (m-80) REVERT: E 470 GLU cc_start: 0.8511 (tt0) cc_final: 0.7618 (tm-30) REVERT: E 508 MET cc_start: 0.7714 (mmp) cc_final: 0.7452 (mmm) REVERT: E 515 LEU cc_start: 0.9107 (mm) cc_final: 0.8824 (mm) REVERT: E 516 PHE cc_start: 0.8622 (m-80) cc_final: 0.8354 (m-80) REVERT: E 517 TYR cc_start: 0.6656 (p90) cc_final: 0.6357 (p90) REVERT: E 538 ASN cc_start: 0.8753 (t0) cc_final: 0.8226 (m-40) REVERT: E 542 ILE cc_start: 0.9168 (tp) cc_final: 0.8927 (tp) REVERT: E 550 MET cc_start: 0.4033 (mmm) cc_final: 0.3286 (tpp) REVERT: E 560 ARG cc_start: 0.9635 (ttt-90) cc_final: 0.9288 (tpp80) REVERT: E 563 PHE cc_start: 0.9382 (m-10) cc_final: 0.8982 (m-80) REVERT: E 579 LEU cc_start: 0.9014 (pt) cc_final: 0.8787 (mm) REVERT: E 678 MET cc_start: 0.4897 (mtp) cc_final: 0.4077 (ttm) REVERT: E 736 PHE cc_start: 0.8810 (m-80) cc_final: 0.8370 (m-10) REVERT: E 740 MET cc_start: 0.7941 (mmp) cc_final: 0.7135 (mmp) REVERT: A 50 GLN cc_start: 0.9311 (pp30) cc_final: 0.9051 (pp30) REVERT: A 64 ARG cc_start: 0.8644 (tpt90) cc_final: 0.7774 (mmm160) REVERT: A 158 MET cc_start: 0.8292 (tmm) cc_final: 0.8069 (tmm) REVERT: A 163 PHE cc_start: 0.8814 (m-80) cc_final: 0.7977 (m-80) REVERT: A 221 GLU cc_start: 0.8723 (pm20) cc_final: 0.8457 (pm20) REVERT: A 243 LEU cc_start: 0.9378 (mm) cc_final: 0.9127 (mm) REVERT: A 253 LEU cc_start: 0.9412 (mt) cc_final: 0.8812 (mp) REVERT: A 256 ARG cc_start: 0.9224 (mtm-85) cc_final: 0.8869 (mtm-85) REVERT: A 319 GLU cc_start: 0.9305 (pm20) cc_final: 0.9047 (pm20) REVERT: A 349 ARG cc_start: 0.9159 (ttm110) cc_final: 0.8855 (mmm-85) REVERT: A 366 GLU cc_start: 0.7969 (tt0) cc_final: 0.7617 (tt0) REVERT: A 369 ILE cc_start: 0.9617 (tp) cc_final: 0.9398 (tp) REVERT: A 388 MET cc_start: 0.8577 (mpp) cc_final: 0.7933 (mpp) REVERT: A 417 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8510 (tm-30) REVERT: A 516 PHE cc_start: 0.9180 (m-80) cc_final: 0.8346 (m-80) REVERT: A 651 LYS cc_start: 0.9411 (pttt) cc_final: 0.9051 (tmtt) REVERT: F 204 ASP cc_start: 0.9034 (m-30) cc_final: 0.8172 (p0) REVERT: F 211 LYS cc_start: 0.7464 (mmtt) cc_final: 0.7162 (mmtm) REVERT: F 251 LYS cc_start: 0.9434 (mtmt) cc_final: 0.9179 (mtpt) REVERT: F 267 PHE cc_start: 0.8549 (t80) cc_final: 0.8338 (t80) REVERT: F 269 ILE cc_start: 0.9598 (tp) cc_final: 0.9140 (tp) REVERT: F 304 ASP cc_start: 0.8279 (p0) cc_final: 0.8030 (p0) REVERT: F 349 ARG cc_start: 0.8958 (tpm170) cc_final: 0.8710 (tpp80) REVERT: F 417 GLU cc_start: 0.9664 (mp0) cc_final: 0.9266 (mp0) REVERT: F 442 MET cc_start: 0.8842 (mmp) cc_final: 0.7492 (ptt) REVERT: F 508 MET cc_start: 0.2486 (ttt) cc_final: 0.2008 (ttt) REVERT: F 565 LYS cc_start: 0.9266 (pttp) cc_final: 0.8898 (pttp) REVERT: F 608 MET cc_start: 0.8653 (ptp) cc_final: 0.8156 (ptp) REVERT: F 609 ASP cc_start: 0.9011 (m-30) cc_final: 0.8587 (m-30) REVERT: F 611 MET cc_start: 0.8298 (pmm) cc_final: 0.7972 (pmm) REVERT: F 678 MET cc_start: 0.7954 (mtp) cc_final: 0.7746 (mtp) outliers start: 0 outliers final: 0 residues processed: 674 average time/residue: 0.2164 time to fit residues: 227.9937 Evaluate side-chains 525 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 301 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 371 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS F 317 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.090838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067318 restraints weight = 138774.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.069852 restraints weight = 95884.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.071720 restraints weight = 72240.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.073128 restraints weight = 57948.