Starting phenix.real_space_refine on Mon Jul 6 11:50:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8daw_27278/07_2026/8daw_27278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8daw_27278/07_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_27278/07_2026/8daw_27278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8daw_27278/07_2026/8daw_27278.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8daw_27278/07_2026/8daw_27278.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8daw_27278/07_2026/8daw_27278.cif" model { file = "/net/cci-nas-00/data/ceres_data/8daw_27278/07_2026/8daw_27278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8daw_27278/07_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.48, per 1000 atoms: 0.21 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: 3.86 Conformation dependent library (CDL) restraints added in 1.6 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: 0.80 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: 7.76 Time building geometry restraints manager: 4.86 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: 21577 33.11 - 66.23: 166 66.23 - 99.34: 9 99.34 - 132.45: 16 132.45 - 165.56: 3 Dihedral angle restraints: 21771 sinusoidal: 9013 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 21768 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 37.960 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 10.649 165.564 13507 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/Z covalent geometry : bond 0.00371 / 0.17 (35424) covalent geometry : angle 0.98309 / 0.49 (47923) hydrogen bonds : bond 0.14582 / 9.76 ( 1610) hydrogen bonds : angle 5.45792 / 3.86 ( 4536) metal coordination : bond 0.08400 / 4.24 ( 8) metal coordination : angle 2.97599 / 1.69 ( 6) Misc. bond : bond 0.42572 / 22.35 ( 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 : 1.492 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: 0.2560 time to fit residues: 163.6021 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 : 1.418 ------------------------------------------------------------------------------- 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... 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 = 0.4175 r_free = 0.4175 target = 0.126160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089799 restraints weight = 100182.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090151 restraints weight = 58117.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090411 restraints weight = 39728.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090851 restraints weight = 37214.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091213 restraints weight = 32890.716| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35436 Z= 0.139 Angle : 0.652 9.434 47929 Z= 0.316 Chirality : 0.045 0.151 5403 Planarity : 0.004 0.038 6242 Dihedral : 8.861 156.290 4873 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 1.04 % Allowed : 7.44 % Favored : 91.52 % 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: 1.17 (0.13), residues: 4348 helix: 1.84 (0.12), residues: 2039 sheet: -0.13 (0.22), residues: 570 loop : -0.10 (0.16), residues: 1739 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 0.022 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/Z covalent geometry : bond 0.00306 / 0.14 (35424) covalent geometry : angle 0.65166 / 0.32 (47923) hydrogen bonds : bond 0.03779 / 2.53 ( 1610) hydrogen bonds : angle 4.66956 / 3.28 ( 4536) metal coordination : bond 0.00972 / 0.46 ( 8) metal coordination : angle 2.90972 / 1.80 ( 6) Misc. bond : bond 0.00920 / 0.46 ( 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 341 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 1.433 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 427 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 672 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7813 (ttm170) REVERT: B 113 HIS cc_start: 0.7901 (t70) cc_final: 0.7551 (t-90) REVERT: B 398 MET cc_start: 0.8753 (mtt) cc_final: 0.8453 (mtt) REVERT: B 405 ASP cc_start: 0.8430 (t0) cc_final: 0.8048 (t0) REVERT: B 437 MET cc_start: 0.8177 (tpt) cc_final: 0.7972 (tpp) REVERT: B 752 TYR cc_start: 0.7859 (p90) cc_final: 0.7360 (p90) REVERT: C 405 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8141 (t0) REVERT: C 618 MET cc_start: 0.7938 (tmm) cc_final: 0.7629 (tmm) REVERT: C 758 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8122 (t80) REVERT: D 314 ASP cc_start: 0.8041 (t0) cc_final: 0.7835 (t0) REVERT: D 430 MET cc_start: 0.8993 (tpp) cc_final: 0.8749 (tpp) REVERT: D 459 MET cc_start: 0.6861 (tmm) cc_final: 0.6650 (tmm) REVERT: D 560 MET cc_start: 0.6306 (tpp) cc_final: 0.5434 (mpp) REVERT: D 588 GLU cc_start: 0.8170 (pm20) cc_final: 0.7418 (mm-30) REVERT: E 468 ASN cc_start: 0.8860 (m110) cc_final: 0.8422 (t0) REVERT: E 509 HIS cc_start: 0.3067 (OUTLIER) cc_final: 0.2123 (p90) REVERT: F 208 MET cc_start: 0.8819 (ppp) cc_final: 0.7164 (mmp) REVERT: F 343 ASP cc_start: 0.8483 (t0) cc_final: 0.8190 (m-30) REVERT: F 566 GLU cc_start: 0.8042 (mp0) cc_final: 0.7633 (mp0) REVERT: F 587 ASP cc_start: 0.8487 (t0) cc_final: 0.8111 (t0) REVERT: G 315 GLN cc_start: 0.8097 (tt0) cc_final: 0.7811 (tt0) REVERT: G 543 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: H 258 PHE cc_start: 0.5838 (p90) cc_final: 0.5336 (p90) REVERT: H 309 LYS cc_start: 0.8225 (tppp) cc_final: 0.7849 (tppp) REVERT: I 34 GLU cc_start: 0.7576 (tt0) cc_final: 0.7345 (tt0) outliers start: 39 outliers final: 22 residues processed: 327 average time/residue: 0.2311 time to fit residues: 123.2527 Evaluate side-chains 282 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 323 ARG 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: 5.9990 chunk 375 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 chunk 413 optimal weight: 0.7980 chunk 433 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 385 optimal weight: 0.0770 chunk 269 optimal weight: 0.7980 chunk 330 optimal weight: 7.9990 overall best weight: 1.