Starting phenix.real_space_refine on Fri Mar 6 22:41:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8daw_27278/03_2026/8daw_27278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8daw_27278/03_2026/8daw_27278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8daw_27278/03_2026/8daw_27278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8daw_27278/03_2026/8daw_27278.map" model { file = "/net/cci-nas-00/data/ceres_data/8daw_27278/03_2026/8daw_27278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8daw_27278/03_2026/8daw_27278.cif" } resolution = 3.6 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= -0.016 sd= 1.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 29 5.49 5 S 157 5.16 5 C 21813 2.51 5 N 6060 2.21 5 O 6787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 34848 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5555 Classifications: {'peptide': 712} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 5599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5599 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 680} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4311 Classifications: {'peptide': 555} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 525} Chain breaks: 4 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4240 Classifications: {'peptide': 547} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 517} Chain breaks: 5 Chain: "E" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4113 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 502} Chain breaks: 3 Chain: "F" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4284 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 521} Chain breaks: 5 Chain: "G" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3825 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 453} Chain: "H" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 477 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain breaks: 1 Chain: "I" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 298 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "J" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "L" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28365 SG CYS G 137 48.797 49.156 93.141 1.00 98.79 S ATOM 28425 SG CYS G 145 52.450 49.938 93.137 1.00 77.93 S ATOM 28452 SG CYS G 148 50.393 50.043 96.161 1.00 79.99 S ATOM 28922 SG CYS G 204 76.806 91.382 114.164 1.00103.46 S ATOM 29020 SG CYS G 216 77.041 91.081 110.408 1.00 75.80 S ATOM 29041 SG CYS G 219 74.275 92.965 111.898 1.00 79.10 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ARG K 274 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG K 274 " occ=0.00 residue: pdb=" N GLY K 275 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY K 275 " occ=0.00 residue: pdb=" N GLY K 276 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY K 276 " occ=0.00 Time building chain proxies: 6.78, per 1000 atoms: 0.19 Number of scatterers: 34848 At special positions: 0 Unit cell: (153.216, 169.176, 189.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 157 16.00 P 29 15.00 O 6787 8.00 N 6060 7.00 C 21813 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8264 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 25 sheets defined 53.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.529A pdb=" N MET A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.756A pdb=" N GLU A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 4.163A pdb=" N LYS A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 201 through 207 removed outlier: 3.794A pdb=" N GLU A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 219 through 236 removed outlier: 3.869A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.587A pdb=" N LYS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.885A pdb=" N ILE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 345 removed outlier: 3.535A pdb=" N ARG A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.671A pdb=" N ARG A 369 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 417 through 438 removed outlier: 4.467A pdb=" N ASP A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.553A pdb=" N LEU A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 492 through 509 removed outlier: 4.546A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.834A pdb=" N TYR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.548A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 588 through 593 removed outlier: 3.645A pdb=" N ILE A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 621 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 659 through 671 Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 693 through 718 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.604A pdb=" N PHE A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 786 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 130 through 134 removed outlier: 4.064A pdb=" N GLU B 134 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 4.407A pdb=" N VAL B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 219 through 236 removed outlier: 4.716A pdb=" N LEU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 236 through 244 removed outlier: 4.202A pdb=" N PHE B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 282 through 285 removed outlier: 3.690A pdb=" N MET B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 329 through 345 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 395 Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 417 through 437 Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.504A pdb=" N LEU B 452 " --> pdb=" O ASP B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.648A pdb=" N TYR B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Proline residue: B 506 - end of helix Processing helix chain 'B' and resid 509 through 517 removed outlier: 4.212A pdb=" N TYR B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 removed outlier: 4.120A pdb=" N ALA B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 563 Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 588 through 593 Processing helix chain 'B' and resid 608 through 621 Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.085A pdb=" N ARG B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 670 Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 693 through 718 Processing helix chain 'B' and resid 754 through 764 removed outlier: 4.077A pdb=" N PHE B 758 " --> pdb=" O THR B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 786 Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.574A pdb=" N ILE C 216 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 236 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 236 through 244 removed outlier: 4.445A pdb=" N PHE C 240 " --> pdb=" O HIS C 236 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 290 through 305 Processing helix chain 'C' and resid 315 through 320 removed outlier: 3.965A pdb=" N ILE C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 344 removed outlier: 4.001A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.705A pdb=" N ILE C 363 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 405 through 413 Processing helix chain 'C' and resid 417 through 437 Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'C' and resid 492 through 509 removed outlier: 4.166A pdb=" N GLU C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 509 through 517 removed outlier: 3.972A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.560A pdb=" N VAL C 545 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 563 Processing helix chain 'C' and resid 568 through 579 Processing helix chain 'C' and resid 588 through 593 removed outlier: 4.441A pdb=" N ILE C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 593 " --> pdb=" O LEU C 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 588 through 593' Processing helix chain 'C' and resid 608 through 619 Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 659 through 671 Processing helix chain 'C' and resid 682 through 689 Processing helix chain 'C' and resid 693 through 718 Processing helix chain 'C' and resid 754 through 765 removed outlier: 3.762A pdb=" N PHE C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 786 removed outlier: 3.978A pdb=" N LEU C 774 " --> pdb=" O SER C 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 219 through 236 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 236 through 244 removed outlier: 4.312A pdb=" N PHE D 240 " --> pdb=" O HIS D 236 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 241 " --> pdb=" O PRO