Starting phenix.real_space_refine on Wed Apr 8 00:18:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dck_27326/04_2026/8dck_27326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dck_27326/04_2026/8dck_27326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dck_27326/04_2026/8dck_27326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dck_27326/04_2026/8dck_27326.map" model { file = "/net/cci-nas-00/data/ceres_data/8dck_27326/04_2026/8dck_27326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dck_27326/04_2026/8dck_27326.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.111 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 P 18 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 21126 2.51 5 N 5610 2.21 5 O 5823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32661 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5443 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4490 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 552} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 309 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "D" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "I" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5443 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4490 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 552} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 309 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "E" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5443 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4490 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 552} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 309 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "H" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.59, per 1000 atoms: 0.23 Number of scatterers: 32661 At special positions: 0 Unit cell: (144.3, 152.1, 140.4, 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) S 78 16.00 P 18 15.00 Mg 6 11.99 O 5823 8.00 N 5610 7.00 C 21126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 21 sheets defined 67.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.536A pdb=" N ASN A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 142 through 150 removed outlier: 4.028A pdb=" N ALA A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 181 Proline residue: A 172 - end of helix removed outlier: 3.831A pdb=" N PHE A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 237 removed outlier: 3.613A pdb=" N ALA A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.688A pdb=" N PHE A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 266 removed outlier: 3.501A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 278 Processing helix chain 'A' and resid 279 through 290 removed outlier: 3.657A pdb=" N VAL A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 294 through 339 Proline residue: A 302 - end of helix Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 348 through 403 removed outlier: 3.621A pdb=" N LEU A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 430 Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 430 through 449 removed outlier: 3.851A pdb=" N THR A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 516 removed outlier: 3.698A pdb=" N GLN A 516 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 558 through 564 Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 584 through 590 Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.882A pdb=" N THR A 597 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 607 through 621 Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.568A pdb=" N ILE A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 686 through 692 Processing helix chain 'A' and resid 696 through 702 Processing helix chain 'B' and resid 142 through 150 removed outlier: 4.047A pdb=" N ALA B 146 " --> pdb=" O TRP B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 182 removed outlier: 3.870A pdb=" N PHE B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Proline residue: B 172 - end of helix removed outlier: 3.614A pdb=" N VAL B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 237 removed outlier: 3.619A pdb=" N VAL B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 222 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.649A pdb=" N PHE B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.191A pdb=" N THR B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 278 Processing helix chain 'B' and resid 280 through 290 removed outlier: 3.930A pdb=" N ALA B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 339 Proline residue: B 302 - end of helix Proline residue: B 313 - end of helix removed outlier: 3.685A pdb=" N ALA B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.509A pdb=" N MET B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 403 Processing helix chain 'B' and resid 406 through 429 Proline residue: B 423 - end of helix Processing helix chain 'B' and resid 430 through 449 Processing helix chain 'B' and resid 507 through 516 removed outlier: 3.832A pdb=" N LEU B 511 " --> pdb=" O GLY B 507 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 516 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 558 through 564 Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.803A pdb=" N VAL B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 591 removed outlier: 3.638A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 597 removed outlier: 4.141A pdb=" N THR B 597 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 621 Processing helix chain 'B' and resid 637 through 652 removed outlier: 4.465A pdb=" N HIS B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 692 Processing helix chain 'B' and resid 696 through 706 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 58 through 65 Processing helix chain 'D' and resid 10 through 24 Processing helix chain 'D' and resid 35 through 40 Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 55 through 77 Processing helix chain 'I' and resid 9 through 21 Processing helix chain 'I' and resid 26 through 35 Processing helix chain 'I' and resid 42 through 53 Processing helix chain 'I' and resid 65 through 69 removed outlier: 3.536A pdb=" N ASN I 68 " --> pdb=" O ASP I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 117 Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 142 through 150 removed outlier: 4.028A pdb=" N ALA I 146 " --> pdb=" O TRP I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 181 Proline residue: I 172 - end of helix removed outlier: 3.831A pdb=" N PHE I 175 " --> pdb=" O THR I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 237 removed outlier: 3.613A pdb=" N ALA I 237 " --> pdb=" O ARG I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 246 removed outlier: 3.689A pdb=" N PHE I 243 " --> pdb=" O PRO I 239 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG I 246 " --> pdb=" O TYR I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 266 removed outlier: 3.501A pdb=" N THR I 251 " --> pdb=" O ARG I 247 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU I 258 " --> pdb=" O ARG I 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 278 Processing helix chain 'I' and resid 279 through 290 removed outlier: 3.657A pdb=" N VAL I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 293 No H-bonds generated for 'chain 'I' and resid 291 through 293' Processing helix chain 'I' and resid 294 through 339 Proline residue: I 302 - end of helix Proline residue: I 313 - end of helix Processing helix chain 'I' and resid 339 through 346 Processing helix chain 'I' and resid 348 through 403 removed outlier: 3.621A pdb=" N LEU I 373 " --> pdb=" O LYS I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 430 Proline residue: I 423 - end of helix Processing helix chain 'I' and resid 430 through 449 removed outlier: 3.851A pdb=" N THR I 442 " --> pdb=" O GLY I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 516 removed outlier: 3.698A pdb=" N GLN I 516 " --> pdb=" O THR I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 537 through 544 Processing helix chain 'I' and resid 558 through 564 Processing helix chain 'I' and resid 572 through 582 Processing helix chain 'I' and resid 584 through 590 Processing helix chain 'I' and resid 593 through 597 removed outlier: 3.882A pdb=" N THR I 597 " --> pdb=" O GLY I 594 " (cutoff:3.500A) Processing helix chain 'I' and resid 600 through 604 Processing helix chain 'I' and resid 607 through 621 Processing helix chain 'I' and resid 640 through 652 removed outlier: 3.569A pdb=" N ILE I 644 " --> pdb=" O SER I 640 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS I 649 " --> pdb=" O MET I 645 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS I 650 " --> pdb=" O ARG I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 667 Processing helix chain 'I' and resid 686 through 692 Processing helix chain 'I' and resid 696 through 702 Processing helix chain 'J' and resid 142 through 150 removed outlier: 4.048A pdb=" N ALA J 146 " --> pdb=" O TRP J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 182 removed outlier: 3.870A pdb=" N PHE J 163 " --> pdb=" O VAL J 159 " (cutoff:3.500A) Proline residue: J 172 - end of helix removed outlier: 3.613A pdb=" N VAL J 182 " --> pdb=" O VAL J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 237 removed outlier: 3.619A pdb=" N VAL J 200 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL J 201 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG J 222 " --> pdb=" O HIS