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 100 ASN F 207 ASN F 209 ASN F 394 HIS G 106 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.125124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088905 restraints weight = 100143.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088528 restraints weight = 57309.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.088934 restraints weight = 40682.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.089441 restraints weight = 36703.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089442 restraints weight = 32701.050| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35436 Z= 0.162 Angle : 0.600 7.554 47929 Z= 0.294 Chirality : 0.043 0.165 5403 Planarity : 0.004 0.040 6242 Dihedral : 8.428 149.600 4870 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 1.79 % Allowed : 8.48 % Favored : 89.73 % 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: 1.04 (0.13), residues: 4348 helix: 1.74 (0.12), residues: 2035 sheet: -0.09 (0.22), residues: 570 loop : -0.21 (0.16), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 387 TYR 0.028 0.001 TYR G 507 PHE 0.026 0.001 PHE E 464 TRP 0.034 0.002 TRP B 561 HIS 0.005 0.001 HIS G 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (35424) covalent geometry : angle 0.59863 / 0.29 (47923) hydrogen bonds : bond 0.03643 / 2.45 ( 1610) hydrogen bonds : angle 4.55519 / 3.20 ( 4536) metal coordination : bond 0.01086 / 0.53 ( 8) metal coordination : angle 3.01461 / 1.53 ( 6) Misc. bond : bond 0.00168 / 0.09 ( 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 345 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 278 time to evaluate : 1.558 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: 0.8603 (OUTLIER) cc_final: 0.8076 (t0) REVERT: A 427 GLU cc_start: 0.8238 (tm-30) cc_final: 0.8010 (tp30) REVERT: A 672 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7529 (tpm170) REVERT: B 113 HIS cc_start: 0.8018 (t70) cc_final: 0.7701 (t70) REVERT: B 120 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.5811 (t80) REVERT: B 398 MET cc_start: 0.8774 (mtt) cc_final: 0.8478 (mtt) REVERT: B 405 ASP cc_start: 0.8523 (t0) cc_final: 0.8120 (t0) REVERT: B 550 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7900 (tt) REVERT: B 752 TYR cc_start: 0.7809 (p90) cc_final: 0.7346 (p90) REVERT: C 398 MET cc_start: 0.8643 (mtp) cc_final: 0.8412 (mtm) REVERT: C 405 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8160 (t0) REVERT: C 614 LEU cc_start: 0.8773 (tt) cc_final: 0.8435 (mm) REVERT: C 618 MET cc_start: 0.7814 (tmm) cc_final: 0.7471 (tmm) REVERT: C 758 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8061 (t80) REVERT: D 304 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7902 (pp20) REVERT: D 342 MET cc_start: 0.8902 (mmm) cc_final: 0.8616 (mmm) REVERT: D 430 MET cc_start: 0.8968 (tpp) cc_final: 0.8722 (tpp) REVERT: D 482 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7324 (p) REVERT: D 560 MET cc_start: 0.6238 (tpp) cc_final: 0.5357 (mpp) REVERT: D 588 GLU cc_start: 0.8190 (pm20) cc_final: 0.7513 (mm-30) REVERT: D 618 MET cc_start: 0.7875 (ttp) cc_final: 0.7626 (ttp) REVERT: E 468 ASN cc_start: 0.8934 (m110) cc_final: 0.8572 (t0) REVERT: E 509 HIS cc_start: 0.3026 (OUTLIER) cc_final: 0.2213 (p90) REVERT: E 560 MET cc_start: 0.7662 (mpp) cc_final: 0.7197 (mpp) REVERT: F 343 ASP cc_start: 0.8477 (t0) cc_final: 0.8160 (m-30) REVERT: F 587 ASP cc_start: 0.8508 (t0) cc_final: 0.8091 (t0) REVERT: G 208 HIS cc_start: 0.8099 (p-80) cc_final: 0.7853 (p-80) REVERT: G 315 GLN cc_start: 0.8170 (tt0) cc_final: 0.7813 (tt0) REVERT: G 543 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: H 258 PHE cc_start: 0.5736 (p90) cc_final: 0.5296 (p90) REVERT: H 309 LYS cc_start: 0.8347 (tppp) cc_final: 0.7982 (tppp) REVERT: I 34 GLU cc_start: 0.7722 (tt0) cc_final: 0.7472 (tt0) outliers start: 67 outliers final: 37 residues processed: 329 average time/residue: 0.2224 time to fit residues: 122.3067 Evaluate side-chains 296 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 120 TYR 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 550 ILE Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 323 ARG 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 758 PHE Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 389 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 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 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 449 VAL 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 L residue 328 SER Chi-restraints excluded: chain L residue 355 THR 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: 0.7980 chunk 138 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 71 optimal weight: 0.2980 chunk 157 optimal weight: 3.9990 chunk 370 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 304 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 390 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 F 512 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.123448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087900 restraints weight = 99848.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.087861 restraints weight = 59416.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088081 restraints weight = 42393.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088539 restraints weight = 39041.