D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 288 through 306 Processing helix chain 'D' and resid 315 through 320 removed outlier: 4.028A pdb=" N ILE D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 345 Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 383 through 395 Processing helix chain 'D' and resid 405 through 413 Processing helix chain 'D' and resid 417 through 437 Processing helix chain 'D' and resid 438 through 440 No H-bonds generated for 'chain 'D' and resid 438 through 440' Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 472 through 476 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 492 through 509 removed outlier: 3.786A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Proline residue: D 506 - end of helix Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 533 through 545 Processing helix chain 'D' and resid 554 through 563 removed outlier: 4.085A pdb=" N MET D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 579 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 608 through 620 Processing helix chain 'D' and resid 659 through 671 Processing helix chain 'D' and resid 682 through 689 Processing helix chain 'D' and resid 693 through 718 removed outlier: 4.134A pdb=" N LEU D 697 " --> pdb=" O SER D 693 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 698 " --> pdb=" O GLY D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 765 removed outlier: 4.326A pdb=" N PHE D 758 " --> pdb=" O THR D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 786 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 219 through 236 removed outlier: 4.488A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 290 through 306 removed outlier: 3.794A pdb=" N SER E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU E 296 " --> pdb=" O SER E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 Processing helix chain 'E' and resid 329 through 345 removed outlier: 4.049A pdb=" N ARG E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 363 removed outlier: 4.126A pdb=" N ILE E 363 " --> pdb=" O PRO E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 369 removed outlier: 3.539A pdb=" N ARG E 368 " --> pdb=" O PRO E 365 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG E 369 " --> pdb=" O ALA E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 395 Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 417 through 437 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 448 through 455 removed outlier: 3.672A pdb=" N LEU E 452 " --> pdb=" O ASP E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'E' and resid 492 through 509 removed outlier: 4.331A pdb=" N TYR E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) Proline residue: E 506 - end of helix Processing helix chain 'E' and resid 509 through 516 Processing helix chain 'E' and resid 535 through 546 Processing helix chain 'E' and resid 553 through 563 Processing helix chain 'E' and resid 568 through 579 Processing helix chain 'E' and resid 588 through 593 removed outlier: 3.774A pdb=" N ILE E 592 " --> pdb=" O LEU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 620 Processing helix chain 'E' and resid 640 through 645 removed outlier: 3.926A pdb=" N ARG E 645 " --> pdb=" O ALA E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 672 Processing helix chain 'E' and resid 681 through 689 removed outlier: 3.839A pdb=" N ALA E 688 " --> pdb=" O ALA E 684 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR E 689 " --> pdb=" O ILE E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 718 Processing helix chain 'E' and resid 754 through 764 removed outlier: 3.992A pdb=" N PHE E 758 " --> pdb=" O THR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 786 Processing helix chain 'F' and resid 97 through 102 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 219 through 236 removed outlier: 3.846A pdb=" N LEU F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 236 through 244 removed outlier: 4.404A pdb=" N PHE F 240 " --> pdb=" O HIS F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 281 through 287 Processing helix chain 'F' and resid 288 through 306 removed outlier: 4.428A pdb=" N GLU F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 320 removed outlier: 3.815A pdb=" N ILE F 319 " --> pdb=" O GLU F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 344 removed outlier: 3.666A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 369 removed outlier: 3.750A pdb=" N ARG F 369 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 395 Processing helix chain 'F' and resid 405 through 413 Processing helix chain 'F' and resid 417 through 438 removed outlier: 3.799A pdb=" N ASP F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 454 removed outlier: 3.590A pdb=" N LEU F 452 " --> pdb=" O ASP F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 468 Processing helix chain 'F' and resid 485 through 489 removed outlier: 3.500A pdb=" N VAL F 489 " --> pdb=" O TRP F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 509 removed outlier: 4.489A pdb=" N TYR F 505 " --> pdb=" O GLU F 501 " (cutoff:3.500A) Proline residue: F 506 - end of helix Processing helix chain 'F' and resid 509 through 517 removed outlier: 3.852A pdb=" N TYR F 513 " --> pdb=" O HIS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 546 removed outlier: 3.581A pdb=" N VAL F 545 " --> pdb=" O VAL F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 563 Processing helix chain 'F' and resid 568 through 579 Processing helix chain 'F' and resid 588 through 592 removed outlier: 3.949A pdb=" N ILE F 592 " --> pdb=" O LEU F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 621 Processing helix chain 'F' and resid 640 through 645 Processing helix chain 'F' and resid 659 through 671 Processing helix chain 'F' and resid 682 through 688 Processing helix chain 'F' and resid 693 through 718 Processing helix chain 'F' and resid 754 through 764 Processing helix chain 'F' and resid 770 through 786 removed outlier: 3.607A pdb=" N LEU F 774 " --> pdb=" O SER F 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 124 Processing helix chain 'G' and resid 155 through 163 removed outlier: 3.849A pdb=" N HIS G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.711A pdb=" N TYR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS G 174 " --> pdb=" O HIS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 214 removed outlier: 3.639A pdb=" N GLY G 214 " --> pdb=" O TRP G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 256 Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.619A pdb=" N VAL G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG G 312 " --> pdb=" O LEU G 308 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 Processing helix chain 'G' and resid 402 through 407 Processing helix chain 'G' and resid 500 through 513 Processing helix chain 'G' and resid 516 through 524 Processing helix chain 'G' and resid 526 through 536 Processing helix chain 'G' and resid 540 through 553 Processing helix chain 'G' and resid 555 through 566 removed outlier: 4.183A pdb=" N SER G 559 " --> pdb=" O GLU G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 566 through 579 Processing helix chain 'H' and resid 243 through 254 removed outlier: 3.545A pdb=" N ARG H 252 " --> pdb=" O ALA H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'I' and resid 22 through 31 Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'K' and resid 222 through 235 removed outlier: 3.836A pdb=" N VAL K 226 " --> pdb=" O THR K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 260 removed outlier: 3.635A pdb=" N TYR K 259 " --> pdb=" O THR K 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 335 removed outlier: 3.861A pdb=" N VAL L 326 " --> pdb=" O THR L 322 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 339 No H-bonds generated for 'chain 'L' and resid 337 through 339' Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 166 removed outlier: 5.974A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 280 removed outlier: 6.756A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ASP A 314 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 279 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA A 309 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE A 354 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 311 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ALA A 356 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE A 313 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 357 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 548 through 552 removed outlier: 3.500A