Starting phenix.real_space_refine on Mon Jul 6 04:09:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dck_27326/07_2026/8dck_27326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dck_27326/07_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_27326/07_2026/8dck_27326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dck_27326/07_2026/8dck_27326.map" model { file = "/net/cci-nas-00/data/ceres_data/8dck_27326/07_2026/8dck_27326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dck_27326/07_2026/8dck_27326.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dck_27326/07_2026/8dck_27326.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dck_27326/07_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-dev-6108/lib/python3.11/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: 6.44, per 1000 atoms: 0.20 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: 2.62 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: 1.04 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: 8.13 Time building geometry restraints manager: 3.48 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: 17879 17.45 - 34.89: 1593 34.89 - 52.34: 284 52.34 - 69.79: 65 69.79 - 87.23: 36 Dihedral angle restraints: 19857 sinusoidal: 7932 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 19854 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: 0.05 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.440 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 14.302 87.232 12129 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/Z covalent geometry : bond 0.00358 / 0.20 (33297) covalent geometry : angle 0.74296 / 0.41 (45204) hydrogen bonds : bond 0.12997 / 8.54 ( 2031) hydrogen bonds : angle 5.46982 / 3.96 ( 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 : 1.220 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: 171.4733 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 : 0.824 ------------------------------------------------------------------------------- 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... 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 = 0.156827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127404 restraints weight = 45921.196| |-----------------------------------------------------------------------------| r_work (start): 0.3590 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: 0.7678 moved from start: 0.1225 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= 0.117 Angle : 0.536 9.037 45204 Z= 0.277 Chirality : 0.041 0.196 5334 Planarity : 0.004 0.044 5640 Dihedral : 4.535 41.579 4458 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.25 % Allowed : 9.26 % Favored : 89.49 % 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: 1.41 (0.10), residues: 2532 sheet: -0.07 (0.32), residues: 276 loop : -1.18 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (33297) covalent geometry : angle 0.53597 / 0.28 (45204) hydrogen bonds : bond 0.04131 / 2.68 ( 2031) hydrogen bonds : angle 4.07811 / 2.94 ( 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 515 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 471 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6973 (t80) cc_final: 0.6734 (t80) REVERT: A 139 ASP cc_start: 0.7315 (m-30) cc_final: 0.6904 (m-30) REVERT: A 263 ASN cc_start: 0.8846 (t0) cc_final: 0.8555 (t0) REVERT: A 320 ASP cc_start: 0.8281 (t70) cc_final: 0.7876 (t0) REVERT: A 471 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.6899 (mtm-85) REVERT: A 527 LEU cc_start: 0.8269 (mp) cc_final: 0.7946 (mp) REVERT: B 150 TYR cc_start: 0.8062 (m-80) cc_final: 0.7796 (m-10) REVERT: B 398 HIS cc_start: 0.5978 (t-90) cc_final: 0.5470 (t-170) REVERT: I 77 TRP cc_start: 0.8599 (t-100) cc_final: 0.8219 (t-100) REVERT: I 224 ASP cc_start: 0.8112 (t70) cc_final: 0.7654 (t0) REVERT: I 246 ARG cc_start: 0.7514 (mtt90) cc_final: 0.7187 (mtt90) REVERT: I 263 ASN cc_start: 0.8836 (t0) cc_final: 0.8385 (t0) REVERT: I 278 PHE cc_start: 0.7563 (m-10) cc_final: 0.7200 (m-80) REVERT: I 475 PHE cc_start: 0.8796 (t80) cc_final: 0.8141 (t80) REVERT: J 150 TYR cc_start: 0.7809 (m-80) cc_final: 0.7526 (m-80) REVERT: J 155 ILE cc_start: 0.8689 (mt) cc_final: 0.8458 (mm) REVERT: E 108 VAL cc_start: 0.8254 (t) cc_final: 0.7993 (m) REVERT: E 139 ASP cc_start: 0.7011 (m-30) cc_final: 0.6642 (m-30) REVERT: E 263 ASN cc_start: 0.8986 (t0) cc_final: 0.8594 (t0) REVERT: E 320 ASP