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.088885 restraints weight = 34507.580| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35436 Z= 0.178 Angle : 0.607 10.612 47929 Z= 0.296 Chirality : 0.043 0.190 5403 Planarity : 0.004 0.040 6242 Dihedral : 8.205 145.527 4869 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 2.19 % Allowed : 9.44 % Favored : 88.37 % 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: 1.66 (0.12), residues: 2036 sheet: -0.14 (0.22), residues: 571 loop : -0.26 (0.16), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 274 TYR 0.037 0.001 TYR G 189 PHE 0.027 0.001 PHE E 464 TRP 0.022 0.001 TRP B 561 HIS 0.004 0.001 HIS K 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (35424) covalent geometry : angle 0.60580 / 0.30 (47923) hydrogen bonds : bond 0.03540 / 2.37 ( 1610) hydrogen bonds : angle 4.54128 / 3.19 ( 4536) metal coordination : bond 0.01049 / 0.52 ( 8) metal coordination : angle 2.96074 / 1.49 ( 6) Misc. bond : bond 0.00330 / 0.17 ( 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 345 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 263 time to evaluate : 1.502 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: 0.8674 (OUTLIER) cc_final: 0.8084 (t0) REVERT: A 427 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8039 (tp30) REVERT: A 672 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7560 (tpm170) REVERT: B 113 HIS cc_start: 0.8045 (t70) cc_final: 0.7679 (t70) REVERT: B 287 LYS cc_start: 0.9160 (tttm) cc_final: 0.8756 (tmtt) REVERT: B 398 MET cc_start: 0.8801 (mtt) cc_final: 0.8510 (mtt) REVERT: B 405 ASP cc_start: 0.8537 (t0) cc_final: 0.8121 (t0) REVERT: B 621 MET cc_start: 0.6752 (ppp) cc_final: 0.6448 (ptm) REVERT: B 752 TYR cc_start: 0.7816 (p90) cc_final: 0.7360 (p90) REVERT: C 288 MET cc_start: 0.8014 (mmt) cc_final: 0.7633 (mmt) REVERT: C 405 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8075 (t0) REVERT: C 583 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8285 (m) REVERT: C 758 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.8077 (t80) REVERT: D 342 MET cc_start: 0.8954 (mmm) cc_final: 0.8627 (mmm) REVERT: D 482 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7297 (p) REVERT: D 560 MET cc_start: 0.6126 (tpp) cc_final: 0.5238 (mpp) REVERT: D 588 GLU cc_start: 0.8188 (pm20) cc_final: 0.7546 (mm-30) REVERT: D 618 MET cc_start: 0.7976 (ttp) cc_final: 0.7623 (ttp) REVERT: D 621 MET cc_start: 0.7653 (pmm) cc_final: 0.7346 (ppp) REVERT: E 339 LEU cc_start: 0.8938 (mp) cc_final: 0.8647 (mt) REVERT: E 348 ARG cc_start: 0.8290 (ptp90) cc_final: 0.8067 (mtt90) REVERT: E 468 ASN cc_start: 0.8874 (m110) cc_final: 0.8483 (t0) REVERT: E 509 HIS cc_start: 0.3023 (OUTLIER) cc_final: 0.2180 (p90) REVERT: E 560 MET cc_start: 0.7607 (mpp) cc_final: 0.7179 (mpp) REVERT: E 639 ILE cc_start: 0.5753 (mm) cc_final: 0.4813 (pt) REVERT: F 343 ASP cc_start: 0.8560 (t0) cc_final: 0.8242 (m-30) REVERT: F 587 ASP cc_start: 0.8519 (t0) cc_final: 0.8072 (t0) REVERT: G 315 GLN cc_start: 0.8136 (tt0) cc_final: 0.7749 (tt0) REVERT: G 543 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: H 258 PHE cc_start: 0.5801 (p90) cc_final: 0.5353 (p90) REVERT: H 309 LYS cc_start: 0.8349 (tppp) cc_final: 0.7951 (tppp) REVERT: I 34 GLU cc_start: 0.7718 (tt0) cc_final: 0.7436 (tt0) REVERT: K 215 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7749 (tt) outliers start: 82 outliers final: 51 residues processed: 328 average time/residue: 0.2161 time to fit residues: 119.4943 Evaluate side-chains 312 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 77 THR 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 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 323 ARG 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 389 GLU 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 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 125 GLU 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 296 LEU 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 215 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 305 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 213 optimal weight: 0.0070 chunk 343 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 392 optimal weight: 0.6980 chunk 173 optimal weight: 0.0570 chunk 306 optimal weight: 0.0010 chunk 379 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 432 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 384 optimal weight: 0.8980 overall best weight: 0.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN B 432 GLN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN H 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.125516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.089326 restraints weight = 100087.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089673 restraints weight = 59766.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089628 restraints weight = 41221.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.090280 restraints weight = 36635.