J 218 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 245 removed outlier: 3.649A pdb=" N PHE J 243 " --> pdb=" O PRO J 239 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER J 245 " --> pdb=" O SER J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 266 removed outlier: 4.191A pdb=" N THR J 251 " --> pdb=" O ARG J 247 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP J 259 " --> pdb=" O VAL J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 278 Processing helix chain 'J' and resid 280 through 290 removed outlier: 3.930A pdb=" N ALA J 284 " --> pdb=" O PHE J 280 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL J 285 " --> pdb=" O ILE J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 339 Proline residue: J 302 - end of helix Proline residue: J 313 - end of helix removed outlier: 3.685A pdb=" N ALA J 339 " --> pdb=" O GLU J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 346 removed outlier: 3.510A pdb=" N MET J 346 " --> pdb=" O THR J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 403 Processing helix chain 'J' and resid 406 through 429 Proline residue: J 423 - end of helix Processing helix chain 'J' and resid 430 through 449 Processing helix chain 'J' and resid 507 through 516 removed outlier: 3.831A pdb=" N LEU J 511 " --> pdb=" O GLY J 507 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR J 512 " --> pdb=" O LYS J 508 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN J 516 " --> pdb=" O THR J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 544 Processing helix chain 'J' and resid 558 through 564 Processing helix chain 'J' and resid 571 through 582 removed outlier: 3.803A pdb=" N VAL J 575 " --> pdb=" O SER J 571 " (cutoff:3.500A) Processing helix chain 'J' and resid 584 through 591 removed outlier: 3.638A pdb=" N ILE J 588 " --> pdb=" O ALA J 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 593 through 597 removed outlier: 4.141A pdb=" N THR J 597 " --> pdb=" O GLY J 594 " (cutoff:3.500A) Processing helix chain 'J' and resid 607 through 621 Processing helix chain 'J' and resid 637 through 652 removed outlier: 4.465A pdb=" N HIS J 649 " --> pdb=" O MET J 645 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS J 650 " --> pdb=" O ARG J 646 " (cutoff:3.500A) Processing helix chain 'J' and resid 686 through 692 Processing helix chain 'J' and resid 696 through 706 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 42 through 49 Processing helix chain 'K' and resid 58 through 65 Processing helix chain 'L' and resid 10 through 24 Processing helix chain 'L' and resid 35 through 40 Processing helix chain 'L' and resid 43 through 51 Processing helix chain 'L' and resid 55 through 77 Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.536A pdb=" N ASN E 68 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 117 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 142 through 150 removed outlier: 4.028A pdb=" N ALA E 146 " --> pdb=" O TRP E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 181 Proline residue: E 172 - end of helix removed outlier: 3.831A pdb=" N PHE E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 237 removed outlier: 3.613A pdb=" N ALA E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 removed outlier: 3.689A pdb=" N PHE E 243 " --> pdb=" O PRO E 239 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 246 " --> pdb=" O TYR E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 266 removed outlier: 3.501A pdb=" N THR E 251 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 278 Processing helix chain 'E' and resid 279 through 290 removed outlier: 3.657A pdb=" N VAL E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 293 No H-bonds generated for 'chain 'E' and resid 291 through 293' Processing helix chain 'E' and resid 294 through 339 Proline residue: E 302 - end of helix Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 339 through 346 Processing helix chain 'E' and resid 348 through 403 removed outlier: 3.621A pdb=" N LEU E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 430 Proline residue: E 423 - end of helix Processing helix chain 'E' and resid 430 through 449 removed outlier: 3.851A pdb=" N THR E 442 " --> pdb=" O GLY E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 516 removed outlier: 3.698A pdb=" N GLN E 516 " --> pdb=" O THR E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 544 Processing helix chain 'E' and resid 558 through 564 Processing helix chain 'E' and resid 572 through 582 Processing helix chain 'E' and resid 584 through 590 Processing helix chain 'E' and resid 593 through 597 removed outlier: 3.882A pdb=" N THR E 597 " --> pdb=" O GLY E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 Processing helix chain 'E' and resid 607 through 621 Processing helix chain 'E' and resid 640 through 652 removed outlier: 3.567A pdb=" N ILE E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS E 649 " --> pdb=" O MET E 645 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS E 650 " --> pdb=" O ARG E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 667 Processing helix chain 'E' and resid 686 through 692 Processing helix chain 'E' and resid 696 through 702 Processing helix chain 'F' and resid 142 through 150 removed outlier: 4.047A pdb=" N ALA F 146 " --> pdb=" O TRP F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 182 removed outlier: 3.870A pdb=" N PHE F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Proline residue: F 172 - end of helix removed outlier: 3.614A pdb=" N VAL F 182 " --> pdb=" O VAL F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 237 removed outlier: 3.619A pdb=" N VAL F 200 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG F 222 " --> pdb=" O HIS F 218 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 245 removed outlier: 3.648A pdb=" N PHE F 243 " --> pdb=" O PRO F 239 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 266 removed outlier: 4.191A pdb=" N THR F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 278 Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.930A pdb=" N ALA F 284 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL F 285 " --> pdb=" O ILE F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 339 Proline residue: F 302 - end of helix Proline residue: F 313 - end of helix removed outlier: 3.686A pdb=" N ALA F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 346 removed outlier: 3.510A pdb=" N MET F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 403 Processing helix chain 'F' and resid 406 through 429 Proline residue: F 423 - end of helix Processing helix chain 'F' and resid 430 through 449 Processing helix chain 'F' and resid 507 through 516 removed outlier: 3.831A pdb=" N LEU F 511 " --> pdb=" O GLY F 507 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR F 512 " --> pdb=" O LYS F 508 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN F 516 " --> pdb=" O THR F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 544 Processing helix chain 'F' and resid 558 through 564 Processing helix chain 'F' and resid 571 through 582 removed outlier: 3.802A pdb=" N VAL F 575 " --> pdb=" O SER F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 591 removed outlier: 3.638A pdb=" N ILE F 588 " --> pdb=" O ALA F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 597 removed outlier: 4.141A pdb=" N THR F 597 " --> pdb=" O GLY F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 621 Processing helix chain 'F' and resid 637 through 652 removed outlier: 4.465A pdb=" N HIS F 649 " --> pdb=" O MET F 645 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 692 Processing helix chain 'F' and resid 696 through 706 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 42 through 49 Processing helix chain 'G' and resid 58 through 65 Processing helix chain 'H' and resid 10 through 24 Processing helix chain 'H' and resid 35 through 40 Processing helix chain 'H' and resid 43 through 51 Processing helix chain 'H' and resid 55 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 76 removed outlier: 3.818A pdb=" N PHE A 84 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 97 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 89 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ARG A 95 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 492 removed outlier: 7.085A pdb=" N ASP A 486 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG A 474 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE A 488 " --> pdb=" O ASN A 472 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 472 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 473 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 523 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.492A pdb=" N GLY A 546 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP A 630 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 548 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 627 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE A 660 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A 629 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A 498 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 675 " --> pdb=" O VAL A 682 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.355A pdb=" N ASP B 486 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE B 475 " --> pdb=" O ASP B 486 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 488 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.355A pdb=" N ASP B 486 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE B 475 " --> pdb=" O ASP B 486 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 488 " --> pdb=" O ILE B 473 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE B 470 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 527 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN B 472 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN B 525 " --> pdb=" O ASN B 472 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 548 removed outlier: 6.761A pdb=" N GLY B 546 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP B 630 " --> pdb=" O GLY B 546 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL B 548 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU B 677 " --> pdb=" O ILE B 681 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 56 through 61 Processing sheet with id=AA9, first strand: chain 'I' and resid 74 through 76 removed outlier: 3.819A pdb=" N PHE I 84 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU I 97 " --> pdb=" O THR I 87 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL I 89 " --> pdb=" O ARG I 95 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ARG I 95 " --> pdb=" O VAL I 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 485 through 492 removed outlier: 7.084A pdb=" N ASP I 486 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG I 474 " --> pdb=" O ASP I 486 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE I 488 " --> pdb=" O ASN I 472 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN I 472 " --> pdb=" O ILE I 488 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE I 473 " --> pdb=" O ASN I 523 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN I 523 " --> pdb=" O ILE I 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 545 through 548 removed outlier: 6.491A pdb=" N GLY I 546 " --> pdb=" O ILE I 628 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP I 630 " --> pdb=" O GLY I 546 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL I 548 " --> pdb=" O ASP I 630 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU I 627 " --> pdb=" O ILE I 658 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE I 660 " --> pdb=" O LEU I 627 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE I 629 " --> pdb=" O ILE I 660 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE I 498 " --> pdb=" O ILE I 659 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL I 675 " --> pdb=" O VAL I 682 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 485 through 488 removed outlier: 6.355A pdb=" N ASP J 486 " --> pdb=" O PHE J 475 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE J 475 " --> pdb=" O ASP J 486 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE J 488 " --> pdb=" O ILE J 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 485 through 488 removed outlier: 6.355A pdb=" N ASP J 486 " --> pdb=" O PHE J 475 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE J 475 " --> pdb=" O ASP J 486 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE J 488 " --> pdb=" O ILE J 473 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N PHE J 470 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU J 527 " --> pdb=" O PHE J 470 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN J 472 " --> pdb=" O GLN J 525 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN J 525 " --> pdb=" O ASN J 472 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 545 through 548 removed outlier: 6.761A pdb=" N GLY J 546 " --> pdb=" O ILE J 628 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP J 630 " --> pdb=" O GLY J 546 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL J 548 " --> pdb=" O ASP J 630 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU J 677 " --> pdb=" O ILE J 681 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE J 681 " --> pdb=" O GLU J 677 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 56 through 61 Processing sheet with id=AB7, first strand: chain 'E' and resid 74 through 76 removed outlier: 3.819A pdb=" N PHE E 84 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU E 97 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL E 89 " --> pdb=" O ARG E 95 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ARG E 95 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 485 through 492 removed outlier: 7.084A pdb=" N ASP E 486 " --> pdb=" O ARG E 474 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG E 474 " --> pdb=" O ASP E 486 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE E 488 " --> pdb=" O ASN E 472 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN E 472 " --> pdb=" O ILE E 488 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE E 473 " --> pdb=" O ASN E 523 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN E 523 " --> pdb=" O ILE E 473 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 545 through 548 removed outlier: 6.492A pdb=" N GLY E 546 " --> pdb=" O ILE E 628 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP E 630 " --> pdb=" O GLY E 546 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 548 " --> pdb=" O ASP E 630 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU E 627 " --> pdb=" O ILE E 658 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE E 660 " --> pdb=" O LEU E 627 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE E 629 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE E 498 " --> pdb=" O ILE E 659 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL E 675 " --> pdb=" O VAL E 682 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 485 through 488 removed outlier: 6.355A pdb=" N ASP F 486 " --> pdb=" O PHE F 475 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE F 475 " --> pdb=" O ASP F 486 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE F 488 " --> pdb=" O ILE F 473 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 485 through 488 removed outlier: 6.355A pdb=" N ASP F 486 " --> pdb=" O PHE F 475 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE F 475 " --> pdb=" O ASP F 486 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE F 488 " --> pdb=" O ILE F 473 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N PHE F 470 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU F 527 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN F 472 " --> pdb=" O GLN F 525 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN F 525 " --> pdb=" O ASN F 472 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 545 through 548 removed outlier: 6.761A pdb=" N GLY F 546 " --> pdb=" O ILE F 628 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP F 630 " --> pdb=" O GLY F 546 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL F 548 " --> pdb=" O ASP F 630 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU F 677 " --> pdb=" O ILE F 681 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE F 681 " --> pdb=" O GLU F 677 " (cutoff:3.500A) 2034 hydrogen bonds defined for protein. 5949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.70 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7427 1.33 - 1.45: 6756 1.45 - 1.57: 18937 1.57 - 1.70: 33 1.70 - 1.82: 144 Bond restraints: 33297 Sorted by residual: bond pdb=" CA ARG A 246 " pdb=" C ARG A 246 " ideal model delta sigma weight residual 1.531 1.492 0.040 1.32e-02 5.74e+03 8.97e+00 bond pdb=" CA ARG I 246 " pdb=" C ARG I 246 " ideal model delta sigma weight residual 1.531 1.492 0.039 1.32e-02 5.74e+03 8.93e+00 bond pdb=" CA ARG E 246 " pdb=" C ARG E 246 " ideal model delta sigma weight residual 1.531 1.492 0.039 1.32e-02 5.74e+03 8.87e+00 bond pdb=" CA TYR A 9 " pdb=" C TYR A 9 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.16e-02 7.43e+03 8.80e+00 bond pdb=" CA TYR I 9 " pdb=" C TYR I 9 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.16e-02 7.43e+03 8.78e+00 ... (remaining 33292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 44787 3.13 - 6.25: 375 6.25 - 9.38: 36 9.38 - 12.51: 3 12.51 - 15.63: 3 Bond angle restraints: 45204 Sorted by residual: angle pdb=" CA GLU I 573 " pdb=" CB GLU I 573 " pdb=" CG GLU I 573 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.47e+01 angle pdb=" CA GLU A 573 " pdb=" CB GLU A 573 " pdb=" CG GLU A 573 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.47e+01 angle pdb=" CA GLU E 573 " pdb=" CB GLU E 573 " pdb=" CG GLU E 573 " ideal model delta sigma weight residual 114.10 125.88 -11.78 2.00e+00 2.50e-01 3.47e+01 angle pdb=" C LEU L 42 " pdb=" N PRO L 43 " pdb=" CA PRO L 43 " ideal model delta sigma weight residual 119.92 114.25 5.67 1.07e+00 8.73e-01 2.81e+01 angle pdb=" C LEU H 42 " pdb=" N PRO H 43 " pdb=" CA PRO H 43 " ideal model delta sigma weight residual 119.92 114.27 5.65 1.07e+00 8.73e-01 2.79e+01 ... (remaining 45199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 17924 17.45 - 34.89: 1662 34.89 - 52.34: 344 52.34 - 69.79: 74 69.79 - 87.23: 39 Dihedral angle restraints: 20043 sinusoidal: 8118 harmonic: 11925 Sorted by residual: dihedral pdb=" CA PHE A 264 " pdb=" C PHE A 264 " pdb=" N LEU A 265 " pdb=" CA LEU A 265 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE E 264 " pdb=" C PHE E 264 " pdb=" N LEU E 265 " pdb=" CA LEU E 265 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE I 264 " pdb=" C PHE I 264 " pdb=" N LEU I 265 " pdb=" CA LEU I 265 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 20040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4018 0.049 - 0.098: 1038 0.098 - 0.148: 266 0.148 - 0.197: 6 0.197 - 0.246: 6 Chirality restraints: 5334 Sorted by residual: chirality