pdb=" N VAL A 524 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLY A 523 " --> pdb=" O GLN A 651 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE A 653 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 525 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 51 Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 120 removed outlier: 7.125A pdb=" N LYS B 119 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 154 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 161 through 166 removed outlier: 6.302A pdb=" N VAL B 175 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 127 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 280 removed outlier: 6.352A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP B 314 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 279 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 250 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL B 377 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 548 through 552 removed outlier: 3.771A pdb=" N VAL B 583 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 524 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR B 633 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N PHE B 526 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 275 through 279 removed outlier: 6.104A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE C 277 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 357 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 375 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 524 through 527 Processing sheet with id=AB3, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AB4, first strand: chain 'D' and resid 275 through 279 removed outlier: 6.407A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D 251 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR D 357 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET D 253 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 548 through 553 removed outlier: 6.536A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASP D 587 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 552 " --> pdb=" O ASP D 587 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 582 " --> pdb=" O PHE D 628 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE D 630 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL D 584 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA D 632 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU D 586 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 275 through 279 removed outlier: 6.843A pdb=" N PHE E 275 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE E 312 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE E 277 " --> pdb=" O PHE E 312 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 309 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ILE E 354 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE E 311 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET E 253 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY E 250 " --> pdb=" O ARG E 375 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL E 377 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 252 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 548 through 552 removed outlier: 3.825A pdb=" N VAL E 583 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 524 " --> pdb=" O GLY E 631 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 275 through 280 removed outlier: 6.949A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE F 279 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL F 352 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 356 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA F 355 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY F 250 " --> pdb=" O ARG F 375 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL F 377 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 548 through 552 removed outlier: 3.524A pdb=" N VAL F 583 " --> pdb=" O ASN F 548 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL F 524 " --> pdb=" O VAL F 629 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 463 through 465 removed outlier: 9.304A pdb=" N VAL G 382 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N HIS G 236 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL G 281 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU G 238 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ALA G 283 " --> pdb=" O GLU G 238 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY G 469 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE G 239 " --> pdb=" O GLY G 469 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 290 through 292 Processing sheet with id=AC3, first strand: chain 'G' and resid 414 through 415 Processing sheet with id=AC4, first strand: chain 'G' and resid 441 through 442 Processing sheet with id=AC5, first strand: chain 'J' and resid 112 through 115 removed outlier: 6.061A pdb=" N PHE J 104 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU J 169 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS J 106 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N LEU J 171 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 212 through 215 removed outlier: 6.279A pdb=" N PHE K 204 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU K 269 " --> pdb=" O PHE K 204 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS K 206 " --> pdb=" O LEU K 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 312 through 315 removed outlier: 4.141A pdb=" N LEU L 343 " --> pdb=" O LEU L 350 " (cutoff:3.500A) 1610 hydrogen bonds defined for protein. 4536 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: 6.96 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11796 1.34 - 1.46: 6852 1.46 - 1.58: 16447 1.58 - 1.70: 39 1.70 - 1.81: 290 Bond restraints: 35424 Sorted by residual: bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP D 902 " pdb=" C5 ADP D 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP C 902 " pdb=" C5 ADP C 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 35419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.56: 47609 5.56 - 11.12: 247 11.12 - 16.68: 59 16.68 - 22.24: 5 22.24 - 27.81: 3 Bond angle restraints: 47923 Sorted by residual: angle pdb=" C ILE E 639 " pdb=" N ASP E 640 " pdb=" CA ASP E 640 " ideal model delta sigma weight residual 121.80 149.61 -27.81 2.44e+00 1.68e-01 1.30e+02 angle pdb=" C GLU L 364 " pdb=" N SER L 365 " pdb=" CA SER L 365 " ideal model delta sigma weight residual 121.32 143.96 -22.64 2.10e+00 2.27e-01 1.16e+02 angle pdb=" C LEU B 36 " pdb=" N LEU B 37 " pdb=" CA LEU B 37 " ideal model delta sigma weight residual 121.32 143.64 -22.32 2.10e+00 2.27e-01 1.13e+02 angle pdb=" C PRO E 248 " pdb=" N ARG E 249 " pdb=" CA ARG E 249 " ideal model delta sigma weight residual 122.58 144.56 -21.98 2.07e+00 2.33e-01 1.13e+02 angle pdb=" C GLU E 331 " pdb=" N ARG E 332 " pdb=" CA ARG E 332 " ideal model delta sigma weight residual 121.54 141.36 -19.82 1.91e+00 2.74e-01 1.08e+02 ... (remaining 47918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.11: 21656 33.11 - 66.23: 226 66.23 - 99.34: 25 99.34 - 132.45: 16 132.45 - 165.56: 3 Dihedral angle restraints: 21926 sinusoidal: 9168 harmonic: 12758 Sorted by residual: dihedral pdb=" CA ALA F 307 " pdb=" C ALA F 307 " pdb=" N PRO F 308 " pdb=" CA PRO F 308 " ideal model delta harmonic sigma weight residual 180.00 140.99 39.01 0 5.00e+00 4.00e-02 6.09e+01 dihedral pdb=" C2' ADP E 901 " pdb=" C1' ADP E 901 " pdb=" N9 ADP E 901 " pdb=" C4 ADP E 901 " ideal model delta sinusoidal sigma weight residual 91.55 -102.89 -165.56 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 153.01 146.98 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 21923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.346: 5246 0.346 - 0.692: 80 0.692 - 1.038: 0 1.038 - 1.384: 12 1.384 - 1.731: 65 Chirality restraints: 5403 Sorted by residual: chirality pdb=" CG LEU F 589 " pdb=" CB LEU F 589 " pdb=" CD1 LEU F 589 " pdb=" CD2 LEU F 589 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.49e+01 chirality pdb=" CB ILE K 236 " pdb=" CA ILE K 236 " pdb=" CG1 ILE K 236 " pdb=" CG2 ILE K 236 " both_signs ideal model delta sigma weight residual False 2.64 0.92 1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" CG LEU E 339 " pdb=" CB LEU E 339 " pdb=" CD1 LEU E 339 " pdb=" CD2 LEU E 339 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.41e+01 ... (remaining 5400 not shown) Planarity restraints: 6242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 329 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLU B 329 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU B 329 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 330 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 506 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LYS G 506 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS G 506 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR G 507 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 507 " 0.019 2.00e-02 2.50e+03 1.23e-02 3.02e+00 pdb=" CG TYR G 507 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR G 507 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR G 507 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 507 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR G 507 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G 507 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 507 " 0.004 2.00e-02 2.50e+03 ... (remaining 6239 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 444 2.55 - 3.14: 30696 3.14 - 3.72: 53701 3.72 - 4.31: 70582 4.31 - 4.90: 119538 Nonbonded interactions: 274961 Sorted by model distance: nonbonded pdb=" OG1 THR D 754 " pdb=" OE1 GLU D 756 " model vdw 1.960 3.040 nonbonded pdb=" OG1 THR B 66 " pdb=" O CYS B 115 " model vdw 1.974 3.040 nonbonded pdb=" OG1 THR B 262 " pdb=" O2G ATP B 901 " model vdw 1.975 3.040 nonbonded pdb=" OG1 THR D 262 " pdb=" O2G ATP D 901 " model vdw 1.989 3.040 nonbonded pdb=" OG SER G 417 " pdb=" O MET G 422 " model vdw 1.991 3.040 ... (remaining 274956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 440 or resid 447 through 902)) selection = (chain 'B' and resid 33 through 902) } ncs_group { reference = (chain 'C' and (resid 207 through 440 or resid 447 through 786 or resid 902)) selection = (chain 'D' and (resid 207 through 786 or resid 902)) selection = (chain 'E' and (resid 207 through 786 or resid 902)) selection = (chain 'F' and (resid 207 through 786 or resid 902)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 3.380 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: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 32.460 Find NCS groups from input model: 0.830 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.006 0.836 35436 Z= 0.484 Angle : 0.984 27.806 47929 Z= 0.494 Chirality : 0.199 1.731 5403 Planarity : 0.003 0.039 6242 Dihedral : 11.527 165.564 13662 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 0.48 % Allowed : 4.27 % Favored : 95.25 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.14), residues: 4348 helix: 2.37 (0.12), residues: 1985 sheet: -0.29 (0.22), residues: 582 loop : -0.09 (0.16), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 492 TYR 0.029 0.001 TYR G 507 PHE 0.014 0.001 PHE G 248 TRP 0.005 0.001 TRP G 489 HIS 0.003 0.001 HIS G 170 Details of bonding type rmsd covalent geometry : bond 0.00371 (35424) covalent geometry : angle 0.98309 (47923) hydrogen bonds : bond 0.14582 ( 1610) hydrogen bonds : angle 5.45792 ( 4536) metal coordination : bond 0.08400 ( 8) metal coordination : angle 2.97599 ( 6) Misc. bond : bond 0.42572 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 392 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: -0.2088 (mtt) cc_final: -0.2290 (mpp) REVERT: A 254 TYR cc_start: 0.8642 (p90) cc_final: 0.8347 (p90) REVERT: A 672 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7906 (ttm110) REVERT: B 113 HIS cc_start: 0.8033 (t70) cc_final: 0.7621 (t-90) REVERT: B 153 TYR cc_start: 0.6193 (m-80) cc_final: 0.5657 (t80) REVERT: B 332 ARG cc_start: 0.7112 (mtm110) cc_final: 0.6816 (ttp-170) REVERT: B 398 MET cc_start: 0.8705 (mtt) cc_final: 0.8427 (mtt) REVERT: B 405 ASP cc_start: 0.8367 (t0) cc_final: 0.8042 (t0) REVERT: B 752 TYR cc_start: 0.7835 (p90) cc_final: 0.7304 (p90) REVERT: B 762 MET cc_start: 0.7189 (ptm) cc_final: 0.6939 (ptm) REVERT: B 784 MET cc_start: 0.7982 (mmm) cc_final: 0.7671 (mmp) REVERT: C 301 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7895 (tm-30) REVERT: C 405 ASP cc_start: 0.8288 (t70) cc_final: 0.7909 (t0) REVERT: C 618 MET cc_start: 0.8119 (tmm) cc_final: 0.7869 (tmm) REVERT: D 264 MET cc_start: 0.7921 (ttm) cc_final: 0.7678 (ttm) REVERT: D 314 ASP cc_start: 0.8276 (t0) cc_final: 0.8012 (t0) REVERT: D 560 MET cc_start: 0.6002 (tpp) cc_final: 0.5228 (mpp) REVERT: D 753 ILE cc_start: 0.7134 (mp) cc_final: 0.6649 (tt) REVERT: E 437 MET cc_start: 0.7859 (ptp) cc_final: 0.7647 (ptt) REVERT: E 468 ASN cc_start: 0.8581 (m110) cc_final: 0.8180 (t0) REVERT: E 762 MET cc_start: 0.5085 (ppp) cc_final: 0.4879 (ppp) REVERT: F 311 ILE cc_start: 0.8322 (mt) cc_final: 0.7931 (tt) REVERT: F 343 ASP cc_start: 0.8445 (t0) cc_final: 0.8241 (m-30) REVERT: F 587 ASP cc_start: 0.8349 (t0) cc_final: 0.7940 (t0) REVERT: G 108 TYR cc_start: 0.7658 (m-80) cc_final: 0.7165 (m-80) REVERT: G 315 GLN cc_start: 0.8007 (tt0) cc_final: 0.7735 (tt0) REVERT: G 543 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: G 574 MET cc_start: 0.8476 (tmm) cc_final: 0.8109 (tmm) REVERT: H 258 PHE cc_start: 0.6016 (p90) cc_final: 0.5393 (p90) outliers start: 18 outliers final: 7 residues processed: 408 average time/residue: 0.2375 time to fit residues: 151.3570 Evaluate side-chains 278 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 355 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 0.0030 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 4.9990 overall best weight: 0.8074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 548 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS F 207 ASN F 209 ASN F 634 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 528 HIS H 298 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.126088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089696 restraints weight = 100236.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090034 restraints weight = 58681.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090316 restraints weight = 39816.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090724 restraints weight = 37449.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.091095 restraints weight = 33204.701| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35436 Z= 0.138 Angle : 0.643 10.296 47929 Z= 0.313 Chirality : 0.044 0.154 5403 Planarity : 0.004 0.038 6242 Dihedral : 10.803 156.841 5028 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 1.01 % Allowed : 7.31 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.13), residues: 4348 helix: 1.88 (0.12), residues: 2039 sheet: -0.14 (0.22), residues: 579 loop : -0.08 (0.16), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 663 TYR 0.021 0.001 TYR G 507 PHE 0.021 0.001 PHE E 464 TRP 0.026 0.002 TRP B 561 HIS 0.006 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00304 (35424) covalent geometry : angle 0.64229 (47923) hydrogen bonds : bond 0.03955 ( 1610) hydrogen bonds : angle 4.67949 ( 4536) metal coordination : bond 0.01014 ( 8) metal coordination : angle 2.92501 ( 6) Misc. bond : bond 0.00452 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 299 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 672 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7812 (ttm170) REVERT: B 113 HIS cc_start: 0.7899 (t70) cc_final: 0.7549 (t-90) REVERT: B 398 MET cc_start: 0.8755 (mtt) cc_final: 0.8452 (mtt) REVERT: B 405 ASP cc_start: 0.8440 (t0) cc_final: 0.8042 (t0) REVERT: B 752 TYR cc_start: 0.7860 (p90) cc_final: 0.7361 (p90) REVERT: C 405 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8095 (t0) REVERT: C 618 MET cc_start: 0.7939 (tmm) cc_final: 0.7631 (tmm) REVERT: C 758 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8126 (t80) REVERT: D 430 MET cc_start: 0.8975 (tpp) cc_final: 0.8727 (tpp) REVERT: D 560 MET cc_start: 0.6290 (tpp) cc_final: 0.5427 (mpp) REVERT: D 588 GLU cc_start: 0.8172 (pm20) cc_final: 0.7416 (mm-30) REVERT: E 285 MET cc_start: 0.6770 (mmp) cc_final: 0.6181 (mtt) REVERT: E 288 MET cc_start: 0.5467 (mmt) cc_final: 0.5179 (mmt) REVERT: E 437 MET cc_start: 0.7907 (ptp) cc_final: 0.7619 (ptt) REVERT: E 468 ASN cc_start: 0.8796 (m110) cc_final: 0.8339 (t0) REVERT: E 509 HIS cc_start: 0.3076 (OUTLIER) cc_final: 0.2125 (p90) REVERT: E 560 MET cc_start: 0.7609 (mpp) cc_final: 0.7129 (mpp) REVERT: F 343 ASP cc_start: 0.8505 (t0) cc_final: 0.8219 (m-30) REVERT: F 587 ASP cc_start: 0.8489 (t0) cc_final: 0.8113 (t0) REVERT: G 315 GLN cc_start: 0.8104 (tt0) cc_final: 0.7823 (tt0) REVERT: G 543 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: H 258 PHE cc_start: 0.5869 (p90) cc_final: 0.5351 (p90) REVERT: H 309 LYS cc_start: 0.8216 (tppp) cc_final: 0.7848 (tppp) REVERT: I 34 GLU cc_start: 0.7583 (tt0) cc_final: 0.7354 (tt0) outliers start: 38 outliers final: 21 residues processed: 324 average time/residue: 0.2106 time to fit residues: 110.9570 Evaluate side-chains 280 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 119 optimal weight: 9.9990 chunk 375 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 413 optimal weight: 0.9980 chunk 433 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 385 optimal weight: 0.9980 chunk 269 optimal weight: 0.6980 chunk 330 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 HIS F 207 ASN F 209 ASN F 394 HIS F 512 GLN G 106 HIS G 170 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.123827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086854 restraints weight = 99920.