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090390 restraints weight = 32835.401| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35436 Z= 0.103 Angle : 0.579 12.870 47929 Z= 0.277 Chirality : 0.042 0.223 5403 Planarity : 0.003 0.043 6242 Dihedral : 7.813 139.405 4869 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 1.68 % Allowed : 10.43 % Favored : 87.89 % 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: 1.09 (0.13), residues: 4348 helix: 1.72 (0.12), residues: 2038 sheet: -0.06 (0.22), residues: 573 loop : -0.11 (0.16), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 434 TYR 0.019 0.001 TYR A 183 PHE 0.024 0.001 PHE E 464 TRP 0.028 0.001 TRP B 486 HIS 0.004 0.001 HIS G 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (35424) covalent geometry : angle 0.57820 / 0.28 (47923) hydrogen bonds : bond 0.03004 / 2.03 ( 1610) hydrogen bonds : angle 4.30193 / 3.03 ( 4536) metal coordination : bond 0.00647 / 0.29 ( 8) metal coordination : angle 2.40696 / 1.47 ( 6) Misc. bond : bond 0.00109 / 0.06 ( 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 348 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 285 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8050 (mp0) cc_final: 0.7769 (mp0) REVERT: A 405 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8155 (t0) REVERT: A 427 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8013 (tp30) REVERT: A 560 MET cc_start: 0.7543 (mtt) cc_final: 0.7224 (mtt) REVERT: A 672 ARG cc_start: 0.8314 (mtp85) cc_final: 0.7829 (ttm170) REVERT: B 113 HIS cc_start: 0.8060 (t70) cc_final: 0.7711 (t70) REVERT: B 287 LYS cc_start: 0.9126 (tttm) cc_final: 0.8775 (tmtt) REVERT: B 398 MET cc_start: 0.8812 (mtt) cc_final: 0.8558 (mtt) REVERT: B 405 ASP cc_start: 0.8553 (t0) cc_final: 0.8134 (t0) REVERT: B 437 MET cc_start: 0.7832 (tpp) cc_final: 0.7581 (tpp) REVERT: B 752 TYR cc_start: 0.7944 (p90) cc_final: 0.7471 (p90) REVERT: C 282 PRO cc_start: 0.8570 (Cg_exo) cc_final: 0.8330 (Cg_endo) REVERT: C 288 MET cc_start: 0.7952 (mmt) cc_final: 0.7586 (mmt) REVERT: C 405 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8051 (t0) REVERT: C 583 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8245 (m) REVERT: C 590 ASP cc_start: 0.8308 (p0) cc_final: 0.8033 (m-30) REVERT: C 758 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8110 (t80) REVERT: D 315 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7705 (mm-30) REVERT: D 342 MET cc_start: 0.8915 (mmm) cc_final: 0.8580 (mmm) REVERT: D 460 ASP cc_start: 0.9179 (t0) cc_final: 0.8884 (p0) REVERT: D 482 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7120 (p) REVERT: D 560 MET cc_start: 0.6204 (tpp) cc_final: 0.5135 (mpp) REVERT: D 588 GLU cc_start: 0.8210 (pm20) cc_final: 0.7578 (mm-30) REVERT: D 621 MET cc_start: 0.7655 (pmm) cc_final: 0.7439 (ppp) REVERT: E 348 ARG cc_start: 0.8288 (ptp90) cc_final: 0.8079 (mtt90) REVERT: E 468 ASN cc_start: 0.8900 (m110) cc_final: 0.8579 (t0) REVERT: E 560 MET cc_start: 0.7652 (mpp) cc_final: 0.7294 (mpp) REVERT: E 639 ILE cc_start: 0.5644 (mm) cc_final: 0.4745 (pt) REVERT: F 343 ASP cc_start: 0.8533 (t0) cc_final: 0.8164 (m-30) REVERT: F 587 ASP cc_start: 0.8499 (t0) cc_final: 0.8055 (t0) REVERT: G 315 GLN cc_start: 0.8069 (tt0) cc_final: 0.7708 (tt0) REVERT: G 543 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: H 258 PHE cc_start: 0.5733 (p90) cc_final: 0.5276 (p90) REVERT: H 309 LYS cc_start: 0.8350 (tppp) cc_final: 0.8039 (tppp) REVERT: I 34 GLU cc_start: 0.7446 (tt0) cc_final: 0.7172 (tt0) REVERT: K 215 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7728 (tt) outliers start: 63 outliers final: 31 residues processed: 333 average time/residue: 0.2145 time to fit residues: 119.7194 Evaluate side-chains 298 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 56 MET 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 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 612 ASN 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 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 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 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 447 ILE 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 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: 6.9990 chunk 176 optimal weight: 0.6980 chunk 341 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 318 optimal weight: 1.9990 chunk 405 optimal weight: 0.9990 chunk 348 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.125664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088990 restraints weight = 99378.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088713 restraints weight = 55585.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.089124 restraints weight = 38206.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089560 restraints weight = 35565.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089616 restraints weight = 31204.765| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35436 Z= 0.146 Angle : 0.594 14.477 47929 Z= 0.285 Chirality : 0.042 0.192 5403 Planarity : 0.003 0.040 6242 Dihedral : 7.561 136.583 4865 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 1.76 % Allowed : 11.15 % Favored : 87.09 % 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: 1.71 (0.12), residues: 2039 sheet: -0.08 (0.22), residues: 564 loop : -0.16 (0.16), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 375 TYR 0.026 0.001 TYR G 507 PHE 0.026 0.001 PHE E 464 TRP 0.021 0.001 TRP B 561 HIS 0.005 0.001 HIS K 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (35424) covalent geometry : angle 0.59340 / 0.28 (47923) hydrogen bonds : bond 0.03172 / 2.13 ( 1610) hydrogen bonds : angle 4.34386 / 3.07 ( 4536) metal coordination : bond 0.01024 / 0.47 ( 8) metal coordination : angle 2.89221 / 1.43 ( 6) Misc. bond : bond 0.00080 / 0.04 ( 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 332 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 1.453 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 229 MET cc_start: 0.8480 (tpp) cc_final: 0.8270 (tpp) REVERT: A 405 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8112 (t0) REVERT: A 427 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8043 (tp30) REVERT: A 672 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7617 (tpm170) REVERT: B 113 HIS cc_start: 0.8156 (t70) cc_final: 0.7675 (t70) REVERT: B 114 PRO cc_start: 