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.074173 restraints weight = 48675.637| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32516 Z= 0.193 Angle : 0.800 12.771 43942 Z= 0.405 Chirality : 0.051 0.263 4978 Planarity : 0.006 0.073 5767 Dihedral : 7.937 176.522 4446 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.13), residues: 4015 helix: -1.19 (0.12), residues: 1730 sheet: -1.74 (0.22), residues: 484 loop : -1.33 (0.15), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 225 TYR 0.024 0.002 TYR C 203 PHE 0.030 0.002 PHE A 563 TRP 0.022 0.001 TRP D 476 HIS 0.014 0.002 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00410 (32516) covalent geometry : angle 0.80040 (43942) hydrogen bonds : bond 0.03931 ( 1085) hydrogen bonds : angle 5.99737 ( 3153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 677 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8319 (mmp) cc_final: 0.8046 (mmm) REVERT: B 84 MET cc_start: 0.8799 (mmp) cc_final: 0.8305 (mmm) REVERT: B 130 LEU cc_start: 0.9009 (tt) cc_final: 0.8664 (mt) REVERT: B 244 TYR cc_start: 0.8867 (p90) cc_final: 0.8632 (p90) REVERT: B 302 PHE cc_start: 0.8765 (t80) cc_final: 0.8159 (t80) REVERT: B 305 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8223 (mm-30) REVERT: B 351 ASN cc_start: 0.9380 (p0) cc_final: 0.9082 (p0) REVERT: B 359 ARG cc_start: 0.8197 (ptm-80) cc_final: 0.7836 (ptt90) REVERT: B 363 PHE cc_start: 0.8148 (m-10) cc_final: 0.7695 (m-80) REVERT: B 366 GLU cc_start: 0.8787 (pm20) cc_final: 0.8387 (pm20) REVERT: B 379 GLU cc_start: 0.9290 (tp30) cc_final: 0.8483 (tt0) REVERT: B 386 LYS cc_start: 0.9448 (tppp) cc_final: 0.9144 (tppp) REVERT: B 388 MET cc_start: 0.8559 (mmp) cc_final: 0.7192 (mmm) REVERT: B 426 LYS cc_start: 0.9652 (mptt) cc_final: 0.9395 (mmtt) REVERT: B 514 VAL cc_start: 0.8149 (p) cc_final: 0.7810 (p) REVERT: B 515 LEU cc_start: 0.9330 (mm) cc_final: 0.9129 (mm) REVERT: B 524 LYS cc_start: 0.9070 (mttt) cc_final: 0.7906 (pttt) REVERT: B 538 ASN cc_start: 0.9357 (t0) cc_final: 0.8948 (t0) REVERT: B 611 MET cc_start: 0.9360 (pmm) cc_final: 0.9126 (pmm) REVERT: B 620 ILE cc_start: 0.9084 (mp) cc_final: 0.8694 (mp) REVERT: B 678 MET cc_start: 0.7618 (mtt) cc_final: 0.6896 (ptt) REVERT: B 757 MET cc_start: 0.8363 (ttt) cc_final: 0.8081 (tmm) REVERT: C 117 LEU cc_start: 0.8247 (mt) cc_final: 0.7872 (mt) REVERT: C 131 PHE cc_start: 0.8171 (m-10) cc_final: 0.7904 (m-10) REVERT: C 163 PHE cc_start: 0.8915 (m-80) cc_final: 0.8303 (m-80) REVERT: C 190 LYS cc_start: 0.9633 (pptt) cc_final: 0.9386 (pptt) REVERT: C 203 TYR cc_start: 0.8886 (m-80) cc_final: 0.8668 (m-80) REVERT: C 221 GLU cc_start: 0.8106 (pt0) cc_final: 0.7738 (pp20) REVERT: C 243 LEU cc_start: 0.9633 (mt) cc_final: 0.9287 (mt) REVERT: C 260 ASN cc_start: 0.8792 (m-40) cc_final: 0.8331 (m110) REVERT: C 261 GLU cc_start: 0.8309 (pt0) cc_final: 0.7568 (mp0) REVERT: C 265 PHE cc_start: 0.8284 (t80) cc_final: 0.8048 (t80) REVERT: C 269 ILE cc_start: 0.9431 (mp) cc_final: 0.9169 (mp) REVERT: C 328 LEU cc_start: 0.9458 (mt) cc_final: 0.9231 (mt) REVERT: C 362 ARG cc_start: 0.8291 (mpp-170) cc_final: 0.7949 (mpt180) REVERT: C 369 ILE cc_start: 0.8466 (mp) cc_final: 0.8264 (tp) REVERT: C 449 MET cc_start: 0.8871 (mmp) cc_final: 0.8165 (mmm) REVERT: C 515 LEU cc_start: 0.9211 (mm) cc_final: 0.8985 (mm) REVERT: C 609 ASP cc_start: 0.9045 (m-30) cc_final: 0.8402 (m-30) REVERT: C 639 LEU cc_start: 0.6838 (mm) cc_final: 0.6542 (mm) REVERT: C 662 ARG cc_start: 0.9016 (tmm160) cc_final: 0.8483 (tmt-80) REVERT: D 135 LEU cc_start: 0.8570 (mt) cc_final: 0.8101 (mt) REVERT: D 139 PHE cc_start: 0.9084 (m-80) cc_final: 0.8593 (m-80) REVERT: D 199 ASN cc_start: 0.8865 (p0) cc_final: 0.8509 (p0) REVERT: D 209 CYS cc_start: 0.8658 (m) cc_final: 0.8349 (m) REVERT: D 219 MET cc_start: 0.8712 (pmm) cc_final: 0.8314 (pmm) REVERT: D 251 LYS cc_start: 0.9598 (mppt) cc_final: 0.9297 (mtmt) REVERT: D 268 LEU cc_start: 0.9404 (tt) cc_final: 0.8584 (tt) REVERT: D 287 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8671 (ttm-80) REVERT: D 302 PHE cc_start: 0.8616 (t80) cc_final: 0.7800 (t80) REVERT: D 319 GLU cc_start: 0.9557 (pp20) cc_final: 0.9212 (pp20) REVERT: D 344 MET cc_start: 0.8914 (ppp) cc_final: 0.8397 (ppp) REVERT: D 366 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8541 (mp0) REVERT: D 382 GLN cc_start: 0.8899 (mp10) cc_final: 0.8400 (pm20) REVERT: D 386 LYS cc_start: 0.9427 (ptmt) cc_final: 0.9094 (ptmt) REVERT: D 388 MET cc_start: 0.9008 (mpp) cc_final: 0.8567 (mpp) REVERT: D 516 PHE cc_start: 0.8543 (m-80) cc_final: 0.8333 (m-10) REVERT: D 543 LYS cc_start: 