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086657 restraints weight = 56597.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086592 restraints weight = 41520.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086901 restraints weight = 41807.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.087615 restraints weight = 33981.670| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35436 Z= 0.225 Angle : 0.650 8.342 47929 Z= 0.322 Chirality : 0.045 0.188 5403 Planarity : 0.004 0.040 6242 Dihedral : 10.326 149.262 5021 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 1.97 % Allowed : 8.75 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.13), residues: 4348 helix: 1.58 (0.12), residues: 2037 sheet: -0.24 (0.22), residues: 570 loop : -0.31 (0.16), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 463 TYR 0.036 0.002 TYR G 507 PHE 0.027 0.002 PHE E 464 TRP 0.031 0.002 TRP B 561 HIS 0.007 0.001 HIS G 139 Details of bonding type rmsd covalent geometry : bond 0.00524 (35424) covalent geometry : angle 0.64878 (47923) hydrogen bonds : bond 0.04037 ( 1610) hydrogen bonds : angle 4.72899 ( 4536) metal coordination : bond 0.01451 ( 8) metal coordination : angle 4.01823 ( 6) Misc. bond : bond 0.00228 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 274 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8116 (t0) REVERT: A 672 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7641 (tpm170) REVERT: B 113 HIS cc_start: 0.7973 (t70) cc_final: 0.7601 (t70) REVERT: B 398 MET cc_start: 0.8798 (mtt) cc_final: 0.8481 (mtt) REVERT: B 405 ASP cc_start: 0.8585 (t0) cc_final: 0.8185 (t0) REVERT: B 437 MET cc_start: 0.8086 (tpp) cc_final: 0.7874 (tpp) REVERT: B 752 TYR cc_start: 0.7893 (p90) cc_final: 0.7412 (p90) REVERT: C 405 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8095 (t0) REVERT: C 583 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8309 (m) REVERT: C 614 LEU cc_start: 0.8785 (tt) cc_final: 0.8449 (mm) REVERT: C 618 MET cc_start: 0.7867 (tmm) cc_final: 0.7459 (tmm) REVERT: C 758 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8140 (t80) REVERT: D 304 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7920 (pp20) REVERT: D 323 ARG cc_start: 0.6378 (mmt90) cc_final: 0.6169 (mmt90) REVERT: D 342 MET cc_start: 0.8923 (mmm) cc_final: 0.8607 (mmm) REVERT: D 430 MET cc_start: 0.9000 (tpp) cc_final: 0.8741 (tpp) REVERT: D 482 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7295 (p) REVERT: D 560 MET cc_start: 0.6282 (tpp) cc_final: 0.5353 (mpp) REVERT: D 588 GLU cc_start: 0.8219 (pm20) cc_final: 0.7566 (mm-30) REVERT: D 618 MET cc_start: 0.7901 (ttp) cc_final: 0.7675 (ttp) REVERT: E 339 LEU cc_start: 0.8920 (mp) cc_final: 0.8702 (mt) REVERT: E 468 ASN cc_start: 0.8839 (m110) cc_final: 0.8538 (t0) REVERT: E 509 HIS cc_start: 0.3019 (OUTLIER) cc_final: 0.2219 (p90) REVERT: E 560 MET cc_start: 0.7509 (mpp) cc_final: 0.7062 (mpp) REVERT: E 639 ILE cc_start: 0.5772 (mm) cc_final: 0.4856 (pt) REVERT: F 254 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.6752 (p90) REVERT: F 343 ASP cc_start: 0.8548 (t0) cc_final: 0.8233 (m-30) REVERT: F 359 ARG cc_start: 0.9094 (tpp-160) cc_final: 0.8869 (tpp80) REVERT: F 587 ASP cc_start: 0.8555 (t0) cc_final: 0.8099 (t0) REVERT: G 208 HIS cc_start: 0.8132 (p-80) cc_final: 0.7899 (p-80) REVERT: G 315 GLN cc_start: 0.8141 (tt0) cc_final: 0.7726 (tt0) REVERT: G 543 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: H 258 PHE cc_start: 0.5748 (p90) cc_final: 0.5285 (p90) REVERT: H 309 LYS cc_start: 0.8334 (tppp) cc_final: 0.7954 (tppp) REVERT: I 34 GLU cc_start: 0.7799 (tt0) cc_final: 0.7508 (tt0) outliers start: 74 outliers final: 44 residues processed: 333 average time/residue: 0.1972 time to fit residues: 110.2871 Evaluate side-chains 295 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 361 ILE Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 166 optimal weight: 0.4980 chunk 138 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 71 optimal weight: 0.0570 chunk 157 optimal weight: 0.9980 chunk 370 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 304 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 390 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.125363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.089606 restraints weight = 98900.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088348 restraints weight = 52365.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089068 restraints weight = 43541.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.089364 restraints weight = 34927.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089437 restraints weight = 31423.947| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35436 Z= 0.124 Angle : 0.588 11.459 47929 Z= 0.286 Chirality : 0.042 0.154 5403 Planarity : 0.004 0.047 6242 Dihedral : 9.892 144.623 5020 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.75 % Rotamer: Outliers : 1.84 % Allowed : 9.90 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 4348 helix: 1.68 (0.12), residues: 2025 sheet: -0.15 (0.22), residues: 572 loop : -0.21 (0.16), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 372 TYR 0.023 0.001 TYR G 507 PHE 0.022 0.001 PHE E 464 TRP 0.026 0.002 TRP B 486 HIS 0.004 0.001 HIS K 268 Details of bonding type rmsd covalent geometry : bond 0.00278 (35424) covalent geometry : angle 0.58774 (47923) hydrogen bonds : bond 0.03389 ( 1610) hydrogen bonds : angle 4.47722 ( 4536) metal coordination : bond 0.00587 ( 8) metal coordination : angle 2.66023 ( 6) Misc. bond : bond 0.00198 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 268 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8409 (m-30) cc_final: 0.8102 (m-30) REVERT: A 405 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8059 (t0) REVERT: A 672 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7575 (tpm170) REVERT: B 113 HIS cc_start: 0.8085 (t70) cc_final: 0.7719 (t70) REVERT: B 287 LYS cc_start: 0.9144 (tttm) cc_final: 0.8783 (tmtt) REVERT: B 398 MET cc_start: 0.8813 (mtt) cc_final: 0.8526 (mtt) REVERT: B 405 ASP cc_start: 0.8563 (t0) cc_final: 0.8135 (t0) REVERT: B 621 MET cc_start: 0.6911 (ppp) cc_final: 0.6622 (ptm) REVERT: B 752 TYR cc_start: 0.7979 (p90) cc_final: 0.7462 (p90) REVERT: C 405 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8091 (t0) REVERT: C 758 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8154 (t80) REVERT: D 342 MET cc_start: 0.8934 (mmm) cc_final: 0.8631 (mmm) REVERT: D 482 VAL cc_start: 0.7630 (OUTLIER) cc_final: 0.7115 (p) REVERT: D 560 MET cc_start: 0.6197 (tpp) cc_final: 0.5169 (mpp) REVERT: D 588 GLU cc_start: 0.8206 (pm20) cc_final: 0.7460 (mm-30) REVERT: D 618 MET cc_start: 0.7877 (ttp) cc_final: 0.7629 (ttp) REVERT: E 285 MET cc_start: 0.7028 (mmp) cc_final: 0.6264 (mtt) REVERT: E 288 MET cc_start: 0.5009 (mmt) cc_final: 0.4765 (mmt) REVERT: E 468 ASN cc_start: 0.8950 (m110) cc_final: 0.8529 (t0) REVERT: E 509 HIS cc_start: 0.2993 (OUTLIER) cc_final: 0.2204 (p90) REVERT: E 560 MET cc_start: 0.7629 (mpp) cc_final: 0.7275 (mpp) REVERT: E 639 ILE cc_start: 0.5599 (mm) cc_final: 0.4675 (pt) REVERT: F 343 ASP cc_start: 0.8550 (t0) cc_final: 0.8235 (m-30) REVERT: F 587 ASP cc_start: 0.8515 (t0) cc_final: 0.8058 (t0) REVERT: G 315 GLN cc_start: 0.8134 (tt0) cc_final: 0.7721 (tt0) REVERT: G 543 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: H 258 PHE cc_start: 0.5803 (p90) cc_final: 0.5284 (p90) REVERT: H 309 LYS cc_start: 0.8346 (tppp) cc_final: 0.7950 (tppp) REVERT: I 34 GLU cc_start: 0.7593 (tt0) cc_final: 0.7306 (tt0) REVERT: K 215 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7715 (tt) outliers start: 69 outliers final: 35 residues processed: 324 average time/residue: 0.1950 time to fit residues: 106.6325 Evaluate side-chains 298 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 213 optimal weight: 0.7980 chunk 343 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 392 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 306 optimal weight: 0.3980 chunk 379 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 432 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 384 optimal weight: 0.8980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 209 ASN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN H 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.124499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.087705 restraints weight = 99509.