0.7406 (Cg_exo) cc_final: 0.6935 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9141 (tttm) cc_final: 0.8750 (tmtt) REVERT: B 398 MET cc_start: 0.8792 (mtt) cc_final: 0.8522 (mtt) REVERT: B 405 ASP cc_start: 0.8574 (t0) cc_final: 0.8160 (t0) REVERT: B 437 MET cc_start: 0.7944 (tpp) cc_final: 0.7726 (tpp) REVERT: B 588 GLU cc_start: 0.8013 (tt0) cc_final: 0.7770 (tt0) REVERT: B 752 TYR cc_start: 0.7954 (p90) cc_final: 0.7458 (p90) REVERT: C 288 MET cc_start: 0.7979 (mmt) cc_final: 0.7613 (mmt) REVERT: C 405 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8068 (t0) REVERT: C 583 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8180 (m) REVERT: C 590 ASP cc_start: 0.8329 (p0) cc_final: 0.8059 (m-30) REVERT: C 618 MET cc_start: 0.8060 (tmm) cc_final: 0.7858 (tmm) REVERT: C 758 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8131 (t80) REVERT: D 342 MET cc_start: 0.8955 (mmm) cc_final: 0.8597 (mmm) REVERT: D 460 ASP cc_start: 0.9189 (t0) cc_final: 0.8883 (p0) REVERT: D 482 VAL cc_start: 0.7651 (OUTLIER) cc_final: 0.7110 (p) REVERT: D 560 MET cc_start: 0.6232 (tpp) cc_final: 0.5143 (mpp) REVERT: E 285 MET cc_start: 0.6235 (mmt) cc_final: 0.5827 (mpp) REVERT: E 468 ASN cc_start: 0.8948 (m110) cc_final: 0.8596 (t0) REVERT: E 560 MET cc_start: 0.7636 (mpp) cc_final: 0.7263 (mpp) REVERT: E 639 ILE cc_start: 0.5612 (mm) cc_final: 0.4770 (pt) REVERT: E 784 MET cc_start: 0.7772 (mmp) cc_final: 0.7221 (mmm) REVERT: F 343 ASP cc_start: 0.8504 (t0) cc_final: 0.8183 (m-30) REVERT: F 587 ASP cc_start: 0.8502 (t0) cc_final: 0.8038 (t0) REVERT: G 315 GLN cc_start: 0.8097 (tt0) cc_final: 0.7720 (tt0) REVERT: G 543 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: H 258 PHE cc_start: 0.5706 (p90) cc_final: 0.5321 (p90) REVERT: H 309 LYS cc_start: 0.8367 (tppp) cc_final: 0.8058 (tppp) REVERT: I 34 GLU cc_start: 0.7481 (tt0) cc_final: 0.7157 (tt0) REVERT: K 215 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7689 (tt) outliers start: 66 outliers final: 41 residues processed: 315 average time/residue: 0.1978 time to fit residues: 104.5762 Evaluate side-chains 306 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 56 MET 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 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 612 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 389 GLU 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 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 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 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 117 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 172 optimal weight: 3.9990 chunk 394 optimal weight: 0.3980 chunk 202 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN B 209 ASN B 432 GLN B 461 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.124998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087633 restraints weight = 99351.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.088134 restraints weight = 55051.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.088438 restraints weight = 37367.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.088898 restraints weight = 37418.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.088866 restraints weight = 32487.612| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35436 Z= 0.150 Angle : 0.594 15.563 47929 Z= 0.286 Chirality : 0.042 0.175 5403 Planarity : 0.004 0.040 6242 Dihedral : 7.318 132.632 4865 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 1.84 % Allowed : 11.18 % 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: 0.95 (0.13), residues: 4348 helix: 1.59 (0.12), residues: 2048 sheet: -0.13 (0.22), residues: 565 loop : -0.19 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 348 TYR 0.027 0.001 TYR G 507 PHE 0.024 0.001 PHE E 464 TRP 0.030 0.002 TRP A 561 HIS 0.005 0.001 HIS K 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (35424) covalent geometry : angle 0.59346 / 0.29 (47923) hydrogen bonds : bond 0.03191 / 2.15 ( 1610) hydrogen bonds : angle 4.35992 / 3.09 ( 4536) metal coordination : bond 0.00725 / 0.37 ( 8) metal coordination : angle 2.88479 / 1.42 ( 6) Misc. bond : bond 0.00085 / 0.04 ( 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 335 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8544 (tpp) cc_final: 0.8086 (tpp) REVERT: A 405 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8117 (t0) REVERT: A 427 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8062 (tp30) REVERT: A 672 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7620 (tpm170) REVERT: B 113 HIS cc_start: 0.8184 (t70) cc_final: 0.7689 (t70) REVERT: B 114 PRO cc_start: 0.7421 (Cg_exo) cc_final: 0.6956 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9124 (tttm) cc_final: 0.8735 (tmtt) REVERT: B 398 MET cc_start: 0.8809 (mtt) cc_final: 0.8529 (mtt) REVERT: B 405 ASP cc_start: 0.8576 (t0) cc_final: 0.8175 (t0) REVERT: B 588 GLU cc_start: 0.8031 (tt0) cc_final: 0.7796 (tt0) REVERT: B 752 TYR cc_start: 0.8028 (p90) cc_final: 0.7536 (p90) REVERT: C 405 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8101 (t0) REVERT: C 583 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8181 (m) REVERT: C 590 ASP cc_start: 0.8377 (p0) cc_final: 0.8110 (m-30) REVERT: C 618 MET cc_start: 0.8092 (tmm) cc_final: 0.7838 (tmm) REVERT: C 758 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8141 (t80) REVERT: D 482 VAL cc_start: 0.7597 (OUTLIER) cc_final: 0.7075 (p) REVERT: D 560 MET cc_start: 0.6259 (tpp) cc_final: 0.5142 (mpp) REVERT: D 621 MET cc_start: 0.7750 (pmm) cc_final: 0.7411 (ppp) REVERT: E 254 TYR cc_start: 0.8297 (p90) cc_final: 0.8073 (p90) REVERT: E 285 MET cc_start: 0.6252 (mmt) cc_final: 0.5921 (mpp) REVERT: E 468 ASN cc_start: 0.8988 (m110) cc_final: 0.8644 (t0) REVERT: E 560 MET cc_start: 0.7560 (mpp) cc_final: 0.7211 (mpp) REVERT: E 621 MET cc_start: 0.7055 (tpp) cc_final: 0.6826 (tpp) REVERT: E 639 ILE cc_start: 0.5774 (mm) cc_final: 0.4947 (pt) REVERT: F 343 ASP cc_start: 0.8524 (t0) cc_final: 0.8183 (m-30) REVERT: F 587 ASP cc_start: 0.8525 (t0) cc_final: 0.8063 (t0) REVERT: G 315 GLN cc_start: 0.8118 (tt0) cc_final: 0.7723 (tt0) REVERT: G 543 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: H 258 PHE cc_start: 0.5665 (p90) cc_final: 0.5309 (p90) REVERT: H 309 LYS cc_start: 0.8332 (tppp) cc_final: 0.7942 (tppp) REVERT: I 34 GLU cc_start: 0.7314 (tt0) cc_final: 0.7001 (tt0) REVERT: K 215 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7726 (tt) outliers start: 69 outliers final: 48 residues processed: 321 average time/residue: 0.1969 time to fit residues: 106.1703 Evaluate side-chains 309 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 56 MET 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 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 389 GLU 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 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 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 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 215 LEU Chi-restraints excluded: chain K residue 255 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 195 optimal weight: 0.9980 chunk 3 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 146 optimal weight: 0.3980 chunk 142 optimal weight: 9.9990 chunk 277 optimal weight: 0.7980 chunk 164 optimal weight: 0.5980 chunk 194 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 177 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 668 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.126387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088489 restraints weight = 99215.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.089324 restraints weight = 54723.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089509 restraints weight = 36827.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.090050 restraints weight = 34133.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090032 restraints weight = 32427.088| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35436 Z= 0.110 Angle : 0.592 17.770 47929 Z= 0.281 Chirality : 0.042 0.177 5403 Planarity : 0.003 0.040 6242 Dihedral : 6.961 128.822 4865 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 1.39 % Allowed : 12.00 % Favored : 86.61 % 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: 1.63 (0.12), residues: 2045 sheet: -0.05 (0.22), residues: 572 loop : -0.14 (0.16), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 274 TYR 0.022 0.001 TYR G 507 PHE 0.021 0.001 PHE A 144 TRP 0.036 0.002 TRP A 561 HIS 0.004 0.001 HIS K 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (35424) covalent geometry : angle 0.59179 / 0.28 (47923) hydrogen bonds : bond 0.02951 / 1.99 ( 1610) hydrogen bonds : angle 4.27577 / 3.03 ( 4536) metal coordination : bond 0.00467 / 0.23 ( 8) metal coordination : angle 2.27852 / 1.23 ( 6) Misc. bond : bond 0.00262 / 0.13 ( 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 322 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 0.905 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 229 MET cc_start: 0.8389 (tpp) cc_final: 0.7995 (tpp) REVERT: A 405 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8108 (t0) REVERT: A 427 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8068 (tp30) REVERT: A 672 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7633 (tpm170) REVERT: B 113 HIS cc_start: 0.8217 (t70) cc_final: 0.7728 (t70) REVERT: B 114 PRO cc_start: 0.7470 (Cg_exo) cc_final: 0.7012 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9122 (tttm) cc_final: 0.8735 (tmtt) REVERT: B 398 MET cc_start: 0.8778 (mtt) cc_final: 0.8503 (mtt) REVERT: B 405 ASP cc_start: 0.8535 (t0) cc_final: 0.8110 (t0) REVERT: B 588 GLU cc_start: 0.8028 (tt0) cc_final: 0.7773 (tt0) REVERT: B 752 TYR cc_start: 0.8061 (p90) cc_final: 0.7539 (p90) REVERT: C 405 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8112 (t0) REVERT: C 583 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8103 (m) REVERT: C 590 ASP cc_start: 0.8391 (p0) cc_final: 0.8067 (m-30) REVERT: C 618 MET cc_start: 0.8070 (tmm) cc_final: 0.7777 (tmm) REVERT: C 758 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8203 (t80) REVERT: D 323 ARG cc_start: 0.6513 (mmt90) cc_final: 0.6135 (mmt-90) REVERT: D 482 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.6873 (p) REVERT: D 560 MET cc_start: 0.6300 (tpp) cc_final: 0.5188 (mpp) REVERT: E 229 MET cc_start: 0.7152 (ttt) cc_final: 0.6853 (tmm) REVERT: E 285 MET cc_start: 0.6194 (mmt) cc_final: 0.5890 (mpp) REVERT: E 468 ASN cc_start: 0.8998 (m110) cc_final: 0.8658 (t0) REVERT: E 560 MET cc_start: 0.7628 (mpp) cc_final: 0.7299 (mpp) REVERT: E 621 MET cc_start: 0.6981 (tpp) cc_final: 0.6744 (tpp) REVERT: E 639 ILE cc_start: 0.5672 (mm) cc_final: 0.4836 (pt) REVERT: E 784 MET cc_start: 0.7650 (mmp) cc_final: 0.7082 (mmm) REVERT: F 587 ASP cc_start: 0.8510 (t0) cc_final: 0.8034 (t0) REVERT: G 315 GLN cc_start: 0.8053 (tt0) cc_final: 0.7665 (tt0) REVERT: H 258 PHE cc_start: 0.5596 (p90) cc_final: 0.5253 (p90) REVERT: H 309 LYS cc_start: 0.8351 (tppp) cc_final: 0.8054 (tppp) REVERT: I 34 GLU cc_start: 0.7263 (tt0) cc_final: 0.6978 (tt0) REVERT: K 215 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7655 (tt) outliers start: 52 outliers final: 36 residues processed: 308 average time/residue: 0.2091 time to fit residues: 107.8217 Evaluate side-chains 301 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 56 MET 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 583 VAL Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 389 GLU 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 D residue 674 THR 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 G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 273 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 32 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 398 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 254 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 262 optimal weight: 0.0980 chunk 332 optimal weight: 7.9990 chunk 148 optimal weight: 0.3980 chunk 210 optimal weight: 0.0870 chunk 83 optimal weight: 7.