0.9206 (mppt) cc_final: 0.8976 (mmmt) REVERT: D 550 MET cc_start: 0.6970 (pmm) cc_final: 0.6730 (pmm) REVERT: D 565 LYS cc_start: 0.9312 (ptmt) cc_final: 0.8920 (tptt) REVERT: D 575 PHE cc_start: 0.8799 (t80) cc_final: 0.7944 (t80) REVERT: D 609 ASP cc_start: 0.8933 (p0) cc_final: 0.8732 (p0) REVERT: D 678 MET cc_start: 0.3160 (ptt) cc_final: 0.2918 (ptt) REVERT: D 700 ARG cc_start: 0.9212 (ppt170) cc_final: 0.8868 (ptm-80) REVERT: E 158 MET cc_start: 0.8814 (tpp) cc_final: 0.8258 (tpp) REVERT: E 218 GLU cc_start: 0.9409 (tt0) cc_final: 0.8969 (tm-30) REVERT: E 219 MET cc_start: 0.9230 (ppp) cc_final: 0.8643 (ptm) REVERT: E 243 LEU cc_start: 0.8486 (mt) cc_final: 0.8172 (mt) REVERT: E 275 MET cc_start: 0.9333 (mpp) cc_final: 0.9024 (mpp) REVERT: E 291 GLU cc_start: 0.9203 (pt0) cc_final: 0.8254 (tp30) REVERT: E 315 LYS cc_start: 0.7341 (mmtm) cc_final: 0.7086 (mmmt) REVERT: E 379 GLU cc_start: 0.9217 (tp30) cc_final: 0.8844 (tp30) REVERT: E 384 HIS cc_start: 0.8875 (t-90) cc_final: 0.8322 (t-170) REVERT: E 388 MET cc_start: 0.8999 (mmp) cc_final: 0.8632 (mmm) REVERT: E 449 MET cc_start: 0.8920 (mmp) cc_final: 0.8559 (mmp) REVERT: E 452 PHE cc_start: 0.7406 (m-80) cc_final: 0.7015 (m-80) REVERT: E 470 GLU cc_start: 0.8472 (tt0) cc_final: 0.7588 (tm-30) REVERT: E 515 LEU cc_start: 0.9109 (mm) cc_final: 0.8818 (mm) REVERT: E 516 PHE cc_start: 0.8610 (m-80) cc_final: 0.8335 (m-80) REVERT: E 517 TYR cc_start: 0.6649 (p90) cc_final: 0.6378 (p90) REVERT: E 538 ASN cc_start: 0.8759 (t0) cc_final: 0.8243 (m-40) REVERT: E 542 ILE cc_start: 0.9148 (tp) cc_final: 0.8912 (tp) REVERT: E 550 MET cc_start: 0.3994 (mmm) cc_final: 0.3294 (tpp) REVERT: E 560 ARG cc_start: 0.9633 (ttt-90) cc_final: 0.9267 (tpp-160) REVERT: E 563 PHE cc_start: 0.9333 (m-10) cc_final: 0.8989 (m-80) REVERT: E 564 ASP cc_start: 0.9172 (m-30) cc_final: 0.8856 (m-30) REVERT: E 579 LEU cc_start: 0.8965 (pt) cc_final: 0.8765 (mm) REVERT: E 615 LYS cc_start: 0.8503 (mptt) cc_final: 0.7862 (mptt) REVERT: E 678 MET cc_start: 0.4832 (mtp) cc_final: 0.4194 (ttm) REVERT: E 736 PHE cc_start: 0.8840 (m-80) cc_final: 0.8383 (m-10) REVERT: E 740 MET cc_start: 0.7995 (mmp) cc_final: 0.7481 (mmp) REVERT: A 50 GLN cc_start: 0.9272 (pp30) cc_final: 0.9020 (pp30) REVERT: A 64 ARG cc_start: 0.8624 (tpt90) cc_final: 0.8278 (tpt170) REVERT: A 84 MET cc_start: 0.9006 (mpp) cc_final: 0.8597 (mpp) REVERT: A 163 PHE cc_start: 0.8795 (m-80) cc_final: 0.7934 (m-80) REVERT: A 253 LEU cc_start: 0.9252 (mt) cc_final: 0.8637 (mt) REVERT: A 256 ARG cc_start: 0.9179 (mtm-85) cc_final: 0.8822 (mtm-85) REVERT: A 319 GLU cc_start: 0.9279 (pm20) cc_final: 0.9014 (pm20) REVERT: A 344 MET cc_start: 0.8996 (mmp) cc_final: 0.7828 (mmp) REVERT: A 349 ARG cc_start: 0.9243 (ttm110) cc_final: 0.9038 (ttm110) REVERT: A 366 GLU cc_start: 0.7918 (tt0) cc_final: 0.7628 (tt0) REVERT: A 388 MET cc_start: 0.8622 (mpp) cc_final: 0.7918 (mpp) REVERT: A 417 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8447 (tm-30) REVERT: A 459 SER cc_start: 0.9487 (t) cc_final: 0.9173 (m) REVERT: A 516 PHE cc_start: 0.8980 (m-80) cc_final: 0.7921 (m-80) REVERT: A 564 ASP cc_start: 0.9262 (t0) cc_final: 0.9015 (t0) REVERT: A 575 PHE cc_start: 0.9426 (t80) cc_final: 0.9214 (t80) REVERT: A 651 LYS cc_start: 0.9402 (pttt) cc_final: 0.9019 (tmtt) REVERT: F 204 ASP cc_start: 0.9064 (m-30) cc_final: 0.8248 (p0) REVERT: F 211 LYS cc_start: 0.7464 (mmtt) cc_final: 0.7160 (mmtm) REVERT: F 222 LEU cc_start: 0.9579 (tp) cc_final: 0.8862 (tp) REVERT: F 251 LYS cc_start: 0.9426 (mtmt) cc_final: 0.9156 (mtpt) REVERT: F 304 ASP cc_start: 0.7955 (p0) cc_final: 0.7739 (p0) REVERT: F 349 ARG cc_start: 0.8970 (tpm170) cc_final: 0.8619 (tpp80) REVERT: F 427 MET cc_start: 0.7069 (tpp) cc_final: 0.6120 (tpp) REVERT: F 442 MET cc_start: 0.8923 (mmp) cc_final: 0.7690 (ptt) REVERT: F 565 LYS cc_start: 0.9305 (pttp) cc_final: 0.8927 (pttp) REVERT: F 567 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8218 (mtt90) REVERT: F 608 MET cc_start: 0.8810 (ptp) cc_final: 0.8576 (ptm) REVERT: F 609 ASP cc_start: 0.9012 (m-30) cc_final: 0.8621 (m-30) outliers start: 0 outliers final: 0 residues processed: 677 average time/residue: 0.2163 time to fit residues: 228.3622 Evaluate side-chains 522 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 157 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 371 optimal weight: 0.7980 chunk 262 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 330 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 391 optimal weight: 5.9990 chunk 34 optimal weight: 0.0270 chunk 98 optimal weight: 4.9990 overall best weight: 2.