pdb=" CA VAL B 526 " pdb=" N VAL B 526 " pdb=" C VAL B 526 " pdb=" CB VAL B 526 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL J 526 " pdb=" N VAL J 526 " pdb=" C VAL J 526 " pdb=" CB VAL J 526 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL F 526 " pdb=" N VAL F 526 " pdb=" C VAL F 526 " pdb=" CB VAL F 526 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5331 not shown) Planarity restraints: 5640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 245 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C SER E 245 " -0.042 2.00e-02 2.50e+03 pdb=" O SER E 245 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG E 246 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 245 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C SER I 245 " 0.042 2.00e-02 2.50e+03 pdb=" O SER I 245 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG I 246 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 245 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C SER A 245 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 245 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 246 " 0.014 2.00e-02 2.50e+03 ... (remaining 5637 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 249 2.59 - 3.17: 27423 3.17 - 3.74: 53028 3.74 - 4.32: 68472 4.32 - 4.90: 114100 Nonbonded interactions: 263272 Sorted by model distance: nonbonded pdb=" OE1 GLN J 550 " pdb="MG MG J 802 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLN B 550 " pdb="MG MG B 802 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLN F 550 " pdb="MG MG F 802 " model vdw 2.013 2.170 nonbonded pdb=" O2B ATP F 801 " pdb="MG MG F 802 " model vdw 2.031 2.170 nonbonded pdb=" O2B ATP B 801 " pdb="MG MG B 802 " model vdw 2.031 2.170 ... (remaining 263267 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'L' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.040 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 30.470 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.004 0.056 33297 Z= 0.200 Angle : 0.743 15.632 45204 Z= 0.415 Chirality : 0.045 0.246 5334 Planarity : 0.004 0.055 5640 Dihedral : 14.840 87.232 12315 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.06 % Allowed : 1.50 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.17 (0.13), residues: 4071 helix: 0.82 (0.10), residues: 2541 sheet: 0.10 (0.33), residues: 270 loop : -1.24 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 128 TYR 0.022 0.002 TYR J 477 PHE 0.025 0.002 PHE B 188 TRP 0.016 0.001 TRP E 394 HIS 0.002 0.000 HIS I 398 Details of bonding type rmsd covalent geometry : bond 0.00358 (33297) covalent geometry : angle 0.74296 (45204) hydrogen bonds : bond 0.12997 ( 2031) hydrogen bonds : angle 5.46982 ( 5949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 583 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6607 (m-30) cc_final: 0.6308 (m-30) REVERT: A 263 ASN cc_start: 0.8522 (t0) cc_final: 0.8242 (t0) REVERT: A 320 ASP cc_start: 0.7779 (t70) cc_final: 0.7501 (t0) REVERT: B 150 TYR cc_start: 0.7939 (m-80) cc_final: 0.7589 (m-80) REVERT: B 645 MET cc_start: 0.7342 (mmm) cc_final: 0.7122 (mmm) REVERT: D 24 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8059 (mtmm) REVERT: D 48 LEU cc_start: 0.8391 (tp) cc_final: 0.8030 (tp) REVERT: I 263 ASN cc_start: 0.8483 (t0) cc_final: 0.8120 (t0) REVERT: J 648 MET cc_start: 0.7893 (tpp) cc_final: 0.7620 (tpt) REVERT: E 108 VAL cc_start: 0.8201 (t) cc_final: 0.7916 (m) REVERT: E 139 ASP cc_start: 0.6554 (m-30) cc_final: 0.6334 (m-30) REVERT: E 263 ASN cc_start: 0.8701 (t0) cc_final: 0.8355 (t0) REVERT: E 320 ASP cc_start: 0.7579 (t70) cc_final: 0.7336 (t0) REVERT: E 469 THR cc_start: 0.7960 (p) cc_final: 0.7747 (p) REVERT: F 150 TYR cc_start: 0.8078 (m-80) cc_final: 0.7809 (m-80) outliers start: 2 outliers final: 0 residues processed: 585 average time/residue: 0.1754 time to fit residues: 171.4919 Evaluate side-chains 413 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 0.0470 chunk 388 optimal weight: 0.4980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.4980 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 516 GLN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN I 516 GLN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN E 516 GLN ** F 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 GLN ** 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 = 0.3913 r_free = 0.3913 target = 0.156787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127389 restraints weight = 45938.211| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.48 r_work: 0.3471 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33297 Z= 0.119 Angle : 0.540 9.118 45204 Z= 0.279 Chirality : 0.041 0.196 5334 Planarity : 0.004 0.044 5640 Dihedral : 7.177 70.310 4644 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.27 % Allowed : 9.32 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.77 (0.13), residues: 4071 helix: 1.42 (0.10), residues: 2532 sheet: -0.06 (0.32), residues: 276 loop : -1.19 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 325 TYR 0.023 0.001 TYR J 477 PHE 0.018 0.001 PHE F 475 TRP 0.014 0.001 TRP A 394 HIS 0.003 0.000 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00257 (33297) covalent geometry : angle 0.53964 (45204) hydrogen bonds : bond 0.04087 ( 2031) hydrogen bonds : angle 4.06802 ( 5949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 472 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6881 (t80) cc_final: 0.6633 (t80) REVERT: A 139 ASP cc_start: 0.7307 (m-30) cc_final: 0.6905 (m-30) REVERT: A 263 ASN cc_start: 0.8845 (t0) cc_final: 0.8555 (t0) REVERT: A 320 ASP cc_start: 0.8282 (t70) cc_final: 0.7877 (t0) REVERT: A 471 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.6878 (mtt90) REVERT: B 150 TYR cc_start: 0.8057 (m-80) cc_final: 0.7736 (m-10) REVERT: B 398 HIS cc_start: 0.5981 (t-90) cc_final: 0.5469 (t-170) REVERT: I 77 TRP cc_start: 0.8601 (t-100) cc_final: 0.8221 (t-100) REVERT: I 224 ASP cc_start: 0.8113 (t70) cc_final: 0.7654 (t0) REVERT: I 246 ARG cc_start: 0.7509 (mtt90) cc_final: 0.7182 (mtt90) REVERT: I 263 ASN cc_start: 0.8836 (t0) cc_final: 0.8387 (t0) REVERT: I 278 PHE cc_start: 0.7566 (m-10) cc_final: 0.7240 (m-80) REVERT: I 475 PHE cc_start: 0.8794 (t80) cc_final: 0.8138 (t80) REVERT: I 645 MET cc_start: 0.8863 (mmp) cc_final: 0.8630 (mmm) REVERT: J 150 TYR cc_start: 0.7815 (m-80) cc_final: 0.7550 (m-80) REVERT: J 155 ILE cc_start: 0.8688 (mt) cc_final: 0.8458 (mm) REVERT: L 65 MET cc_start: 0.6434 (ttt) cc_final: 0.6117 (ttp) REVERT: E 108 VAL cc_start: 0.8252 (t) cc_final: 0.7987 (m) REVERT: E 139 ASP cc_start: 0.7014 (m-30) cc_final: 0.6645 (m-30) REVERT: E 263 ASN cc_start: 0.8998 (t0) cc_final: 0.8593 (t0) REVERT: E 320 ASP cc_start: 0.7995 (t70) cc_final: 0.7617 (t0) REVERT: E 415 MET cc_start: 0.6785 (ptp) cc_final: 0.6349 (ptp) REVERT: E 648 MET cc_start: 0.8496 (tpt) cc_final: 0.8205 (mmt) REVERT: F 150 TYR cc_start: 0.8164 (m-80) cc_final: 0.7635 (m-80) REVERT: F 268 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7513 (mm-40) REVERT: F 385 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8000 (tm-30) REVERT: F 398 HIS cc_start: 0.6247 (t-90) cc_final: 0.5837 (t-170) REVERT: F 598 ILE cc_start: 0.7436 (mm) cc_final: 0.7218 (mm) REVERT: H 47 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8160 (tm-30) REVERT: H 55 ARG cc_start: 0.6592 (tpt170) cc_final: 0.6336 (tpp-160) REVERT: H 65 MET cc_start: 0.6632 (ttt) cc_final: 0.6107 (ttp) outliers start: 45 outliers final: 33 residues processed: 498 average time/residue: 0.1688 time to fit residues: 141.6579 Evaluate side-chains 449 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 416 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 702 TYR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 673 ILE Chi-restraints excluded: chain F residue 676 MET Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 202 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 363 optimal weight: 3.9990 chunk 401 optimal weight: 0.0050 chunk 191 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 GLN ** F 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124885 restraints weight = 47212.304| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.52 r_work: 0.3435 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.114 Angle : 0.514 10.852 45204 Z= 0.262 Chirality : 0.040 0.158 5334 Planarity : 0.003 0.044 5640 Dihedral : 6.811 66.371 4644 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.21 % Allowed : 10.96 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 4071 helix: 1.68 (0.10), residues: 2538 sheet: -0.08 (0.32), residues: 276 loop : -1.15 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 325 TYR 0.013 0.001 TYR J 288 PHE 0.019 0.001 PHE E 84 TRP 0.013 0.001 TRP A 394 HIS 0.002 0.000 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00252 (33297) covalent geometry : angle 0.51400 (45204) hydrogen bonds : bond 0.03882 ( 2031) hydrogen bonds : angle 3.80471 ( 5949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 463 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6724 (t80) cc_final: 0.6488 (t80) REVERT: A 139 ASP cc_start: 0.7246 (m-30) cc_final: 0.6812 (m-30) REVERT: A 320 ASP cc_start: 0.8329 (t70) cc_final: 0.7912 (t0) REVERT: A 471 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7020 (mtt90) REVERT: B 150 TYR cc_start: 0.8204 (m-80) cc_final: 0.7657 (m-10) REVERT: B 167 PHE cc_start: 0.8099 (m-10) cc_final: 0.7801 (m-10) REVERT: B 205 GLU cc_start: 0.7974 (tp30) cc_final: 0.7631 (tp30) REVERT: B 286 MET cc_start: 0.7668 (mmt) cc_final: 0.7322 (mmt) REVERT: C 65 MET cc_start: 0.2781 (mmt) cc_final: 0.2181 (mtt) REVERT: D 24 LYS cc_start: 0.8414 (mtmm) cc_final: 0.8168 (mtmm) REVERT: D 65 MET cc_start: 0.6787 (ttt) cc_final: 0.6229 (ttp) REVERT: I 12 TYR cc_start: 0.6947 (t80) cc_final: 0.6728 (t80) REVERT: I 77 TRP cc_start: 0.8645 (t-100) cc_final: 0.8255 (t-100) REVERT: I 224 ASP cc_start: 0.8158 (t70) cc_final: 0.7745 (t0) REVERT: I 246 ARG cc_start: 0.7464 (mtt90) cc_final: 0.7058 (mtt90) REVERT: I 263 ASN cc_start: 0.8829 (t0) cc_final: 0.8351 (t0) REVERT: I 268 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7661 (mt0) REVERT: I 645 MET cc_start: 0.8951 (mmp) cc_final: 0.8670 (mmm) REVERT: J 150 TYR cc_start: 0.7941 (m-80) cc_final: 0.7576 (m-80) REVERT: J 155 ILE cc_start: 0.8663 (mt) cc_final: 0.8376 (mm) REVERT: J 549 LEU cc_start: 0.7787 (mt) cc_final: 0.7543 (mp) REVERT: J 592 ARG cc_start: 0.8200 (ttt-90) cc_final: 0.7562 (tmt170) REVERT: K 65 MET cc_start: 0.2597 (mmt) cc_final: 0.2362 (mtt) REVERT: E 88 LYS cc_start: 0.7821 (tptm) cc_final: 0.7164 (ttpp) REVERT: E 108 VAL cc_start: 0.8468 (t) cc_final: 0.8194 (m) REVERT: E 139 ASP cc_start: 0.7190 (m-30) cc_final: 0.6956 (m-30) REVERT: E 320 ASP cc_start: 0.8021 (t70) cc_final: 0.7618 (t0) REVERT: E 352 MET cc_start: 0.8343 (mmm) cc_final: 0.8110 (mmm) REVERT: E 415 MET cc_start: 0.6664 (ptp) cc_final: 0.6426 (ptp) REVERT: E 648 MET cc_start: 0.8534 (tpt) cc_final: 0.8311 (mmt) REVERT: F 150 TYR cc_start: 0.8078 (m-80) cc_final: 0.7550 (m-80) REVERT: F 156 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8260 (tp30) REVERT: F 205 GLU cc_start: 0.8058 (tp30) cc_final: 0.7599 (tp30) REVERT: F 385 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7867 (tm-30) REVERT: F 586 ASP cc_start: 0.8148 (p0) cc_final: 0.7884 (p0) REVERT: F 598 ILE cc_start: 0.7457 (mm) cc_final: 0.7243 (mm) REVERT: H 55 ARG cc_start: 0.6725 (tpt170) cc_final: 0.6326 (tpp-160) REVERT: H 65 MET cc_start: 0.6525 (ttt) cc_final: 0.6032 (ttp) outliers start: 78 outliers final: 49 residues processed: 517 average time/residue: 0.1651 time to fit residues: 145.2502 Evaluate side-chains 474 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 424 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 702 TYR Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 123 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 332 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 284 optimal weight: 0.6980 chunk 384 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 305 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 539 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.152498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122732 restraints weight = 46230.844| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.49 r_work: 0.3405 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.126 Angle : 0.523 11.047 45204 Z= 0.265 Chirality : 0.041 0.170 5334 Planarity : 0.003 0.043 5640 Dihedral : 6.727 69.713 4644 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.21 % Allowed : 13.40 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.16 (0.14), residues: 4071 helix: 1.76 (0.10), residues: 2547 sheet: -0.09 (0.31), residues: 276 loop : -1.12 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 58 TYR 0.015 0.001 TYR B 288 PHE 0.021 0.001 PHE A 84 TRP 0.012 0.001 TRP A 394 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00289 (33297) covalent geometry : angle 0.52307 (45204) hydrogen bonds : bond 0.03867 ( 2031) hydrogen bonds : angle 3.74015 ( 5949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 467 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6721 (t80) cc_final: 0.6502 (t80) REVERT: A 139 ASP cc_start: 0.7291 (m-30) cc_final: 0.6850 (m-30) REVERT: A 320 ASP cc_start: 0.8383 (t70) cc_final: 0.7929 (t0) REVERT: A 471 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7134 (mtt90) REVERT: B 150 TYR cc_start: 0.8356 (m-80) cc_final: 0.7852 (m-10) REVERT: B 167 PHE cc_start: 0.8062 (m-10) cc_final: 0.7845 (m-10) REVERT: B 205 GLU cc_start: 0.7967 (tp30) cc_final: 0.7571 (tp30) REVERT: B 286 MET cc_start: 0.7736 (mmt) cc_final: 0.7377 (mmt) REVERT: B 385 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 592 ARG cc_start: 0.7995 (ttt-90) cc_final: 0.7682 (tmt170) REVERT: B 643 ILE cc_start: 0.8080 (mm) cc_final: 0.7679 (mm) REVERT: B 703 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8315 (mp10) REVERT: C 65 MET cc_start: 0.2827 (mmt) cc_final: 0.2288 (mtt) REVERT: D 24 LYS cc_start: 0.8314 (mtmm) cc_final: 0.8044 (mtmm) REVERT: D 55 ARG cc_start: 0.7099 (tpt170) cc_final: 0.6389 (tpp-160) REVERT: D 65 MET cc_start: 0.6855 (ttt) cc_final: 0.6264 (ttp) REVERT: I 77 TRP cc_start: 0.8668 (t-100) cc_final: 0.8318 (t-100) REVERT: I 88 LYS cc_start: 0.7855 (tptm) cc_final: 0.7382 (ttpp) REVERT: I 246 ARG cc_start: 0.7420 (mtt90) cc_final: 0.7045 (mtt90) REVERT: I 263 ASN cc_start: 0.9005 (t0) cc_final: 0.8540 (t0) REVERT: I 268 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7714 (mt0) REVERT: I 270 LEU cc_start: 0.7837 (mt) cc_final: 0.7585 (mt) REVERT: I 645 MET cc_start: 0.9034 (mmp) cc_final: 0.8824 (mmm) REVERT: J 150 TYR cc_start: 0.8083 (m-80) cc_final: 0.7608 (m-80) REVERT: J 167 PHE cc_start: 0.8049 (m-10) cc_final: 0.7815 (m-10) REVERT: J 262 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.7149 (ttm110) REVERT: J 389 MET cc_start: 0.8122 (tmm) cc_final: 0.7493 (tmm) REVERT: J 592 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.8054 (ttt-90) REVERT: J 703 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: K 65 MET cc_start: 0.2613 (mmt) cc_final: 0.2366 (mtt) REVERT: L 55 ARG cc_start: 0.6738 (tpt170) cc_final: 0.6173 (tpp-160) REVERT: E 88 LYS cc_start: 0.7818 (tptm) cc_final: 0.7188 (ttpp) REVERT: E 108 VAL cc_start: 0.8543 (t) cc_final: 0.8277 (m) REVERT: E 139 ASP cc_start: 0.7282 (m-30) cc_final: 0.7020 (m-30) REVERT: E 320 ASP cc_start: 0.8058 (t70) cc_final: 0.7627 (t0) REVERT: E 415 MET cc_start: 0.6682 (ptp) cc_final: 0.6368 (ptp) REVERT: E 541 LEU cc_start: 0.7912 (tt) cc_final: 0.7414 (tt) REVERT: E 676 MET cc_start: 0.8973 (mtp) cc_final: 0.8490 (mtp) REVERT: F 150 TYR cc_start: 0.8285 (m-80) cc_final: 0.7912 (m-80) REVERT: F 156 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: F 415 MET cc_start: 0.7938 (mmt) cc_final: 0.7459 (mtp) REVERT: F 477 TYR cc_start: 0.8404 (m-80) cc_final: 0.8019 (m-10) REVERT: F 586 ASP cc_start: 0.8200 (p0) cc_final: 0.7903 (p0) REVERT: F 598 ILE cc_start: 0.7476 (mm) cc_final: 0.7267 (mm) REVERT: F 643 ILE cc_start: 0.8283 (mm) cc_final: 0.7922 (mm) REVERT: F 703 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: H 47 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8049 (tm-30) REVERT: H 55 ARG cc_start: 0.6749 (tpt170) cc_final: 0.6349 (tpp-160) outliers start: 78 outliers final: 61 residues processed: 522 average time/residue: 0.1727 time to fit residues: 151.0946 Evaluate side-chains 493 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 428 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 702 TYR Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 305 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 390 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 348 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 472 ASN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121862 restraints weight = 46300.855| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.49 r_work: 0.3383 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.134 Angle : 0.536 10.676 45204 Z= 0.271 Chirality : 0.041 0.204 5334 Planarity : 0.003 0.049 5640 Dihedral : 6.671 74.013 4644 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.69 % Allowed : 14.87 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.21 (0.13), residues: 4071 helix: 1.80 (0.10), residues: 2556 sheet: -0.11 (0.31), residues: 276 loop : -1.12 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 256 TYR 0.014 0.001 TYR B 477 PHE 0.021 0.001 PHE I 84 TRP 0.010 0.001 TRP A 394 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00310 (33297) covalent geometry : angle 0.53590 (45204) hydrogen bonds : bond 0.03888 ( 2031) hydrogen bonds : angle 3.72928 ( 5949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 472 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7385 (m-30) cc_final: 0.6917 (m-30) REVERT: A 204 PHE cc_start: 0.7490 (m-80) cc_final: 0.7099 (t80) REVERT: A 320 ASP cc_start: 0.8383 (t70) cc_final: 0.7930 (t0) REVERT: A 471 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.7149 (mtt90) REVERT: B 150 TYR cc_start: 0.8441 (m-80) cc_final: 0.8008 (m-10) REVERT: B 205 GLU cc_start: 0.7962 (tp30) cc_final: 0.7560 (tp30) REVERT: B 286 MET cc_start: 0.7719 (mmt) cc_final: 0.7485 (mmt) REVERT: B 385 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 592 ARG cc_start: 0.8218 (ttt-90) cc_final: 0.7798 (tmt170) REVERT: B 643 ILE cc_start: 0.8110 (mm) cc_final: 0.7713 (mm) REVERT: B 703 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: C 65 MET cc_start: 0.2979 (mmt) cc_final: 0.2468 (mtt) REVERT: D 24 LYS cc_start: 0.8317 (mtmm) cc_final: 0.8114 (mtmm) REVERT: D 50 GLU cc_start: 0.7964 (tt0) cc_final: 0.7553 (tp30) REVERT: D 55 ARG cc_start: 0.7005 (tpt170) cc_final: 0.6238 (tpp-160) REVERT: D 65 MET cc_start: 0.6745 (ttt) cc_final: 0.6132 (ttp) REVERT: I 72 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8058 (mm) REVERT: I 77 TRP cc_start: 0.8648 (t-100) cc_final: 0.8265 (t-100) REVERT: I 88 LYS cc_start: 0.7913 (tptm) cc_final: 0.7445 (ttpp) REVERT: I 263 ASN cc_start: 0.9021 (t0) cc_final: 0.8529 (t0) REVERT: I 268 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7851 (mt0) REVERT: I 570 MET cc_start: 0.7943 (ppp) cc_final: 0.6635 (ppp) REVERT: J 150 TYR cc_start: 0.8177 (m-80) cc_final: 0.7682 (m-80) REVERT: J 155 ILE cc_start: 0.8701 (mt) cc_final: 0.8379 (mm) REVERT: J 205 GLU cc_start: 0.8061 (tp30) cc_final: 0.7858 (tm-30) REVERT: J 389 MET cc_start: 0.7953 (tmm) cc_final: 0.7355 (tmm) REVERT: J 549 LEU cc_start: 0.7767 (mt) cc_final: 0.7536 (mp) REVERT: J 592 ARG cc_start: 0.8330 (ttt-90) cc_final: 0.8059 (ttt-90) REVERT: J 703 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8388 (mp10) REVERT: K 65 MET cc_start: 0.2497 (mmt) cc_final: 0.2245 (mtt) REVERT: L 55 ARG cc_start: 0.6715 (tpt170) cc_final: 0.6170 (tpp-160) REVERT: E 72 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8004 (mm) REVERT: E 88 LYS cc_start: 0.7898 (tptm) cc_final: 0.7298 (ttpp) REVERT: E 108 VAL cc_start: 0.8617 (t) cc_final: 0.8359 (m) REVERT: E 139 ASP cc_start: 0.7426 (m-30) cc_final: 0.7147 (m-30) REVERT: E 320 ASP cc_start: 0.8037 (t70) cc_final: 0.7595 (t0) REVERT: E 415 MET cc_start: 0.6583 (ptp) cc_final: 0.6306 (ptp) REVERT: E 541 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7315 (tt) REVERT: E 633 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8326 (m) REVERT: E 676 MET cc_start: 0.9017 (mtp) cc_final: 0.8603 (mtp) REVERT: F 150 TYR cc_start: 0.8289 (m-80) cc_final: 0.7964 (m-80) REVERT: F 156 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: F 205 GLU cc_start: 0.8318 (tp30) cc_final: 0.7779 (tp30) REVERT: F 415 MET cc_start: 0.7961 (mmt) cc_final: 0.7440 (mtp) REVERT: F 477 TYR cc_start: 0.8435 (m-80) cc_final: 0.8176 (m-10) REVERT: F 586 ASP cc_start: 0.8358 (p0) cc_final: 0.8057 (p0) REVERT: F 598 ILE cc_start: 0.7430 (mm) cc_final: 0.7223 (mm) REVERT: F 643 ILE cc_start: 0.8196 (mm) cc_final: 0.7867 (mm) REVERT: H 29 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7884 (mp) REVERT: H 47 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7906 (tm-30) REVERT: H 55 ARG cc_start: 0.6959 (tpt170) cc_final: 0.6386 (tpp-160) outliers start: 95 outliers final: 67 residues processed: 543 average time/residue: 0.1660 time to fit residues: 151.6484 Evaluate side-chains 515 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 440 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 14 optimal weight: 0.9990 chunk 393 optimal weight: 0.0170 chunk 342 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 376 optimal weight: 0.5980 chunk 284 optimal weight: 0.0970 chunk 375 optimal weight: 4.9990 chunk 305 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 GLN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123352 restraints weight = 46109.640| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.47 r_work: 0.3402 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.112 Angle : 0.520 11.064 45204 Z= 0.262 Chirality : 0.041 0.200 5334 Planarity : 0.003 0.051 5640 Dihedral : 6.591 77.195 4644 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.32 % Allowed : 16.48 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.33 (0.14), residues: 4071 helix: 1.93 (0.10), residues: 2553 sheet: -0.07 (0.31), residues: 276 loop : -1.12 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 246 TYR 0.015 0.001 TYR B 288 PHE 0.030 0.001 PHE A 475 TRP 0.008 0.001 TRP A 394 HIS 0.004 0.001 HIS I 185 Details of bonding type rmsd covalent geometry : bond 0.00251 (33297) covalent geometry : angle 0.51953 (45204) hydrogen bonds : bond 0.03688 ( 2031) hydrogen bonds : angle 3.65270 ( 5949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 453 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7383 (m-30) cc_final: 0.6910 (m-30) REVERT: A 175 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.6693 (t80) REVERT: A 204 PHE cc_start: 0.7505 (m-80) cc_final: 0.6991 (t80) REVERT: A 320 ASP cc_start: 0.8375 (t70) cc_final: 0.7883 (t0) REVERT: A 384 ILE cc_start: 0.8009 (mm) cc_final: 0.7798 (mt) REVERT: A 471 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.7143 (mtt180) REVERT: B 150 TYR cc_start: 0.8322 (m-80) cc_final: 0.8104 (m-10) REVERT: B 205 GLU cc_start: 0.7967 (tp30) cc_final: 0.7594 (tp30) REVERT: B 286 MET cc_start: 0.7701 (mmt) cc_final: 0.7415 (mmt) REVERT: B 385 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 475 PHE cc_start: 0.8492 (t80) cc_final: 0.8210 (t80) REVERT: B 592 ARG cc_start: 0.8181 (ttt-90) cc_final: 0.7771 (tmt170) REVERT: B 643 ILE cc_start: 0.8102 (mm) cc_final: 0.7708 (mm) REVERT: B 703 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: C 65 MET cc_start: 0.2970 (mmt) cc_final: 0.2696 (mtt) REVERT: D 24 LYS cc_start: 0.8357 (mtmm) cc_final: 0.8103 (mtmm) REVERT: D 50 GLU cc_start: 0.8007 (tt0) cc_final: 0.7667 (tp30) REVERT: D 55 ARG cc_start: 0.6940 (tpt170) cc_final: 0.6163 (tpp-160) REVERT: D 65 MET cc_start: 0.6686 (ttt) cc_final: 0.6077 (ttp) REVERT: I 72 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7967 (mm) REVERT: I 77 TRP cc_start: 0.8641 (t-100) cc_final: 0.8312 (t-100) REVERT: I 88 LYS cc_start: 0.7897 (tptm) cc_final: 0.7401 (ttpp) REVERT: I 246 ARG cc_start: 0.7348 (mtt90) cc_final: 0.7043 (mtt90) REVERT: I 261 ILE cc_start: 0.7872 (mt) cc_final: 0.7608 (tt) REVERT: I 263 ASN cc_start: 0.8898 (t0) cc_final: 0.8420 (t0) REVERT: I 268 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7885 (mt0) REVERT: I 384 ILE cc_start: 0.7827 (mm) cc_final: 0.7599 (mt) REVERT: I 570 MET cc_start: 0.8043 (ppp) cc_final: 0.7136 (ppp) REVERT: J 150 TYR cc_start: 0.8136 (m-80) cc_final: 0.7592 (m-80) REVERT: J 286 MET cc_start: 0.7488 (mmt) cc_final: 0.7222 (mmt) REVERT: J 389 MET cc_start: 0.7954 (tmm) cc_final: 0.7353 (tmm) REVERT: J 549 LEU cc_start: 0.7793 (mt) cc_final: 0.7531 (mp) REVERT: J 592 ARG cc_start: 0.8308 (ttt-90) cc_final: 0.8094 (ttt-90) REVERT: J 703 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: L 55 ARG cc_start: 0.6767 (tpt170) cc_final: 0.6135 (tpp-160) REVERT: E 72 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7936 (mm) REVERT: E 88 LYS cc_start: 0.7901 (tptm) cc_final: 0.7294 (ttpp) REVERT: E 108 VAL cc_start: 0.8611 (t) cc_final: 0.8339 (m) REVERT: E 139 ASP cc_start: 0.7436 (m-30) cc_final: 0.7150 (m-30) REVERT: E 320 ASP cc_start: 0.7987 (t70) cc_final: 0.7557 (t0) REVERT: E 415 MET cc_start: 0.6549 (ptp) cc_final: 0.6303 (ptp) REVERT: E 541 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7099 (tt) REVERT: E 633 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8158 (m) REVERT: E 676 MET cc_start: 0.8995 (mtp) cc_final: 0.8638 (mtp) REVERT: F 150 TYR cc_start: 0.8204 (m-80) cc_final: 0.7898 (m-80) REVERT: F 156 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: F 205 GLU cc_start: 0.8263 (tp30) cc_final: 0.7719 (tp30) REVERT: F 415 MET cc_start: 0.8010 (mmt) cc_final: 0.7497 (mtp) REVERT: F 477 TYR cc_start: 0.8389 (m-80) cc_final: 0.8160 (m-10) REVERT: F 586 ASP cc_start: 0.8358 (p0) cc_final: 0.8071 (p0) REVERT: F 598 ILE cc_start: 0.7432 (mm) cc_final: 0.7223 (mm) REVERT: F 643 ILE cc_start: 0.8292 (mm) cc_final: 0.7961 (mm) REVERT: F 703 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: H 47 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7879 (tm-30) REVERT: H 55 ARG cc_start: 0.6941 (tpt170) cc_final: 0.6369 (tpp-160) outliers start: 82 outliers final: 62 residues processed: 517 average time/residue: 0.1749 time to fit residues: 151.7149 Evaluate side-chains 503 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 432 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 165 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 0.1980 chunk 135 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 392 optimal weight: 9.9990 chunk 233 optimal weight: 0.7980 chunk 374 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 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 = 0.3858 r_free = 0.3858 target = 0.152001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122411 restraints weight = 46342.170| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.48 r_work: 0.3384 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.121 Angle : 0.528 10.465 45204 Z= 0.267 Chirality : 0.041 0.205 5334 Planarity : 0.003 0.051 5640 Dihedral : 6.570 81.506 4644 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.61 % Allowed : 17.02 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.35 (0.14), residues: 4071 helix: 1.94 (0.10), residues: 2553 sheet: -0.10 (0.31), residues: 279 loop : -1.10 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 246 TYR 0.017 0.001 TYR B 288 PHE 0.019 0.001 PHE B 413 TRP 0.008 0.001 TRP A 431 HIS 0.002 0.001 HIS J 662 Details of bonding type rmsd covalent geometry : bond 0.00276 (33297) covalent geometry : angle 0.52756 (45204) hydrogen bonds : bond 0.03702 ( 2031) hydrogen bonds : angle 3.64567 ( 5949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 451 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7435 (m-30) cc_final: 0.7036 (m-30) REVERT: A 320 ASP cc_start: 0.8363 (t70) cc_final: 0.7882 (t0) REVERT: A 471 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.7167 (mtt180) REVERT: A 472 ASN cc_start: 0.7931 (t0) cc_final: 0.7681 (t0) REVERT: B 150 TYR cc_start: 0.8390 (m-80) cc_final: 0.7966 (m-10) REVERT: B 385 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 592 ARG cc_start: 0.8185 (ttt-90) cc_final: 0.7965 (ttt-90) REVERT: B 643 ILE cc_start: 0.8146 (mm) cc_final: 0.7750 (mm) REVERT: B 703 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: C 42 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6467 (mp) REVERT: D 24 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8146 (mtmm) REVERT: D 50 GLU cc_start: 0.8174 (tt0) cc_final: 0.7778 (tp30) REVERT: D 55 ARG cc_start: 0.7059 (tpt170) cc_final: 0.6278 (tpp-160) REVERT: D 65 MET cc_start: 0.6678 (ttt) cc_final: 0.6074 (ttp) REVERT: I 72 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8000 (mm) REVERT: I 77 TRP cc_start: 0.8647 (t-100) cc_final: 0.8278 (t-100) REVERT: I 88 LYS cc_start: 0.7975 (tptm) cc_final: 0.7506 (ttpp) REVERT: I 261 ILE cc_start: 0.7933 (mt) cc_final: 0.7673 (tt) REVERT: I 268 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7898 (mt0) REVERT: I 384 ILE cc_start: 0.7900 (mm) cc_final: 0.7672 (mt) REVERT: I 570 MET cc_start: 0.7998 (ppp) cc_final: 0.6793 (ppp) REVERT: J 150 TYR cc_start: 0.8204 (m-80) cc_final: 0.7686 (m-80) REVERT: J 276 LEU cc_start: 0.7557 (tt) cc_final: 0.7335 (tt) REVERT: J 286 MET cc_start: 0.7651 (mmt) cc_final: 0.7304 (mmt) REVERT: J 389 MET cc_start: 0.8002 (tmm) cc_final: 0.7405 (tmm) REVERT: J 549 LEU cc_start: 0.7842 (mt) cc_final: 0.7573 (mp) REVERT: J 592 ARG cc_start: 0.8348 (ttt-90) cc_final: 0.8129 (ttt-90) REVERT: J 621 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7976 (p) REVERT: J 703 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: L 47 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7928 (tm-30) REVERT: L 55 ARG cc_start: 0.6764 (tpt170) cc_final: 0.6187 (tpp-160) REVERT: E 72 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7995 (mm) REVERT: E 88 LYS cc_start: 0.7941 (tptm) cc_final: 0.7353 (ttpp) REVERT: E 108 VAL cc_start: 0.8562 (t) cc_final: 0.8285 (m) REVERT: E 139 ASP cc_start: 0.7505 (m-30) cc_final: 0.7213 (m-30) REVERT: E 320 ASP cc_start: 0.8014 (t70) cc_final: 0.7590 (t0) REVERT: E 415 MET cc_start: 0.6638 (ptp) cc_final: 0.6360 (ptp) REVERT: E 633 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8169 (m) REVERT: E 676 MET cc_start: 0.8988 (mtp) cc_final: 0.8667 (mtp) REVERT: F 156 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8366 (tp30) REVERT: F 205 GLU cc_start: 0.8278 (tp30) cc_final: 0.7717 (tp30) REVERT: F 415 MET cc_start: 0.8098 (mmt) cc_final: 0.7570 (mtp) REVERT: F 586 ASP cc_start: 0.8293 (p0) cc_final: 0.7994 (p0) REVERT: F 643 ILE cc_start: 0.8332 (mm) cc_final: 0.7993 (mm) REVERT: F 703 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: G 34 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7351 (mtm-85) REVERT: H 47 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8266 (tm-30) REVERT: H 55 ARG cc_start: 0.7004 (tpt170) cc_final: 0.6442 (tpp-160) outliers start: 92 outliers final: 68 residues processed: 525 average time/residue: 0.1698 time to fit residues: 149.9031 Evaluate side-chains 506 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 429 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 357 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 251 optimal weight: 0.9990 chunk 372 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 235 optimal weight: 0.0570 chunk 221 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 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 = 0.3869 r_free = 0.3869 target = 0.153010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123629 restraints weight = 46100.108| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.48 r_work: 0.3401 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33297 Z= 0.110 Angle : 0.525 10.607 45204 Z= 0.263 Chirality : 0.041 0.254 5334 Planarity : 0.003 0.048 5640 Dihedral : 6.495 83.382 4644 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.41 % Allowed : 17.53 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.44 (0.14), residues: 4071 helix: 2.01 (0.10), residues: 2553 sheet: 0.04 (0.32), residues: 276 loop : -1.10 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 246 TYR 0.016 0.001 TYR B 288 PHE 0.019 0.001 PHE B 413 TRP 0.008 0.001 TRP H 23 HIS 0.002 0.000 HIS J 662 Details of bonding type rmsd covalent geometry : bond 0.00246 (33297) covalent geometry : angle 0.52463 (45204) hydrogen bonds : bond 0.03580 ( 2031) hydrogen bonds : angle 3.59285 ( 5949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 467 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 139 ASP cc_start: 0.7475 (m-30) cc_final: 0.7050 (m-30) REVERT: A 175 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 204 PHE cc_start: 0.7582 (m-80) cc_final: 0.7271 (t80) REVERT: A 320 ASP cc_start: 0.8343 (t70) cc_final: 0.7883 (t0) REVERT: A 472 ASN cc_start: 0.7902 (t0) cc_final: 0.7606 (t0) REVERT: B 150 TYR cc_start: 0.8344 (m-80) cc_final: 0.7921 (m-10) REVERT: B 205 GLU cc_start: 0.8086 (tp30) cc_final: 0.7717 (tp30) REVERT: B 385 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 486 ASP cc_start: 0.8000 (t0) cc_final: 0.7751 (t0) REVERT: B 643 ILE cc_start: 0.8141 (mm) cc_final: 0.7742 (mm) REVERT: B 703 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8246 (mp10) REVERT: D 24 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8016 (mtmm) REVERT: D 50 GLU cc_start: 0.8196 (tt0) cc_final: 0.7833 (tp30) REVERT: D 55 ARG cc_start: 0.7053 (tpt170) cc_final: 0.6308 (tpp-160) REVERT: D 65 MET cc_start: 0.6700 (ttt) cc_final: 0.6121 (ttp) REVERT: I 72 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7955 (mm) REVERT: I 77 TRP cc_start: 0.8574 (t-100) cc_final: 0.8224 (t-100) REVERT: I 88 LYS cc_start: 0.7994 (tptm) cc_final: 0.7532 (ttpp) REVERT: I 261 ILE cc_start: 0.7887 (mt) cc_final: 0.7646 (tt) REVERT: I 268 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7912 (mt0) REVERT: I 384 ILE cc_start: 0.7856 (mm) cc_final: 0.7641 (mt) REVERT: I 389 MET cc_start: 0.7280 (tmm) cc_final: 0.6998 (tmm) REVERT: I 570 MET cc_start: 0.7885 (ppp) cc_final: 0.6697 (ppp) REVERT: J 150 TYR cc_start: 0.8225 (m-80) cc_final: 0.7679 (m-80) REVERT: J 256 ARG cc_start: 0.7922 (mmp80) cc_final: 0.7631 (mmp80) REVERT: J 276 LEU cc_start: 0.7531 (tt) cc_final: 0.7310 (tt) REVERT: J 286 MET cc_start: 0.7629 (mmt) cc_final: 0.7291 (mmt) REVERT: J 308 SER cc_start: 0.8869 (t) cc_final: 0.8332 (p) REVERT: J 389 MET cc_start: 0.8002 (tmm) cc_final: 0.7409 (tmm) REVERT: J 549 LEU cc_start: 0.7845 (mt) cc_final: 0.7587 (mp) REVERT: J 683 GLU cc_start: 0.7091 (mp0) cc_final: 0.6317 (mp0) REVERT: J 703 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: L 47 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7941 (tm-30) REVERT: L 55 ARG cc_start: 0.6589 (tpt170) cc_final: 0.6144 (tpp-160) REVERT: E 72 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7966 (mm) REVERT: E 88 LYS cc_start: 0.7955 (tptm) cc_final: 0.7371 (ttpp) REVERT: E 108 VAL cc_start: 0.8560 (t) cc_final: 0.8292 (m) REVERT: E 139 ASP cc_start: 0.7505 (m-30) cc_final: 0.7220 (m-30) REVERT: E 320 ASP cc_start: 0.8006 (t70) cc_final: 0.7575 (t0) REVERT: E 633 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8133 (m) REVERT: E 676 MET cc_start: 0.8997 (mtp) cc_final: 0.8572 (mtm) REVERT: F 156 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: F 205 GLU cc_start: 0.8266 (tp30) cc_final: 0.7711 (tp30) REVERT: F 415 MET cc_start: 0.8142 (mmt) cc_final: 0.7630 (mtp) REVERT: F 586 ASP cc_start: 0.8291 (p0) cc_final: 0.7998 (p0) REVERT: F 643 ILE cc_start: 0.8323 (mm) cc_final: 0.7989 (mm) REVERT: F 703 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: G 34 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7330 (mtm-85) REVERT: H 55 ARG cc_start: 0.6996 (tpt170) cc_final: 0.6436 (tpp-160) outliers start: 85 outliers final: 66 residues processed: 534 average time/residue: 0.1690 time to fit residues: 151.5424 Evaluate side-chains 506 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 432 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 9 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 290 optimal weight: 0.5980 chunk 348 optimal weight: 3.9990 chunk 281 optimal weight: 0.5980 chunk 243 optimal weight: 0.7980 chunk 229 optimal weight: 5.9990 chunk 395 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 360 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.149653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119994 restraints weight = 46406.897| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.46 r_work: 0.3352 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33297 Z= 0.148 Angle : 0.567 10.962 45204 Z= 0.286 Chirality : 0.042 0.226 5334 Planarity : 0.004 0.050 5640 Dihedral : 6.564 88.373 4644 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.44 % Allowed : 18.15 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.28 (0.14), residues: 4071 helix: 1.87 (0.10), residues: 2553 sheet: -0.11 (0.31), residues: 279 loop : -1.11 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 592 TYR 0.016 0.001 TYR B 288 PHE 0.026 0.001 PHE D 67 TRP 0.014 0.001 TRP A 431 HIS 0.003 0.001 HIS E 234 Details of bonding type rmsd covalent geometry : bond 0.00352 (33297) covalent geometry : angle 0.56710 (45204) hydrogen bonds : bond 0.03913 ( 2031) hydrogen bonds : angle 3.70387 ( 5949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 444 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8082 (tptm) cc_final: 0.7556 (ttpp) REVERT: A 139 ASP cc_start: 0.7459 (m-30) cc_final: 0.7060 (m-30) REVERT: A 204 PHE cc_start: 0.7609 (m-80) cc_final: 0.7110 (t80) REVERT: A 320 ASP cc_start: 0.8388 (t70) cc_final: 