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.126051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089541 restraints weight = 98910.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089818 restraints weight = 53970.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090053 restraints weight = 37608.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090387 restraints weight = 37763.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090491 restraints weight = 32559.615| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35436 Z= 0.111 Angle : 0.593 20.223 47929 Z= 0.281 Chirality : 0.042 0.150 5403 Planarity : 0.003 0.041 6242 Dihedral : 6.643 124.937 4862 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 1.36 % Allowed : 12.11 % Favored : 86.53 % 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: 1.62 (0.12), residues: 2042 sheet: 0.01 (0.22), residues: 572 loop : -0.12 (0.16), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.022 0.001 TYR G 507 PHE 0.019 0.001 PHE E 464 TRP 0.039 0.002 TRP A 561 HIS 0.004 0.001 HIS K 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (35424) covalent geometry : angle 0.59268 / 0.28 (47923) hydrogen bonds : bond 0.02910 / 1.96 ( 1610) hydrogen bonds : angle 4.24175 / 3.01 ( 4536) metal coordination : bond 0.00439 / 0.22 ( 8) metal coordination : angle 2.28784 / 1.20 ( 6) Misc. bond : bond 0.00264 / 0.13 ( 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 323 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 1.383 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 229 MET cc_start: 0.8408 (tpp) cc_final: 0.8029 (tpp) REVERT: A 405 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8082 (t0) REVERT: A 427 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7992 (tp30) REVERT: A 672 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7620 (tpm170) REVERT: B 113 HIS cc_start: 0.8140 (t70) cc_final: 0.7617 (t70) REVERT: B 114 PRO cc_start: 0.7335 (Cg_exo) cc_final: 0.6863 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9103 (tttm) cc_final: 0.8730 (tmtt) REVERT: B 398 MET cc_start: 0.8691 (mtt) cc_final: 0.8477 (mtt) REVERT: B 405 ASP cc_start: 0.8450 (t0) cc_final: 0.8059 (t0) REVERT: B 588 GLU cc_start: 0.8059 (tt0) cc_final: 0.7832 (tt0) REVERT: B 752 TYR cc_start: 0.7961 (p90) cc_final: 0.7502 (p90) REVERT: C 405 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8029 (t0) REVERT: C 583 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8192 (m) REVERT: C 590 ASP cc_start: 0.8331 (p0) cc_final: 0.8111 (m-30) REVERT: C 618 MET cc_start: 0.8030 (tmm) cc_final: 0.7710 (tmm) REVERT: C 758 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.8094 (t80) REVERT: D 482 VAL cc_start: 0.7623 (OUTLIER) cc_final: 0.7092 (p) REVERT: D 560 MET cc_start: 0.6179 (tpp) cc_final: 0.5101 (mpp) REVERT: E 285 MET cc_start: 0.6083 (mmt) cc_final: 0.5852 (mpp) REVERT: E 468 ASN cc_start: 0.8953 (m110) cc_final: 0.8639 (t0) REVERT: E 560 MET cc_start: 0.7607 (mpp) cc_final: 0.7194 (mpp) REVERT: E 621 MET cc_start: 0.6893 (tpp) cc_final: 0.6606 (tpp) REVERT: E 639 ILE cc_start: 0.5752 (mm) cc_final: 0.4954 (pt) REVERT: E 784 MET cc_start: 0.7743 (mmp) cc_final: 0.7199 (mmm) REVERT: F 587 ASP cc_start: 0.8476 (t0) cc_final: 0.8056 (t0) REVERT: G 315 GLN cc_start: 0.8041 (tt0) cc_final: 0.7682 (tt0) REVERT: H 309 LYS cc_start: 0.8323 (tppp) cc_final: 0.8042 (tppp) REVERT: I 34 GLU cc_start: 0.7205 (tt0) cc_final: 0.6955 (tt0) REVERT: K 215 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7602 (tt) outliers start: 51 outliers final: 42 residues processed: 311 average time/residue: 0.2143 time to fit residues: 111.6795 Evaluate side-chains 307 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 56 MET 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 627 VAL 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 612 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 389 GLU 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 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 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 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 273 THR 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 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 139 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 199 optimal weight: 0.0980 chunk 133 optimal weight: 20.0000 chunk 202 optimal weight: 0.0370 chunk 412 optimal weight: 0.0270 chunk 71 optimal weight: 0.0170 chunk 358 optimal weight: 5.9990 chunk 1 optimal weight: 30.0000 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.127669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.091931 restraints weight = 99482.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.092270 restraints weight = 54813.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.092460 restraints weight = 38906.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.092909 restraints weight = 36324.