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN D 327 GLN D 443 ASN D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.090831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.067219 restraints weight = 137373.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069742 restraints weight = 94522.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071599 restraints weight = 71126.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073049 restraints weight = 57178.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.074078 restraints weight = 47842.988| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32516 Z= 0.181 Angle : 0.808 12.389 43942 Z= 0.407 Chirality : 0.051 0.290 4978 Planarity : 0.006 0.093 5767 Dihedral : 7.955 177.665 4446 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 24.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 4015 helix: -1.20 (0.12), residues: 1739 sheet: -1.77 (0.22), residues: 471 loop : -1.34 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 365 TYR 0.018 0.002 TYR A 495 PHE 0.041 0.002 PHE E 302 TRP 0.022 0.001 TRP D 476 HIS 0.012 0.002 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00389 (32516) covalent geometry : angle 0.80758 (43942) hydrogen bonds : bond 0.03904 ( 1085) hydrogen bonds : angle 5.99482 ( 3153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8408 (mmp) cc_final: 0.8049 (mmm) REVERT: B 80 GLU cc_start: 0.8957 (pm20) cc_final: 0.8689 (pm20) REVERT: B 84 MET cc_start: 0.8789 (mmp) cc_final: 0.8282 (mmm) REVERT: B 130 LEU cc_start: 0.8942 (tt) cc_final: 0.8729 (mp) REVERT: B 275 MET cc_start: 0.9500 (mpp) cc_final: 0.9051 (mpp) REVERT: B 302 PHE cc_start: 0.8798 (t80) cc_final: 0.8233 (t80) REVERT: B 305 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8162 (mm-30) REVERT: B 351 ASN cc_start: 0.9384 (p0) cc_final: 0.9087 (p0) REVERT: B 363 PHE cc_start: 0.8174 (m-10) cc_final: 0.7717 (m-80) REVERT: B 366 GLU cc_start: 0.8894 (pm20) cc_final: 0.8531 (pm20) REVERT: B 379 GLU cc_start: 0.9269 (tp30) cc_final: 0.8461 (tt0) REVERT: B 388 MET cc_start: 0.8519 (mmp) cc_final: 0.7202 (mmm) REVERT: B 426 LYS cc_start: 0.9651 (mptt) cc_final: 0.9403 (mmtt) REVERT: B 508 MET cc_start: 0.5064 (mtt) cc_final: 0.4737 (mtp) REVERT: B 514 VAL cc_start: 0.8346 (p) cc_final: 0.8070 (p) REVERT: B 524 LYS cc_start: 0.9080 (mttt) cc_final: 0.7898 (pttt) REVERT: B 538 ASN cc_start: 0.9342 (t0) cc_final: 0.8985 (t0) REVERT: B 565 LYS cc_start: 0.9693 (pptt) cc_final: 0.9454 (pptt) REVERT: B 608 MET cc_start: 0.8432 (ptt) cc_final: 0.8140 (ppp) REVERT: B 611 MET cc_start: 0.9439 (pmm) cc_final: 0.8902 (pmm) REVERT: B 620 ILE cc_start: 0.9050 (mp) cc_final: 0.8637 (mp) REVERT: B 639 LEU cc_start: 0.9421 (mp) cc_final: 0.9148 (mp) REVERT: B 678 MET cc_start: 0.7590 (mtt) cc_final: 0.6888 (ptt) REVERT: B 757 MET cc_start: 0.8359 (ttt) cc_final: 0.8077 (tmm) REVERT: C 117 LEU cc_start: 0.8307 (mt) cc_final: 0.7937 (mt) REVERT: C 131 PHE cc_start: 0.8074 (m-10) cc_final: 0.7819 (m-10) REVERT: C 163 PHE cc_start: 0.8913 (m-80) cc_final: 0.8290 (m-80) REVERT: C 201 VAL cc_start: 0.9086 (m) cc_final: 0.8542 (p) REVERT: C 203 TYR cc_start: 0.9078 (m-80) cc_final: 0.8324 (m-80) REVERT: C 221 GLU cc_start: 0.7905 (pt0) cc_final: 0.7583 (pp20) REVERT: C 243 LEU cc_start: 0.9645 (mt) cc_final: 0.9322 (mt) REVERT: C 244 TYR cc_start: 0.7503 (p90) cc_final: 0.7179 (p90) REVERT: C 260 ASN cc_start: 0.8716 (m-40) cc_final: 0.8498 (m110) REVERT: C 261 GLU cc_start: 0.8493 (pt0) cc_final: 0.7024 (pt0) REVERT: C 265 PHE cc_start: 0.8252 (t80) cc_final: 0.8014 (t80) REVERT: C 269 ILE cc_start: 0.9412 (mp) cc_final: 0.9085 (mp) REVERT: C 362 ARG cc_start: 