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088078 restraints weight = 57102.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087831 restraints weight = 42698.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.088344 restraints weight = 39826.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088770 restraints weight = 33807.414| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35436 Z= 0.117 Angle : 0.578 11.398 47929 Z= 0.278 Chirality : 0.042 0.227 5403 Planarity : 0.003 0.040 6242 Dihedral : 9.464 139.575 5020 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.52 % Rotamer: Outliers : 2.00 % Allowed : 10.54 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.13), residues: 4348 helix: 1.70 (0.12), residues: 2027 sheet: -0.13 (0.22), residues: 571 loop : -0.15 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 348 TYR 0.022 0.001 TYR G 507 PHE 0.025 0.001 PHE E 464 TRP 0.023 0.001 TRP B 561 HIS 0.005 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00263 (35424) covalent geometry : angle 0.57705 (47923) hydrogen bonds : bond 0.03163 ( 1610) hydrogen bonds : angle 4.34376 ( 4536) metal coordination : bond 0.00544 ( 8) metal coordination : angle 2.45633 ( 6) Misc. bond : bond 0.00093 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 269 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8623 (ttm) cc_final: 0.8392 (ttm) REVERT: A 405 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8167 (t0) REVERT: A 427 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8061 (tp30) REVERT: A 672 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7630 (tpm170) REVERT: B 113 HIS cc_start: 0.8099 (t70) cc_final: 0.7740 (t70) REVERT: B 287 LYS cc_start: 0.9136 (tttm) cc_final: 0.8745 (tmtt) REVERT: B 398 MET cc_start: 0.8823 (mtt) cc_final: 0.8549 (mtt) REVERT: B 405 ASP cc_start: 0.8566 (t0) cc_final: 0.8134 (t0) REVERT: B 437 MET cc_start: 0.7844 (tpp) cc_final: 0.7580 (tpp) REVERT: B 752 TYR cc_start: 0.8019 (p90) cc_final: 0.7516 (p90) REVERT: C 282 PRO cc_start: 0.8570 (Cg_exo) cc_final: 0.8338 (Cg_endo) REVERT: C 398 MET cc_start: 0.8635 (mtp) cc_final: 0.8427 (mtm) REVERT: C 405 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8072 (t0) REVERT: C 583 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8261 (m) REVERT: C 590 ASP cc_start: 0.8312 (p0) cc_final: 0.8024 (m-30) REVERT: C 758 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8165 (t80) REVERT: D 342 MET cc_start: 0.8962 (mmm) cc_final: 0.8620 (mmm) REVERT: D 460 ASP cc_start: 0.9201 (t0) cc_final: 0.8934 (p0) REVERT: D 482 VAL cc_start: 0.7574 (OUTLIER) cc_final: 0.7054 (p) REVERT: D 560 MET cc_start: 0.6247 (tpp) cc_final: 0.5145 (mpp) REVERT: D 588 GLU cc_start: 0.8236 (pm20) cc_final: 0.7531 (mm-30) REVERT: D 621 MET cc_start: 0.7766 (pmm) cc_final: 0.7486 (ppp) REVERT: E 223 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8748 (mmm) REVERT: E 468 ASN cc_start: 0.8958 (m110) cc_final: 0.8573 (t0) REVERT: E 560 MET cc_start: 0.7596 (mpp) cc_final: 0.7253 (mpp) REVERT: E 639 ILE cc_start: 0.5624 (mm) cc_final: 0.4721 (pt) REVERT: F 343 ASP cc_start: 0.8540 (t0) cc_final: 0.8177 (m-30) REVERT: F 587 ASP cc_start: 0.8517 (t0) cc_final: 0.8053 (t0) REVERT: G 208 HIS cc_start: 0.8006 (p-80) cc_final: 0.7679 (p-80) REVERT: G 315 GLN cc_start: 0.8147 (tt0) cc_final: 0.7751 (tt0) REVERT: G 543 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: H 258 PHE cc_start: 0.5756 (p90) cc_final: 0.5322 (p90) REVERT: H 309 LYS cc_start: 0.8351 (tppp) cc_final: 0.8030 (tppp) REVERT: I 34 GLU cc_start: 0.7563 (tt0) cc_final: 0.7271 (tt0) REVERT: K 215 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7687 (tt) outliers start: 75 outliers final: 37 residues processed: 328 average time/residue: 0.1982 time to fit residues: 109.1803 Evaluate side-chains 300 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 6.9990 chunk 427 optimal weight: 4.9990 chunk 176 optimal weight: 0.0060 chunk 341 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 405 optimal weight: 0.9980 chunk 348 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.128732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091647 restraints weight = 101971.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.090940 restraints weight = 51814.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.091852 restraints weight = 43495.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.091881 restraints weight = 35312.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.092132 restraints weight = 32930.661| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35436 Z= 0.133 Angle : 0.588 13.090 47929 Z= 0.283 Chirality : 0.042 0.177 5403 Planarity : 0.003 0.040 6242 Dihedral : 9.244 136.712 5020 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % Rotamer: Outliers : 1.76 % Allowed : 11.26 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.13), residues: 4348 helix: 1.66 (0.12), residues: 2040 sheet: -0.12 (0.22), residues: 564 loop : -0.18 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 434 TYR 0.024 0.001 TYR G 507 PHE 0.023 0.001 PHE E 464 TRP 0.023 0.001 TRP B 561 HIS 0.004 0.001 HIS K 268 Details of bonding type rmsd covalent geometry : bond 0.00306 (35424) covalent geometry : angle 0.58700 (47923) hydrogen bonds : bond 0.03190 ( 1610) hydrogen bonds : angle 4.34778 ( 4536) metal coordination : bond 0.00763 ( 8) metal coordination : angle 2.66719 ( 6) Misc. bond : bond 0.00403 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 265 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8558 (ttm) cc_final: 0.8325 (ttm) REVERT: A 405 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8104 (t0) REVERT: A 427 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8046 (tp30) REVERT: A 672 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7612 (tpm170) REVERT: B 113 HIS cc_start: 0.8142 (t70) cc_final: 0.7661 (t70) REVERT: B 114 PRO cc_start: 0.7411 (Cg_exo) cc_final: 0.6943 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9140 (tttm) cc_final: 0.8769 (tmtt) REVERT: B 398 MET cc_start: 0.8791 (mtt) cc_final: 0.8521 (mtt) REVERT: B 405 ASP cc_start: 0.8558 (t0) cc_final: 0.8156 (t0) REVERT: B 483 ASN cc_start: 0.8488 (t0) cc_final: 0.8271 (t0) REVERT: B 752 TYR cc_start: 0.7958 (p90) cc_final: 0.7482 (p90) REVERT: C 398 MET cc_start: 0.8604 (mtp) cc_final: 0.8396 (mtm) REVERT: C 405 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8072 (t0) REVERT: C 583 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8239 (m) REVERT: C 590 ASP cc_start: 0.8306 (p0) cc_final: 0.8063 (m-30) REVERT: C 618 MET cc_start: 0.8305 (ptp) cc_final: 0.7576 (tmm) REVERT: C 758 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8115 (t80) REVERT: D 342 MET cc_start: 0.8934 (mmm) cc_final: 0.8592 (mmm) REVERT: D 460 ASP cc_start: 0.9108 (t0) cc_final: 0.8894 (p0) REVERT: D 482 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7168 (p) REVERT: D 560 MET cc_start: 0.6217 (tpp) cc_final: 0.5153 (mpp) REVERT: D 588 GLU cc_start: 0.8239 (pm20) cc_final: 0.7597 (mm-30) REVERT: E 468 ASN cc_start: 0.8922 (m110) cc_final: 0.8577 (t0) REVERT: E 560 MET cc_start: 0.7630 (mpp) cc_final: 0.7247 (mpp) REVERT: E 639 ILE cc_start: 0.5720 (mm) cc_final: 0.4838 (pt) REVERT: F 343 ASP cc_start: 0.8488 (t0) cc_final: 0.8157 (m-30) REVERT: F 587 ASP cc_start: 0.8495 (t0) cc_final: 0.8046 (t0) REVERT: G 315 GLN cc_start: 0.8103 (tt0) cc_final: 0.7719 (tt0) REVERT: G 543 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: G 574 MET cc_start: 0.8784 (tmm) cc_final: 0.8537 (tmm) REVERT: H 258 PHE cc_start: 0.5632 (p90) cc_final: 0.5345 (p90) REVERT: H 309 LYS cc_start: 0.8334 (tppp) cc_final: 0.7948 (tppp) REVERT: I 34 GLU cc_start: 0.7439 (tt0) cc_final: 0.7114 (tt0) REVERT: K 215 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7661 (tt) outliers start: 66 outliers final: 41 residues processed: 316 average time/residue: 0.1897 time to fit residues: 101.9804 Evaluate side-chains 301 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 172 optimal weight: 3.9990 chunk 394 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 181 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.125779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089161 restraints weight = 99162.