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.093008 restraints weight = 32364.293| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 35436 Z= 0.101 Angle : 0.598 22.382 47929 Z= 0.282 Chirality : 0.042 0.188 5403 Planarity : 0.003 0.041 6242 Dihedral : 6.427 119.594 4862 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 1.25 % Allowed : 12.54 % Favored : 86.21 % 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: 1.11 (0.13), residues: 4348 helix: 1.65 (0.12), residues: 2044 sheet: 0.09 (0.22), residues: 574 loop : -0.03 (0.16), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.019 0.001 TYR G 507 PHE 0.015 0.001 PHE H 258 TRP 0.043 0.002 TRP A 561 HIS 0.004 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (35424) covalent geometry : angle 0.59776 / 0.28 (47923) hydrogen bonds : bond 0.02751 / 1.85 ( 1610) hydrogen bonds : angle 4.18398 / 2.97 ( 4536) metal coordination : bond 0.00416 / 0.21 ( 8) metal coordination : angle 1.96954 / 1.21 ( 6) Misc. bond : bond 0.00191 / 0.10 ( 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 328 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 1.442 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 56 MET cc_start: -0.0418 (pmm) cc_final: -0.0622 (pmm) REVERT: A 229 MET cc_start: 0.8416 (tpp) cc_final: 0.8039 (tpp) REVERT: A 405 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8090 (t0) REVERT: A 427 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7971 (tp30) REVERT: B 113 HIS cc_start: 0.8138 (t70) cc_final: 0.7607 (t70) REVERT: B 114 PRO cc_start: 0.7298 (Cg_exo) cc_final: 0.6814 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9104 (tttm) cc_final: 0.8771 (tmtt) REVERT: B 405 ASP cc_start: 0.8351 (t0) cc_final: 0.7965 (t0) REVERT: B 588 GLU cc_start: 0.7984 (tt0) cc_final: 0.7764 (tt0) REVERT: B 752 TYR cc_start: 0.7892 (p90) cc_final: 0.7456 (p90) REVERT: C 405 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8058 (t0) REVERT: C 583 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8162 (m) REVERT: C 590 ASP cc_start: 0.8299 (p0) cc_final: 0.8084 (m-30) REVERT: C 618 MET cc_start: 0.8023 (tmm) cc_final: 0.7708 (tmm) REVERT: C 758 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8069 (t80) REVERT: D 323 ARG cc_start: 0.6453 (mmt90) cc_final: 0.6108 (mmt-90) REVERT: D 482 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7096 (p) REVERT: D 560 MET cc_start: 0.6079 (tpp) cc_final: 0.4977 (mpp) REVERT: E 315 GLU cc_start: 0.8204 (mp0) cc_final: 0.8004 (mp0) REVERT: E 323 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8251 (ttp80) REVERT: E 468 ASN cc_start: 0.8918 (m110) cc_final: 0.8628 (t0) REVERT: E 560 MET cc_start: 0.7531 (mpp) cc_final: 0.7152 (mpp) REVERT: E 621 MET cc_start: 0.6904 (tpp) cc_final: 0.6654 (tpp) REVERT: E 639 ILE cc_start: 0.5611 (mm) cc_final: 0.4901 (pt) REVERT: E 784 MET cc_start: 0.7722 (mmp) cc_final: 0.7185 (mmm) REVERT: G 315 GLN cc_start: 0.8071 (tt0) cc_final: 0.7789 (tt0) REVERT: H 309 LYS cc_start: 0.8354 (tppp) cc_final: 0.8068 (tppp) REVERT: K 215 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7577 (tt) outliers start: 47 outliers final: 34 residues processed: 317 average time/residue: 0.2137 time to fit residues: 112.6806 Evaluate side-chains 299 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 482 VAL Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 584 VAL 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 612 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 389 GLU 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 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 281 VAL 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 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain J residue 136 ILE 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: 0.2980 chunk 140 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 388 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 241 optimal weight: 0.0670 chunk 85 optimal weight: 30.0000 chunk 211 optimal weight: 0.9990 chunk 362 optimal weight: 5.9990 chunk 364 optimal weight: 0.5980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.126809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.090410 restraints weight = 98985.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090204 restraints weight = 57489.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091182 restraints weight = 41879.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.091193 restraints weight = 32557.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.091501 restraints weight = 32100.730| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2730 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= 0.104 Angle : 0.598 21.850 47929 Z= 0.281 Chirality : 0.041 0.146 5403 Planarity : 0.003 0.043 6242 Dihedral : 6.312 115.294 4862 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 1.17 % Allowed : 12.78 % Favored : 86.05 % 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: 1.15 (0.13), residues: 4348 helix: 1.68 (0.12), residues: 2046 sheet: 0.10 (0.22), residues: 576 loop : -0.01 (0.16), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 672 TYR 0.021 0.001 TYR G 507 PHE 0.014 0.001 PHE E 464 TRP 0.039 0.002 TRP A 561 HIS 0.004 0.000 HIS K 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (35424) covalent geometry : angle 0.59745 / 0.28 (47923) hydrogen bonds : bond 0.02758 / 1.86 ( 1610) hydrogen bonds : angle 4.15835 / 2.95 ( 4536) metal coordination : bond 0.00394 / 0.20 ( 8) metal coordination : angle 2.02388 / 1.08 ( 6) Misc. bond : bond 0.00122 / 0.06 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6474.99 seconds wall clock time: 112 minutes 40.43 seconds (6760.43 seconds total)