0.8163 (mpp-170) cc_final: 0.7927 (mmt90) REVERT: C 369 ILE cc_start: 0.8491 (mp) cc_final: 0.8221 (tp) REVERT: C 449 MET cc_start: 0.8923 (mmp) cc_final: 0.8259 (mmm) REVERT: C 516 PHE cc_start: 0.8437 (m-80) cc_final: 0.8105 (m-80) REVERT: C 609 ASP cc_start: 0.9022 (m-30) cc_final: 0.8390 (m-30) REVERT: C 639 LEU cc_start: 0.6762 (mm) cc_final: 0.6482 (mm) REVERT: C 662 ARG cc_start: 0.9042 (tmm160) cc_final: 0.8507 (tmt-80) REVERT: D 135 LEU cc_start: 0.8628 (mt) cc_final: 0.8179 (mt) REVERT: D 139 PHE cc_start: 0.9115 (m-80) cc_final: 0.8635 (m-80) REVERT: D 199 ASN cc_start: 0.8853 (p0) cc_final: 0.8500 (p0) REVERT: D 209 CYS cc_start: 0.8793 (m) cc_final: 0.8510 (m) REVERT: D 219 MET cc_start: 0.8659 (pmm) cc_final: 0.8296 (pmm) REVERT: D 221 GLU cc_start: 0.8957 (pm20) cc_final: 0.8734 (pm20) REVERT: D 268 LEU cc_start: 0.9323 (tt) cc_final: 0.8455 (tt) REVERT: D 287 ARG cc_start: 0.8986 (mmm-85) cc_final: 0.8748 (ttm-80) REVERT: D 302 PHE cc_start: 0.8565 (t80) cc_final: 0.8009 (t80) REVERT: D 319 GLU cc_start: 0.9585 (pp20) cc_final: 0.9154 (pp20) REVERT: D 366 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8601 (mp0) REVERT: D 388 MET cc_start: 0.8969 (mpp) cc_final: 0.8545 (mpp) REVERT: D 516 PHE cc_start: 0.8531 (m-80) cc_final: 0.8311 (m-10) REVERT: D 543 LYS cc_start: 0.9226 (mppt) cc_final: 0.8949 (mmmt) REVERT: D 550 MET cc_start: 0.6976 (pmm) cc_final: 0.6676 (pmm) REVERT: D 565 LYS cc_start: 0.9287 (ptmt) cc_final: 0.8984 (tptt) REVERT: D 574 LEU cc_start: 0.9589 (tp) cc_final: 0.9380 (tp) REVERT: D 575 PHE cc_start: 0.8827 (t80) cc_final: 0.7877 (t80) REVERT: D 609 ASP cc_start: 0.8999 (p0) cc_final: 0.8776 (p0) REVERT: D 700 ARG cc_start: 0.9124 (ppt170) cc_final: 0.8828 (ptm-80) REVERT: E 158 MET cc_start: 0.8810 (tpp) cc_final: 0.8360 (tpp) REVERT: E 218 GLU cc_start: 0.9386 (tt0) cc_final: 0.8903 (tm-30) REVERT: E 219 MET cc_start: 0.9232 (ppp) cc_final: 0.8691 (ptm) REVERT: E 243 LEU cc_start: 0.8538 (mt) cc_final: 0.8240 (mt) REVERT: E 244 TYR cc_start: 0.8536 (p90) cc_final: 0.8315 (p90) REVERT: E 291 GLU cc_start: 0.9189 (pt0) cc_final: 0.8264 (tp30) REVERT: E 379 GLU cc_start: 0.9214 (tp30) cc_final: 0.8827 (tp30) REVERT: E 388 MET cc_start: 0.8993 (mmp) cc_final: 0.8561 (mmm) REVERT: E 449 MET cc_start: 0.8810 (mmp) cc_final: 0.8362 (mmp) REVERT: E 451 ASP cc_start: 0.8421 (m-30) cc_final: 0.8205 (m-30) REVERT: E 452 PHE cc_start: 0.7395 (m-10) cc_final: 0.6940 (m-80) REVERT: E 470 GLU cc_start: 0.8510 (tt0) cc_final: 0.7583 (tm-30) REVERT: E 515 LEU cc_start: 0.9016 (mm) cc_final: 0.8680 (mm) REVERT: E 516 PHE cc_start: 0.8610 (m-80) cc_final: 0.8327 (m-80) REVERT: E 517 TYR cc_start: 0.6508 (p90) cc_final: 0.6239 (p90) REVERT: E 538 ASN cc_start: 0.8704 (t0) cc_final: 0.8244 (m-40) REVERT: E 542 ILE cc_start: 0.9212 (tp) cc_final: 0.8946 (tp) REVERT: E 560 ARG cc_start: 0.9637 (ttt-90) cc_final: 0.9230 (tpp-160) REVERT: E 563 PHE cc_start: 0.9354 (m-10) cc_final: 0.8979 (m-80) REVERT: E 564 ASP cc_start: 0.9105 (m-30) cc_final: 0.8579 (m-30) REVERT: E 678 MET cc_start: 0.4834 (mtp) cc_final: 0.4218 (ttm) REVERT: E 736 PHE cc_start: 0.8907 (m-80) cc_final: 0.8468 (m-10) REVERT: E 740 MET cc_start: 0.7752 (mmp) cc_final: 0.7335 (mmp) REVERT: A 50 GLN cc_start: 0.9214 (pp30) cc_final: 0.8932 (pp30) REVERT: A 64 ARG cc_start: 0.8639 (tpt90) cc_final: 0.7758 (mmm160) REVERT: A 158 MET cc_start: 0.8333 (tmm) cc_final: 0.8099 (tmm) REVERT: A 163 PHE cc_start: 0.8760 (m-80) cc_final: 0.8023 (m-80) REVERT: A 253 LEU cc_start: 0.9225 (mt) cc_final: 0.8796 (mt) REVERT: A 256 ARG cc_start: 0.9191 (mtm-85) cc_final: 0.8855 (mtm-85) REVERT: A 275 MET cc_start: 0.9346 (mmt) cc_final: 0.8982 (mmm) REVERT: A 319 GLU cc_start: 0.9303 (pm20) cc_final: 0.9062 (pm20) REVERT: A 344 MET cc_start: 0.9003 (mmp) cc_final: 0.7844 (mmp) REVERT: A 366 GLU cc_start: 0.7921 (tt0) cc_final: 0.7657 (tt0) REVERT: A 388 MET cc_start: 0.8627 (mpp) cc_final: 0.7937 (mpp) REVERT: A 417 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8638 (tm-30) REVERT: A 459 SER cc_start: 0.9553 (t) cc_final: 0.9197 (m) REVERT: A 516 PHE cc_start: 0.9148 (m-80) cc_final: 