0.7953 (t0) REVERT: A 472 ASN cc_start: 0.7988 (t0) cc_final: 0.7636 (t0) REVERT: B 150 TYR cc_start: 0.8546 (m-80) cc_final: 0.8158 (m-10) REVERT: B 205 GLU cc_start: 0.8115 (tp30) cc_final: 0.7687 (tp30) REVERT: B 286 MET cc_start: 0.7985 (mmt) cc_final: 0.7420 (mmt) REVERT: B 385 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7803 (tm-30) REVERT: B 643 ILE cc_start: 0.8251 (mm) cc_final: 0.7867 (mm) REVERT: B 703 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: C 42 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6486 (mp) REVERT: D 24 LYS cc_start: 0.8315 (mtmm) cc_final: 0.8059 (mtmm) REVERT: D 50 GLU cc_start: 0.8209 (tt0) cc_final: 0.7801 (tp30) REVERT: D 55 ARG cc_start: 0.7189 (tpt170) cc_final: 0.6436 (tpp-160) REVERT: D 65 MET cc_start: 0.6751 (ttt) cc_final: 0.6151 (ttp) REVERT: I 72 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8040 (mm) REVERT: I 77 TRP cc_start: 0.8582 (t-100) cc_final: 0.8184 (t-100) REVERT: I 88 LYS cc_start: 0.8047 (tptm) cc_final: 0.7587 (ttpp) REVERT: I 246 ARG cc_start: 0.7404 (mtt90) cc_final: 0.7006 (mtt90) REVERT: I 268 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8020 (mt0) REVERT: I 320 ASP cc_start: 0.8388 (t70) cc_final: 0.7871 (t0) REVERT: J 150 TYR cc_start: 0.8383 (m-80) cc_final: 0.7825 (m-80) REVERT: J 276 LEU cc_start: 0.7557 (tt) cc_final: 0.7341 (tt) REVERT: J 286 MET cc_start: 0.7684 (mmt) cc_final: 0.7374 (mmt) REVERT: J 308 SER cc_start: 0.8916 (t) cc_final: 0.8336 (p) REVERT: J 389 MET cc_start: 0.8059 (tmm) cc_final: 0.7455 (tmm) REVERT: J 703 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: L 47 GLU cc_start: 0.8571 (tm-30) cc_final: 0.7942 (tm-30) REVERT: L 55 ARG cc_start: 0.6643 (tpt170) cc_final: 0.6235 (tpp-160) REVERT: E 72 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8160 (mm) REVERT: E 88 LYS cc_start: 0.8235 (tptm) cc_final: 0.7629 (ttpp) REVERT: E 108 VAL cc_start: 0.8392 (t) cc_final: 0.8133 (m) REVERT: E 139 ASP cc_start: 0.7581 (m-30) cc_final: 0.7322 (m-30) REVERT: E 176 GLN cc_start: 0.8440 (tt0) cc_final: 0.8210 (tt0) REVERT: E 320 ASP cc_start: 0.8086 (t70) cc_final: 0.7646 (t0) REVERT: E 676 MET cc_start: 0.9095 (mtp) cc_final: 0.8840 (mtp) REVERT: F 150 TYR cc_start: 0.8224 (m-80) cc_final: 0.7963 (m-80) REVERT: F 156 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8389 (tp30) REVERT: F 205 GLU cc_start: 0.8302 (tp30) cc_final: 0.7798 (tp30) REVERT: F 415 MET cc_start: 0.8195 (mmt) cc_final: 0.7615 (mtp) REVERT: F 586 ASP cc_start: 0.8314 (p0) cc_final: 0.8008 (p0) REVERT: F 643 ILE cc_start: 0.8372 (mm) cc_final: 0.8025 (mm) REVERT: F 703 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: H 55 ARG cc_start: 0.7179 (tpt170) cc_final: 0.6674 (tpp-160) outliers start: 86 outliers final: 68 residues processed: 508 average time/residue: 0.1708 time to fit residues: 146.3029 Evaluate side-chains 509 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 434 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 570 MET Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 65 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 353 optimal weight: 0.2980 chunk 230 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 367 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 356 optimal weight: 0.9980 chunk 133 optimal weight: 0.0470 chunk 41 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 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 = 0.3859 r_free = 0.3859 target = 0.152048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122761 restraints weight = 46383.979| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.47 r_work: 0.3397 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 33297 Z= 0.111 Angle : 0.539 10.009 45204 Z= 0.271 Chirality : 0.041 0.222 5334 Planarity : 0.003 0.049 5640 Dihedral : 6.454 86.359 4644 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.98 % Allowed : 18.49 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.44 (0.14), residues: 4071 helix: 2.01 (0.10), residues: 2553 sheet: -0.01 (0.32), residues: 276 loop : -1.08 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 246 TYR 0.019 0.001 TYR B 288 PHE 0.029 0.001 PHE F 475 TRP 0.008 0.001 TRP L 23 HIS 0.003 0.000 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00246 (33297) covalent geometry : angle 0.53858 (45204) hydrogen bonds : bond 0.03590 ( 2031) hydrogen bonds : angle 3.58966 ( 5949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 455 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7378 (tm-30) REVERT: A 88 LYS cc_start: 0.8094 (tptm) cc_final: 0.7581 (ttpp) REVERT: A 139 ASP cc_start: 0.7445 (m-30) cc_final: 0.7171 (m-30) REVERT: A 204 PHE cc_start: 0.7599 (m-80) cc_final: 0.7173 (t80) REVERT: A 320 ASP cc_start: 0.8353 (t70) cc_final: 0.7900 (t0) REVERT: A 472 ASN cc_start: 0.7874 (t0) cc_final: 0.7534 (t0) REVERT: B 150 TYR cc_start: 0.8346 (m-80) cc_final: 0.7923 (m-10) REVERT: B 205 GLU cc_start: 0.8069 (tp30) cc_final: 0.7664 (tp30) REVERT: B 286 MET cc_start: 0.8029 (mmt) cc_final: 0.7525 (mmt) REVERT: B 643 ILE cc_start: 0.8171 (mm) cc_final: 0.7782 (mm) REVERT: B 703 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8246 (mp10) REVERT: C 42 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6338 (mp) REVERT: D 24 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7909 (mtmm) REVERT: D 50 GLU cc_start: 0.8054 (tt0) cc_final: 0.7715 (tp30) REVERT: D 55 ARG cc_start: 0.7080 (tpt170) cc_final: 0.5731 (ttp-170) REVERT: D 65 MET cc_start: 0.6692 (ttt) cc_final: 0.6114 (ttp) REVERT: I 72 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7968 (mm) REVERT: I 77 TRP cc_start: 0.8538 (t-100) cc_final: 0.8176 (t-100) REVERT: I 88 LYS cc_start: 0.8046 (tptm) cc_final: 0.7472 (ttpp) REVERT: I 175 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6506 (t80) REVERT: I 261 ILE cc_start: 0.7874 (mt) cc_final: 0.7630 (tt) REVERT: I 268 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8074 (mt0) REVERT: I 384 ILE cc_start: 0.7820 (mm) cc_final: 0.7614 (mt) REVERT: I 389 MET cc_start: 0.7284 (tmm) cc_final: 0.6997 (tmm) REVERT: I 570 MET cc_start: 0.7912 (ppp) cc_final: 0.7305 (ppp) REVERT: J 150 TYR cc_start: 0.8235 (m-80) cc_final: 0.7714 (m-80) REVERT: J 256 ARG cc_start: 0.8001 (mmp80) cc_final: 0.7723 (mmp80) REVERT: J 276 LEU cc_start: 0.7503 (tt) cc_final: 0.7267 (tt) REVERT: J 286 MET cc_start: 0.7653 (mmt) cc_final: 0.7323 (mmt) REVERT: J 308 SER cc_start: 0.8891 (t) cc_final: 0.8349 (p) REVERT: J 389 MET cc_start: 0.8047 (tmm) cc_final: 0.7454 (tmm) REVERT: J 549 LEU cc_start: 0.7923 (mt) cc_final: 0.7710 (mp) REVERT: J 703 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: L 47 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7927 (tm-30) REVERT: L 55 ARG cc_start: 0.6630 (tpt170) cc_final: 0.6186 (tpp-160) REVERT: E 72 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8066 (mm) REVERT: E 88 LYS cc_start: 0.8217 (tptm) cc_final: 0.7621 (ttpp) REVERT: E 108 VAL cc_start: 0.8426 (t) cc_final: 0.8161 (m) REVERT: E 139 ASP cc_start: 0.7562 (m-30) cc_final: 0.7300 (m-30) REVERT: E 320 ASP cc_start: 0.8036 (t70) cc_final: 0.7598 (t0) REVERT: E 676 MET cc_start: 0.9053 (mtp) cc_final: 0.8672 (mtm) REVERT: F 150 TYR cc_start: 0.8098 (m-80) cc_final: 0.7803 (m-80) REVERT: F 156 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8390 (tp30) REVERT: F 205 GLU cc_start: 0.8235 (tp30) cc_final: 0.7732 (tp30) REVERT: F 415 MET cc_start: 0.8150 (mmt) cc_final: 0.7606 (mtp) REVERT: F 586 ASP cc_start: 0.8294 (p0) cc_final: 0.8001 (p0) REVERT: F 643 ILE cc_start: 0.8335 (mm) cc_final: 0.7992 (mm) REVERT: F 703 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: H 55 ARG cc_start: 0.7113 (tpt170) cc_final: 0.6545 (tpp-160) outliers start: 70 outliers final: 55 residues processed: 505 average time/residue: 0.1740 time to fit residues: 146.9188 Evaluate side-chains 501 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 438 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 65 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 139 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 402 optimal weight: 3.9990 chunk 196 optimal weight: 0.4980 chunk 389 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 271 optimal weight: 0.8980 chunk 294 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 369 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 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 = 0.3849 r_free = 0.3849 target = 0.151209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.121629 restraints weight = 46423.707| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.48 r_work: 0.3374 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33297 Z= 0.124 Angle : 0.546 9.680 45204 Z= 0.275 Chirality : 0.041 0.222 5334 Planarity : 0.003 0.050 5640 Dihedral : 6.444 89.988 4644 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.01 % Allowed : 18.72 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.42 (0.14), residues: 4071 helix: 1.98 (0.10), residues: 2553 sheet: -0.02 (0.32), residues: 276 loop : -1.06 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 246 TYR 0.021 0.001 TYR B 288 PHE 0.024 0.001 PHE F 475 TRP 0.010 0.001 TRP A 431 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00286 (33297) covalent geometry : angle 0.54592 (45204) hydrogen bonds : bond 0.03680 ( 2031) hydrogen bonds : angle 3.60085 ( 5949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5829.08 seconds wall clock time: 101 minutes 7.90 seconds (6067.90 seconds total)