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089037 restraints weight = 57265.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089548 restraints weight = 42958.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089880 restraints weight = 35377.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089991 restraints weight = 33451.216| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35436 Z= 0.116 Angle : 0.592 20.782 47929 Z= 0.282 Chirality : 0.042 0.159 5403 Planarity : 0.003 0.040 6242 Dihedral : 8.861 132.179 5020 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 1.81 % Allowed : 11.71 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.13), residues: 4348 helix: 1.65 (0.12), residues: 2049 sheet: -0.08 (0.22), residues: 572 loop : -0.15 (0.16), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.023 0.001 TYR G 189 PHE 0.030 0.001 PHE C 573 TRP 0.037 0.001 TRP B 486 HIS 0.004 0.001 HIS K 268 Details of bonding type rmsd covalent geometry : bond 0.00262 (35424) covalent geometry : angle 0.59097 (47923) hydrogen bonds : bond 0.03053 ( 1610) hydrogen bonds : angle 4.29862 ( 4536) metal coordination : bond 0.00521 ( 8) metal coordination : angle 2.40961 ( 6) Misc. bond : bond 0.00121 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8554 (ttm) cc_final: 0.8228 (ttm) REVERT: A 405 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8085 (t0) REVERT: A 427 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8060 (tp30) REVERT: A 672 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7638 (tpm170) REVERT: B 113 HIS cc_start: 0.8178 (t70) cc_final: 0.7688 (t70) REVERT: B 114 PRO cc_start: 0.7437 (Cg_exo) cc_final: 0.6974 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9118 (tttm) cc_final: 0.8742 (tmtt) REVERT: B 398 MET cc_start: 0.8790 (mtt) cc_final: 0.8524 (mtt) REVERT: B 405 ASP cc_start: 0.8543 (t0) cc_final: 0.8122 (t0) REVERT: B 437 MET cc_start: 0.7798 (tpp) cc_final: 0.7566 (tpp) REVERT: B 483 ASN cc_start: 0.8494 (t0) cc_final: 0.8279 (t0) REVERT: B 752 TYR cc_start: 0.8004 (p90) cc_final: 0.7512 (p90) REVERT: C 398 MET cc_start: 0.8609 (mtp) cc_final: 0.8398 (mtm) REVERT: C 405 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8093 (t0) REVERT: C 583 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8181 (m) REVERT: C 590 ASP cc_start: 0.8362 (p0) cc_final: 0.8081 (m-30) REVERT: C 758 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.8147 (t80) REVERT: D 264 MET cc_start: 0.8583 (tpp) cc_final: 0.8364 (tpp) REVERT: D 323 ARG cc_start: 0.6324 (mmt90) cc_final: 0.5942 (mmt-90) REVERT: D 342 MET cc_start: 0.8958 (mmm) cc_final: 0.8586 (mmm) REVERT: D 482 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7058 (p) REVERT: D 560 MET cc_start: 0.6270 (tpp) cc_final: 0.5151 (mpp) REVERT: D 588 GLU cc_start: 0.8249 (pm20) cc_final: 0.7623 (mm-30) REVERT: E 468 ASN cc_start: 0.8973 (m110) cc_final: 0.8655 (t0) REVERT: E 560 MET cc_start: 0.7634 (mpp) cc_final: 0.7277 (mpp) REVERT: E 639 ILE cc_start: 0.5744 (mm) cc_final: 0.4910 (pt) REVERT: E 784 MET cc_start: 0.7769 (mmp) cc_final: 0.7243 (mmm) REVERT: F 587 ASP cc_start: 0.8506 (t0) cc_final: 0.8037 (t0) REVERT: G 315 GLN cc_start: 0.8048 (tt0) cc_final: 0.7679 (tt0) REVERT: G 543 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: H 258 PHE cc_start: 0.5620 (p90) cc_final: 0.5294 (p90) REVERT: H 309 LYS cc_start: 0.8350 (tppp) cc_final: 0.8040 (tppp) REVERT: I 34 GLU cc_start: 0.7234 (tt0) cc_final: 0.6969 (tt0) REVERT: K 215 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7661 (tt) outliers start: 68 outliers final: 45 residues processed: 319 average time/residue: 0.1917 time to fit residues: 104.4128 Evaluate side-chains 306 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 195 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 461 ASN B 512 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.124991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087529 restraints weight = 99113.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088203 restraints weight = 56975.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088372 restraints weight = 40548.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088735 restraints weight = 38379.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.088898 restraints weight = 33843.103| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35436 Z= 0.153 Angle : 0.606 15.671 47929 Z= 0.292 Chirality : 0.042 0.176 5403 Planarity : 0.004 0.040 6242 Dihedral : 8.539 128.669 5020 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.78 % Favored : 95.17 % Rotamer: Outliers : 1.81 % Allowed : 12.06 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4348 helix: 1.59 (0.12), residues: 2055 sheet: -0.09 (0.22), residues: 565 loop : -0.20 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 434 TYR 0.026 0.001 TYR G 507 PHE 0.022 0.001 PHE E 464 TRP 0.026 0.001 TRP B 486 HIS 0.005 0.001 HIS K 268 Details of bonding type rmsd covalent geometry : bond 0.00356 (35424) covalent geometry : angle 0.60528 (47923) hydrogen bonds : bond 0.03211 ( 1610) hydrogen bonds : angle 4.38236 ( 4536) metal coordination : bond 0.00718 ( 8) metal coordination : angle 2.74678 ( 6) Misc. bond : bond 0.00104 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8150 (t0) REVERT: A 427 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8084 (tp30) REVERT: A 672 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7631 (tpm170) REVERT: B 113 HIS cc_start: 0.8189 (t70) cc_final: 0.7687 (t70) REVERT: B 114 PRO cc_start: 0.7425 (Cg_exo) cc_final: 0.6946 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9129 (tttm) cc_final: 0.8719 (tmtt) REVERT: B 398 MET cc_start: 0.8809 (mtt) cc_final: 0.8527 (mtt) REVERT: B 405 ASP cc_start: 0.8563 (t0) cc_final: 0.8163 (t0) REVERT: B 437 MET cc_start: 0.7952 (tpp) cc_final: 0.7742 (tpp) REVERT: B 752 TYR cc_start: 0.8018 (p90) cc_final: 0.7531 (p90) REVERT: C 398 MET cc_start: 0.8655 (mtp) cc_final: 0.8450 (mtm) REVERT: C 405 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8086 (t0) REVERT: C 583 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8210 (m) REVERT: C 590 ASP cc_start: 0.8370 (p0) cc_final: 0.8116 (m-30) REVERT: C 758 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8132 (t80) REVERT: D 482 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7106 (p) REVERT: D 560 MET cc_start: 0.6310 (tpp) cc_final: 0.5209 (mpp) REVERT: D 588 GLU cc_start: 0.8171 (pm20) cc_final: 0.7601 (mm-30) REVERT: D 621 MET cc_start: 0.7751 (pmm) cc_final: 0.7397 (ppp) REVERT: E 254 TYR cc_start: 0.8326 (p90) cc_final: 0.8041 (p90) REVERT: E 468 ASN cc_start: 0.8990 (m110) cc_final: 0.8653 (t0) REVERT: E 560 MET cc_start: 0.7470 (mpp) cc_final: 0.7099 (mpp) REVERT: E 621 MET cc_start: 0.7006 (tpp) cc_final: 0.6787 (tpp) REVERT: E 639 ILE cc_start: 0.5759 (mm) cc_final: 0.4958 (pt) REVERT: F 587 ASP cc_start: 0.8531 (t0) cc_final: 0.8079 (t0) REVERT: G 315 GLN cc_start: 0.8148 (tt0) cc_final: 0.7762 (tt0) REVERT: G 543 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: H 258 PHE cc_start: 0.5577 (p90) cc_final: 0.5345 (p90) REVERT: H 309 LYS cc_start: 0.8343 (tppp) cc_final: 0.7953 (tppp) REVERT: K 215 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7686 (tt) outliers start: 68 outliers final: 50 residues processed: 310 average time/residue: 0.2010 time to fit residues: 104.9533 Evaluate side-chains 307 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 250 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 32 optimal weight: 0.0020 chunk 164 optimal weight: 6.9990 chunk 398 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 254 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 262 optimal weight: 0.6980 chunk 332 optimal weight: 6.9990 chunk 148 optimal weight: 0.0010 chunk 210 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN C 668 ASN F 548 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.126288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090525 restraints weight = 98441.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090913 restraints weight = 53945.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.090606 restraints weight = 41221.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091073 restraints weight = 38993.