0.8231 (m-80) REVERT: A 561 GLU cc_start: 0.9058 (tt0) cc_final: 0.8745 (tm-30) REVERT: A 651 LYS cc_start: 0.9401 (pttt) cc_final: 0.8991 (tmtt) REVERT: F 204 ASP cc_start: 0.9011 (m-30) cc_final: 0.8182 (p0) REVERT: F 211 LYS cc_start: 0.7479 (mmtt) cc_final: 0.7168 (mmtm) REVERT: F 222 LEU cc_start: 0.9599 (tp) cc_final: 0.8857 (tp) REVERT: F 251 LYS cc_start: 0.9386 (mtmt) cc_final: 0.9089 (mtpt) REVERT: F 269 ILE cc_start: 0.9645 (tp) cc_final: 0.9436 (tp) REVERT: F 304 ASP cc_start: 0.8029 (p0) cc_final: 0.7828 (p0) REVERT: F 347 THR cc_start: 0.8824 (m) cc_final: 0.8560 (m) REVERT: F 349 ARG cc_start: 0.8933 (tpm170) cc_final: 0.8580 (tpp80) REVERT: F 442 MET cc_start: 0.8937 (mmp) cc_final: 0.7739 (ptt) REVERT: F 452 PHE cc_start: 0.8151 (m-80) cc_final: 0.7609 (m-80) REVERT: F 465 ARG cc_start: 0.6304 (mmt180) cc_final: 0.5499 (mmm160) REVERT: F 508 MET cc_start: 0.1635 (ttm) cc_final: 0.1087 (ttt) REVERT: F 565 LYS cc_start: 0.9304 (pttp) cc_final: 0.8880 (pttp) REVERT: F 567 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8277 (mtt180) REVERT: F 606 THR cc_start: 0.8933 (p) cc_final: 0.8469 (p) outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.2103 time to fit residues: 223.5453 Evaluate side-chains 550 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 16 optimal weight: 0.9990 chunk 278 optimal weight: 0.0010 chunk 116 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 330 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 285 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.093968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.070300 restraints weight = 130631.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073026 restraints weight = 88434.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074980 restraints weight = 65711.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.076481 restraints weight = 52204.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.077554 restraints weight = 43483.858| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32516 Z= 0.143 Angle : 0.809 12.906 43942 Z= 0.400 Chirality : 0.052 0.312 4978 Planarity : 0.006 0.078 5767 Dihedral : 7.773 174.191 4446 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.13), residues: 4015 helix: -1.09 (0.12), residues: 1727 sheet: -1.52 (0.23), residues: 443 loop : -1.31 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 155 TYR 0.020 0.002 TYR C 203 PHE 0.027 0.001 PHE A 563 TRP 0.021 0.001 TRP D 476 HIS 0.011 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00323 (32516) covalent geometry : angle 0.80938 (43942) hydrogen bonds : bond 0.03656 ( 1085) hydrogen bonds : angle 5.83735 ( 3153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 715 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8493 (mmp) cc_final: 0.8068 (mmm) REVERT: B 84 MET cc_start: 0.8648 (mmp) cc_final: 0.8131 (mmm) REVERT: B 244 TYR cc_start: 0.8626 (p90) cc_final: 0.8347 (p90) REVERT: B 256 ARG cc_start: 0.9228 (tpt90) cc_final: 0.9010 (tpp80) REVERT: B 302 PHE cc_start: 0.8762 (t80) cc_final: 0.8150 (t80) REVERT: B 305 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 344 MET cc_start: 0.9392 (tpt) cc_final: 0.8841 (tpt) REVERT: B 351 ASN cc_start: 0.9377 (p0) cc_final: 0.9051 (p0) REVERT: B 363 PHE cc_start: 0.7978 (m-10) cc_final: 0.7729 (m-80) REVERT: B 366 GLU cc_start: 0.8830 (pm20) cc_final: 0.8235 (pm20) REVERT: B 379 GLU cc_start: 0.9239 (tp30) cc_final: 0.8425 (tt0) REVERT: B 388 MET cc_start: 0.8445 (mmp) cc_final: 0.7089 (mmm) REVERT: B 426 LYS cc_start: 0.9603 (mptt) cc_final: 0.9364 (mmtt) REVERT: B 514 VAL cc_start: 0.8267 (p) cc_final: 0.8023 (p) REVERT: B 524 LYS cc_start: 0.9067 (mttt) cc_final: 0.7890 (pttt) REVERT: B 538 ASN cc_start: 0.9273 (t0) cc_final: 0.8893 (t0) REVERT: B 565 LYS cc_start: 0.9654 (pptt) cc_final: 0.9443 (pptt) REVERT: B 611 MET cc_start: 0.9394 (pmm) cc_final: 0.9087 (pmm) REVERT: B 620 ILE cc_start: 0.8940 (mp) cc_final: 0.8545 (mp) REVERT: B 639 LEU cc_start: 0.9422 (mp) cc_final: 0.9180 (mp) REVERT: B 678 MET cc_start: 0.7626 (mtt) cc_final: 0.6820 (ptt) REVERT: B 736 PHE cc_start: 0.8981 (m-80) cc_final: 0.8747 (m-10) REVERT: B 757 MET cc_start: 0.8335 (ttt) cc_final: 0.8047 (tmm) REVERT: C 117 LEU cc_start: 0.8109 (mt) cc_final: 0.7757 (mt) REVERT: C 131 PHE cc_start: 0.7959 (m-10) cc_final: 0.7647 (m-10) REVERT: C 163 PHE cc_start: 0.8887 (m-80) cc_final: 0.8166 (m-80) REVERT: C 201 VAL cc_start: 0.9051 (m) cc_final: 0.8570 (p) REVERT: C 203 TYR cc_start: 0.8984 (m-80) cc_final: 0.8305 (m-80) REVERT: C 221 GLU cc_start: 0.8025 (pt0) cc_final: 0.7634 (pt0) REVERT: C 225 ARG cc_start: 0.8879 (tmm160) cc_final: 0.8332 (tmt-80) REVERT: C 243 LEU cc_start: 0.9628 (mt) cc_final: 0.9299 (mt) REVERT: C 244 TYR cc_start: 0.7514 (p90) cc_final: 0.7137 (p90) REVERT: C 261 GLU cc_start: 0.8654 (pt0) cc_final: 0.7102 (pt0) REVERT: C 265 PHE cc_start: 0.8246 (t80) cc_final: 0.7978 (t80) REVERT: C 269 ILE cc_start: 0.9284 (mp) cc_final: 0.8988 (mp) REVERT: C 328 LEU cc_start: 0.9489 (mt) cc_final: 0.9260 (mt) REVERT: C 362 ARG cc_start: 0.7831 (mpp-170) cc_final: 0.7535 (mmt90) REVERT: C 423 ILE cc_start: 0.9554 (mt) cc_final: 0.9316 (mm) REVERT: C 449 MET cc_start: 0.8853 (mmp) cc_final: 0.8126 (mmm) REVERT: C 516 PHE cc_start: 0.8619 (m-80) cc_final: 0.8386 (m-80) REVERT: C 609 ASP cc_start: 0.8991 (m-30) cc_final: 0.8450 (m-30) REVERT: C 639 LEU cc_start: 0.6608 (mm) cc_final: 0.6347 (mm) REVERT: C 662 ARG cc_start: 0.8971 (tmm160) cc_final: 0.8478 (tmt-80) REVERT: D 135 LEU cc_start: 0.8608 (mt) cc_final: 0.8161 (mt) REVERT: D 139 PHE cc_start: 0.9085 (m-80) cc_final: 0.8646 (m-80) REVERT: D 158 MET cc_start: 0.7319 (ppp) cc_final: 0.6441 (ppp) REVERT: D 199 ASN cc_start: 0.8706 (p0) cc_final: 0.8404 (p0) REVERT: D 209 CYS cc_start: 0.8486 (m) cc_final: 0.8240 (m) REVERT: D 219 MET cc_start: 0.8561 (pmm) cc_final: 0.8190 (pmm) REVERT: D 221 GLU cc_start: 0.8919 (pm20) cc_final: 0.8685 (pm20) REVERT: D 268 LEU cc_start: 0.9337 (tt) cc_final: 0.8472 (tt) REVERT: D 287 ARG cc_start: 0.8996 (mmm-85) cc_final: 0.8564 (mpp80) REVERT: D 302 PHE cc_start: 0.8448 (t80) cc_final: 0.7965 (t80) REVERT: D 313 ARG cc_start: 0.7956 (tmm160) cc_final: 0.7497 (tmt170) REVERT: D 319 GLU cc_start: 0.9538 (pp20) cc_final: 0.9015 (pp20) REVERT: D 366 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8298 (mp0) REVERT: D 388 MET cc_start: 0.8848 (mpp) cc_final: 0.8399 (mpp) REVERT: D 410 ASP cc_start: 0.9000 (p0) cc_final: 0.8787 (p0) REVERT: D 417 GLU cc_start: 0.9309 (pm20) cc_final: 0.9051 (pm20) REVERT: D 543 LYS cc_start: 0.9187 (mppt) cc_final: 0.8895 (mmmt) REVERT: D 565 LYS cc_start: 0.9178 (ptmt) cc_final: 0.8920 (tptt) REVERT: D 575 PHE cc_start: 0.8787 (t80) cc_final: 0.7787 (t80) REVERT: D 687 LEU cc_start: 0.9597 (mt) cc_final: 0.9252 (pp) REVERT: D 700 ARG cc_start: 0.9213 (ppt170) cc_final: 0.8845 (ptm-80) REVERT: E 158 MET cc_start: 0.8778 (tpp) cc_final: 0.8289 (tpp) REVERT: E 218 GLU cc_start: 0.9377 (tt0) cc_final: 0.8934 (tm-30) REVERT: E 219 MET cc_start: 0.9195 (ppp) cc_final: 0.8670 (ptm) REVERT: E 243 LEU cc_start: 0.8460 (mt) cc_final: 0.8185 (mt) REVERT: E 270 ASN cc_start: 0.9507 (t0) cc_final: 0.8754 (t0) REVERT: E 273 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9212 (tp30) REVERT: E 291 GLU cc_start: 0.9176 (pt0) cc_final: 0.8256 (tp30) REVERT: E 315 LYS cc_start: 0.6327 (mmtt) cc_final: 0.5985 (mmmt) REVERT: E 379 GLU cc_start: 0.9121 (tp30) cc_final: 0.8669 (tp30) REVERT: E 383 ILE cc_start: 0.9667 (mt) cc_final: 0.9434 (mt) REVERT: E 388 MET cc_start: 0.8911 (mmp) cc_final: 0.8499 (mmm) REVERT: E 449 MET cc_start: 0.8901 (mmp) cc_final: 0.8406 (mmp) REVERT: E 452 PHE cc_start: 0.7275 (m-80) cc_final: 0.6660 (m-80) REVERT: E 470 GLU cc_start: 0.8574 (tt0) cc_final: 0.7697 (tm-30) REVERT: E 515 LEU cc_start: 0.8949 (mm) cc_final: 0.8632 (mm) REVERT: E 516 PHE cc_start: 0.8604 (m-80) cc_final: 0.8350 (m-80) REVERT: E 517 TYR cc_start: 0.6495 (p90) cc_final: 0.6279 (p90) REVERT: E 538 ASN cc_start: 0.8660 (t0) cc_final: 0.8186 (m-40) REVERT: E 542 ILE cc_start: 0.9118 (tp) cc_final: 0.8907 (tp) REVERT: E 560 ARG cc_start: 0.9632 (ttt-90) cc_final: 0.9269 (tpp-160) REVERT: E 563 PHE cc_start: 0.9391 (m-10) cc_final: 0.8989 (m-80) REVERT: E 564 ASP