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091193 restraints weight = 33629.855| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35436 Z= 0.104 Angle : 0.600 19.405 47929 Z= 0.286 Chirality : 0.042 0.150 5403 Planarity : 0.003 0.040 6242 Dihedral : 8.207 123.820 5020 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 1.47 % Allowed : 12.43 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4348 helix: 1.64 (0.12), residues: 2049 sheet: -0.00 (0.22), residues: 573 loop : -0.11 (0.16), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 375 TYR 0.020 0.001 TYR G 189 PHE 0.019 0.001 PHE A 144 TRP 0.028 0.001 TRP B 486 HIS 0.003 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00227 (35424) covalent geometry : angle 0.59942 (47923) hydrogen bonds : bond 0.02902 ( 1610) hydrogen bonds : angle 4.27089 ( 4536) metal coordination : bond 0.00443 ( 8) metal coordination : angle 2.04840 ( 6) Misc. bond : bond 0.00108 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 265 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8090 (t0) REVERT: A 427 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8047 (tp30) REVERT: A 672 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7756 (ttm170) REVERT: B 113 HIS cc_start: 0.8171 (t70) cc_final: 0.7664 (t70) REVERT: B 114 PRO cc_start: 0.7263 (Cg_exo) cc_final: 0.6733 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9104 (tttm) cc_final: 0.8712 (tmtt) REVERT: B 405 ASP cc_start: 0.8484 (t0) cc_final: 0.8076 (t0) REVERT: B 437 MET cc_start: 0.7908 (tpp) cc_final: 0.7662 (tpp) REVERT: B 752 TYR cc_start: 0.7875 (p90) cc_final: 0.7478 (p90) REVERT: C 405 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8051 (t0) REVERT: C 583 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8221 (m) REVERT: C 590 ASP cc_start: 0.8292 (p0) cc_final: 0.8090 (m-30) REVERT: C 758 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.8052 (t80) REVERT: D 323 ARG cc_start: 0.6535 (mmt90) cc_final: 0.6253 (mmt-90) REVERT: D 560 MET cc_start: 0.6164 (tpp) cc_final: 0.5107 (mpp) REVERT: D 588 GLU cc_start: 0.8228 (pm20) cc_final: 0.7664 (mm-30) REVERT: E 254 TYR cc_start: 0.8253 (p90) cc_final: 0.8003 (p90) REVERT: E 468 ASN cc_start: 0.8940 (m110) cc_final: 0.8634 (t0) REVERT: E 560 MET cc_start: 0.7517 (mpp) cc_final: 0.7138 (mpp) REVERT: E 621 MET cc_start: 0.6902 (tpp) cc_final: 0.6678 (tpp) REVERT: E 639 ILE cc_start: 0.5792 (mm) cc_final: 0.4985 (pt) REVERT: E 784 MET cc_start: 0.7719 (mmp) cc_final: 0.7175 (mmm) REVERT: F 587 ASP cc_start: 0.8469 (t0) cc_final: 0.8058 (t0) REVERT: F 758 PHE cc_start: 0.8620 (m-80) cc_final: 0.8327 (m-80) REVERT: G 315 GLN cc_start: 0.8072 (tt0) cc_final: 0.7701 (tt0) REVERT: G 543 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: H 309 LYS cc_start: 0.8312 (tppp) cc_final: 0.8010 (tppp) REVERT: K 215 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7660 (tt) outliers start: 55 outliers final: 38 residues processed: 307 average time/residue: 0.2011 time to fit residues: 103.5000 Evaluate side-chains 299 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 139 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 180 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 199 optimal weight: 0.5980 chunk 133 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 412 optimal weight: 0.2980 chunk 71 optimal weight: 0.0980 chunk 358 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN D 651 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.126717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090413 restraints weight = 99266.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.090916 restraints weight = 54918.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.091013 restraints weight = 38831.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.091317 restraints weight = 38602.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091428 restraints weight = 33748.730| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35436 Z= 0.105 Angle : 0.614 21.660 47929 Z= 0.291 Chirality : 0.042 0.192 5403 Planarity : 0.003 0.040 6242 Dihedral : 7.973 119.771 5020 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 1.33 % Allowed : 13.04 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.13), residues: 4348 helix: 1.63 (0.12), residues: 2047 sheet: 0.01 (0.22), residues: 575 loop : -0.05 (0.16), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 434 TYR 0.019 0.001 TYR G 507 PHE 0.015 0.001 PHE E 464 TRP 0.024 0.001 TRP B 486 HIS 0.004 0.001 HIS K 268 Details of bonding type rmsd covalent geometry : bond 0.00228 (35424) covalent geometry : angle 0.61367 (47923) hydrogen bonds : bond 0.02852 ( 1610) hydrogen bonds : angle 4.24495 ( 4536) metal coordination : bond 0.00385 ( 8) metal coordination : angle 2.08429 ( 6) Misc. bond : bond 0.00099 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8099 (t0) REVERT: A 427 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8062 (tp30) REVERT: A 672 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7581 (tpm170) REVERT: B 113 HIS cc_start: 0.8153 (t70) cc_final: 0.7634 (t70) REVERT: B 114 PRO cc_start: 0.7212 (Cg_exo) cc_final: 0.6746 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9137 (tttm) cc_final: 0.8785 (tmtt) REVERT: B 405 ASP cc_start: 0.8448 (t0) cc_final: 0.8039 (t0) REVERT: B 437 MET cc_start: 0.7903 (tpp) cc_final: 0.7652 (tpp) REVERT: B 752 TYR cc_start: 0.7969 (p90) cc_final: 0.7524 (p90) REVERT: C 405 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8077 (t0) REVERT: C 583 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8155 (m) REVERT: C 590 ASP cc_start: 0.8358 (p0) cc_final: 0.8105 (m-30) REVERT: C 618 MET cc_start: 0.8489 (ptp) cc_final: 0.8245 (ppp) REVERT: C 758 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8142 (t80) REVERT: D 560 MET cc_start: 0.6216 (tpp) cc_final: 0.5058 (mpp) REVERT: D 588 GLU cc_start: 0.8241 (pm20) cc_final: 0.7617 (mm-30) REVERT: E 288 MET cc_start: 0.4647 (mmt) cc_final: 0.4207 (mpp) REVERT: E 468 ASN cc_start: 0.8969 (m110) cc_final: 0.8661 (t0) REVERT: E 560 MET cc_start: 0.7545 (mpp) cc_final: 0.7182 (mpp) REVERT: E 621 MET cc_start: 0.6924 (tpp) cc_final: 0.6699 (tpp) REVERT: E 639 ILE cc_start: 0.5655 (mm) cc_final: 0.4848 (pt) REVERT: E 784 MET cc_start: 0.7766 (mmp) cc_final: 0.7250 (mmm) REVERT: F 587 ASP cc_start: 0.8508 (t0) cc_final: 0.8083 (p0) REVERT: F 758 PHE cc_start: 0.8659 (m-80) cc_final: 0.8352 (m-80) REVERT: G 315 GLN cc_start: 0.8073 (tt0) cc_final: 0.7751 (tt0) REVERT: G 543 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: H 309 LYS cc_start: 0.8317 (tppp) cc_final: 0.8043 (tppp) REVERT: K 215 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7638 (tt) REVERT: L 370 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8594 (m) outliers start: 50 outliers final: 38 residues processed: 310 average time/residue: 0.1989 time to fit residues: 103.8283 Evaluate side-chains 306 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 379 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 211 optimal weight: 0.9990 chunk 362 optimal weight: 0.7980 chunk 364 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.126291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089055 restraints weight = 98495.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089946 restraints weight = 53300.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.090068 restraints weight = 36778.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.090695 restraints weight = 35141.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090887 restraints weight = 30283.213| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35436 Z= 0.117 Angle : 0.619 21.407 47929 Z= 0.293 Chirality : 0.042 0.170 5403 Planarity : 0.003 0.043 6242 Dihedral : 7.859 116.692 5020 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 1.33 % Allowed : 13.12 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.13), residues: 4348 helix: 1.66 (0.12), residues: 2047 sheet: -0.01 (0.23), residues: 560 loop : -0.05 (0.16), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 123 TYR 0.021 0.001 TYR G 507 PHE 0.016 0.001 PHE E 464 TRP 0.024 0.001 TRP B 486 HIS 0.003 0.001 HIS L 368 Details of bonding type rmsd covalent geometry : bond 0.00268 (35424) covalent geometry : angle 0.61906 (47923) hydrogen bonds : bond 0.02911 ( 1610) hydrogen bonds : angle 4.24777 ( 4536) metal coordination : bond 0.00428 ( 8) metal coordination : angle 2.13404 ( 6) Misc. bond : bond 0.00095 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6153.42 seconds wall clock time: 106 minutes 44.58 seconds (6404.58 seconds total)