cc_start: 0.9195 (m-30) cc_final: 0.8880 (m-30) REVERT: E 635 ARG cc_start: 0.8648 (ptt-90) cc_final: 0.7924 (ptm160) REVERT: E 678 MET cc_start: 0.4362 (mtp) cc_final: 0.3609 (ttm) REVERT: E 736 PHE cc_start: 0.8811 (m-80) cc_final: 0.8418 (m-10) REVERT: E 740 MET cc_start: 0.7687 (mmp) cc_final: 0.7165 (mmp) REVERT: A 50 GLN cc_start: 0.9210 (pp30) cc_final: 0.8903 (pp30) REVERT: A 64 ARG cc_start: 0.8613 (tpt90) cc_final: 0.7711 (mmm160) REVERT: A 163 PHE cc_start: 0.8764 (m-80) cc_final: 0.7873 (m-80) REVERT: A 241 ILE cc_start: 0.8709 (tp) cc_final: 0.8113 (tp) REVERT: A 244 TYR cc_start: 0.8127 (p90) cc_final: 0.7754 (p90) REVERT: A 253 LEU cc_start: 0.9096 (mt) cc_final: 0.8521 (mt) REVERT: A 256 ARG cc_start: 0.9215 (mtm-85) cc_final: 0.8766 (mtm-85) REVERT: A 319 GLU cc_start: 0.9200 (pm20) cc_final: 0.8998 (pm20) REVERT: A 344 MET cc_start: 0.9154 (mmp) cc_final: 0.8150 (mmp) REVERT: A 366 GLU cc_start: 0.7747 (tt0) cc_final: 0.7304 (tt0) REVERT: A 417 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 459 SER cc_start: 0.9499 (t) cc_final: 0.9079 (m) REVERT: A 508 MET cc_start: 0.3167 (ptp) cc_final: 0.1999 (pmm) REVERT: A 516 PHE cc_start: 0.9152 (m-80) cc_final: 0.8293 (m-80) REVERT: A 561 GLU cc_start: 0.9020 (tt0) cc_final: 0.8676 (tm-30) REVERT: A 651 LYS cc_start: 0.9392 (pttt) cc_final: 0.8995 (tmtt) REVERT: A 661 LEU cc_start: 0.7683 (pp) cc_final: 0.7264 (pp) REVERT: F 204 ASP cc_start: 0.9027 (m-30) cc_final: 0.8135 (p0) REVERT: F 222 LEU cc_start: 0.9584 (tp) cc_final: 0.9340 (tp) REVERT: F 251 LYS cc_start: 0.9359 (mtmt) cc_final: 0.9044 (mtpt) REVERT: F 349 ARG cc_start: 0.8874 (tpm170) cc_final: 0.8529 (tpp80) REVERT: F 417 GLU cc_start: 0.9536 (mp0) cc_final: 0.9191 (mp0) REVERT: F 427 MET cc_start: 0.6787 (tpp) cc_final: 0.5810 (tpp) REVERT: F 442 MET cc_start: 0.8816 (mmp) cc_final: 0.7697 (ptt) REVERT: F 452 PHE cc_start: 0.8105 (m-80) cc_final: 0.7748 (m-80) REVERT: F 458 GLN cc_start: 0.8950 (mp10) cc_final: 0.8591 (mp10) REVERT: F 465 ARG cc_start: 0.6314 (mmt180) cc_final: 0.5309 (mmp-170) REVERT: F 508 MET cc_start: 0.1580 (ttm) cc_final: 0.1104 (ttm) REVERT: F 565 LYS cc_start: 0.9266 (pttp) cc_final: 0.8874 (pttp) REVERT: F 567 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8213 (mtt180) REVERT: F 606 THR cc_start: 0.8847 (p) cc_final: 0.8634 (p) REVERT: F 609 ASP cc_start: 0.9213 (m-30) cc_final: 0.8670 (m-30) outliers start: 0 outliers final: 0 residues processed: 715 average time/residue: 0.2210 time to fit residues: 245.0656 Evaluate side-chains 571 residues out of total 3470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 359 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 227 optimal weight: 0.4980 chunk 253 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 288 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 355 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.090566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.067080 restraints weight = 138157.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.069618 restraints weight = 94964.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.071466 restraints weight = 71459.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072890 restraints weight = 57414.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.073961 restraints weight = 48164.663| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32516 Z= 0.205 Angle : 0.834 11.802 43942 Z= 0.421 Chirality : 0.052 0.294 4978 Planarity : 0.006 0.086 5767 Dihedral : 7.889 179.762 4446 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 4015 helix: -1.16 (0.12), residues: 1728 sheet: -1.76 (0.22), residues: 469 loop : -1.26 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 349 TYR 0.050 0.002 TYR E 203 PHE 0.038 0.002 PHE E 302 TRP 0.022 0.002 TRP C 551 HIS 0.013 0.002 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00439 (32516) covalent geometry : angle 0.83438 (43942) hydrogen bonds : bond 0.04062 ( 1085) hydrogen bonds : angle 5.99419 ( 3153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6605.80 seconds wall clock time: 114 minutes 59.27 seconds (6899.27 seconds total)