cc_start: 0.7998 (t70) cc_final: 0.7620 (t0) REVERT: E 415 MET cc_start: 0.6681 (ptp) cc_final: 0.6271 (ptp) REVERT: E 648 MET cc_start: 0.8499 (tpt) cc_final: 0.8206 (mmt) REVERT: F 150 TYR cc_start: 0.8169 (m-80) cc_final: 0.7658 (m-80) REVERT: F 268 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7512 (mm-40) REVERT: F 385 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8001 (tm-30) REVERT: F 398 HIS cc_start: 0.6243 (t-90) cc_final: 0.5836 (t-170) REVERT: F 598 ILE cc_start: 0.7439 (mm) cc_final: 0.7218 (mm) REVERT: H 47 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8110 (tm-30) REVERT: H 55 ARG cc_start: 0.6594 (tpt170) cc_final: 0.6333 (tpp-160) REVERT: H 65 MET cc_start: 0.6630 (ttt) cc_final: 0.6105 (ttp) outliers start: 44 outliers final: 33 residues processed: 497 average time/residue: 0.1684 time to fit residues: 141.0954 Evaluate side-chains 451 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 418 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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: 0.0060 chunk 150 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 363 optimal weight: 3.9990 chunk 401 optimal weight: 8.9990 chunk 191 optimal weight: 0.0770 chunk 138 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 217 optimal weight: 0.0040 overall best weight: 0.3166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3930 r_free = 0.3930 target = 0.158533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129235 restraints weight = 45718.303| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.48 r_work: 0.3469 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33297 Z= 0.103 Angle : 0.505 11.029 45204 Z= 0.255 Chirality : 0.040 0.159 5334 Planarity : 0.003 0.042 5640 Dihedral : 4.332 44.236 4458 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.90 % Allowed : 11.33 % Favored : 86.77 % 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: 1.11 (0.14), residues: 4071 helix: 1.73 (0.10), residues: 2538 sheet: -0.04 (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 I 246 TYR 0.014 0.001 TYR J 477 PHE 0.016 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/Z covalent geometry : bond 0.00217 / 0.10 (33297) covalent geometry : angle 0.50468 / 0.26 (45204) hydrogen bonds : bond 0.03731 / 2.43 ( 2031) hydrogen bonds : angle 3.78657 / 2.73 ( 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 538 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 471 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6717 (t80) cc_final: 0.6469 (t80) REVERT: A 139 ASP cc_start: 0.7382 (m-30) cc_final: 0.6954 (m-30) REVERT: A 263 ASN cc_start: 0.8856 (t0) cc_final: 0.8569 (t0) REVERT: A 278 PHE cc_start: 0.7629 (m-10) cc_final: 0.7212 (m-80) REVERT: A 320 ASP cc_start: 0.8288 (t70) cc_final: 0.7874 (t0) REVERT: B 150 TYR cc_start: 0.8060 (m-80) cc_final: 0.7710 (m-10) REVERT: B 167 PHE cc_start: 0.8032 (m-10) cc_final: 0.7747 (m-10) REVERT: B 205 GLU cc_start: 0.7966 (tp30) cc_final: 0.7576 (tp30) REVERT: B 286 MET cc_start: 0.7749 (mmt) cc_final: 0.7407 (mmt) REVERT: B 385 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8060 (tm-30) REVERT: B 643 ILE cc_start: 0.8013 (mm) cc_final: 0.7624 (mm) REVERT: C 65 MET cc_start: 0.2811 (mmt) cc_final: 0.2165 (mtt) REVERT: D 65 MET cc_start: 0.6767 (ttt) cc_final: 0.6220 (ttp) REVERT: I 77 TRP cc_start: 0.8618 (t-100) cc_final: 0.8248 (t-100) REVERT: I 224 ASP cc_start: 0.8029 (t70) cc_final: 0.7561 (t0) REVERT: I 246 ARG cc_start: 0.7394 (mtt90) cc_final: 0.7038 (mtt90) REVERT: I 261 ILE cc_start: 0.7872 (mt) cc_final: 0.7625 (tt) REVERT: I 263 ASN cc_start: 0.8821 (t0) cc_final: 0.8370 (t0) REVERT: I 268 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7630 (mt0) REVERT: J 150 TYR cc_start: 0.7963 (m-80) cc_final: 0.7724 (m-80) REVERT: J 155 ILE cc_start: 0.8681 (mt) cc_final: 0.8389 (mm) REVERT: J 205 GLU cc_start: 0.8055 (tp30) cc_final: 0.7755 (tp30) REVERT: J 549 LEU cc_start: 0.7729 (mt) cc_final: 0.7493 (mp) REVERT: J 592 ARG cc_start: 0.8087 (ttt-90) cc_final: 0.7663 (tmt170) REVERT: J 648 MET cc_start: 0.7423 (tpp) cc_final: 0.6617 (tpp) REVERT: K 65 MET cc_start: 0.2678 (mmt) cc_final: 0.2470 (mtt) REVERT: E 88 LYS cc_start: 0.7730 (tptm) cc_final: 0.7070 (ttpp) REVERT: E 108 VAL cc_start: 0.8451 (t) cc_final: 0.8200 (m) REVERT: E 139 ASP cc_start: 0.7164 (m-30) cc_final: 0.6918 (m-30) REVERT: E 263 ASN cc_start: 0.8967 (t0) cc_final: 0.8517 (t0) REVERT: E 320 ASP cc_start: 0.7988 (t70) cc_final: 0.7600 (t0) REVERT: E 415 MET cc_start: 0.6569 (ptp) cc_final: 0.6336 (ptp) REVERT: E 648 MET cc_start: 0.8466 (tpt) cc_final: 0.8189 (mmt) REVERT: F 150 TYR cc_start: 0.8036 (m-80) cc_final: 0.7407 (m-80) REVERT: F 205 GLU cc_start: 0.8063 (tp30) cc_final: 0.7583 (tp30) REVERT: F 385 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7976 (tm-30) REVERT: F 416 LEU cc_start: 0.8237 (mp) cc_final: 0.7975 (mm) REVERT: F 586 ASP cc_start: 0.8057 (p0) cc_final: 0.7786 (p0) REVERT: F 703 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: H 55 ARG cc_start: 0.6655 (tpt170) cc_final: 0.6305 (tpp-160) REVERT: H 65 MET cc_start: 0.6541 (ttt) cc_final: 0.6039 (ttp) outliers start: 67 outliers final: 39 residues processed: 518 average time/residue: 0.1697 time to fit residues: 148.5914 Evaluate side-chains 464 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 424 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 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 53 VAL 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 388 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 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 702 TYR 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 264 PHE Chi-restraints excluded: chain E residue 273 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 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 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 123 optimal weight: 0.1980 chunk 145 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 284 optimal weight: 0.8980 chunk 384 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122648 restraints weight = 46190.963| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.48 r_work: 0.3393 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1991 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= 0.138 Angle : 0.543 11.369 45204 Z= 0.274 Chirality : 0.041 0.172 5334 Planarity : 0.003 0.042 5640 Dihedral : 4.354 49.011 4458 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.55 % Allowed : 12.72 % Favored : 84.74 % 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: 1.11 (0.13), residues: 4071 helix: 1.72 (0.10), residues: 2553 sheet: -0.04 (0.31), residues: 276 loop : -1.15 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 262 TYR 0.015 0.001 TYR B 477 PHE 0.025 0.001 PHE A 84 TRP 0.012 0.001 TRP A 394 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (33297) covalent geometry : angle 0.54284 / 0.27 (45204) hydrogen bonds : bond 0.03987 / 2.62 ( 2031) hydrogen bonds : angle 3.76596 / 2.72 ( 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 565 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 475 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6753 (t80) cc_final: 0.6539 (t80) REVERT: A 139 ASP cc_start: 0.7312 (m-30) cc_final: 0.6864 (m-30) REVERT: A 263 ASN cc_start: 0.8746 (t0) cc_final: 0.8526 (t0) REVERT: A 320 ASP cc_start: 0.8369 (t70) cc_final: 0.7931 (t0) REVERT: A 471 ARG cc_start: 0.7418 (mtm-85) cc_final: 0.7123 (mtt90) REVERT: B 150 TYR cc_start: 0.8401 (m-80) cc_final: 0.7904 (m-10) REVERT: B 167 PHE cc_start: 0.8025 (m-10) cc_final: 0.7808 (m-10) REVERT: B 205 GLU cc_start: 0.7961 (tp30) cc_final: 0.7581 (tp30) REVERT: B 286 MET cc_start: 0.7724 (mmt) cc_final: 0.7475 (mmt) REVERT: B 592 ARG cc_start: 0.8002 (ttt-90) cc_final: 0.7658 (tmt170) REVERT: B 643 ILE cc_start: 0.8065 (mm) cc_final: 0.7672 (mm) REVERT: B 703 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8333 (mp10) REVERT: C 65 MET cc_start: 0.2618 (mmt) cc_final: 0.2171 (mtt) REVERT: D 24 LYS cc_start: 0.8312 (mtmm) cc_final: 0.8045 (mtmm) REVERT: D 55 ARG cc_start: 0.7038 (tpt170) cc_final: 0.6306 (tpp-160) REVERT: D 65 MET cc_start: 0.6806 (ttt) cc_final: 0.6219 (ttp) REVERT: I 77 TRP cc_start: 0.8665 (t-100) cc_final: 0.8286 (t-100) REVERT: I 88 LYS cc_start: 0.7837 (tptm) cc_final: 0.7349 (ttpp) REVERT: I 140 PHE cc_start: 0.7671 (m-10) cc_final: 0.7460 (m-10) REVERT: I 224 ASP cc_start: 0.8252 (t70) cc_final: 0.7868 (t0) REVERT: I 246 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7024 (mtt90) REVERT: I 263 ASN cc_start: 0.8973 (t0) cc_final: 0.8493 (t0) REVERT: I 270 LEU cc_start: 0.7850 (mt) cc_final: 0.7596 (mt) REVERT: I 320 ASP cc_start: 0.8388 (t70) cc_final: 0.7822 (t0) REVERT: J 150 TYR cc_start: 0.8156 (m-80) cc_final: 0.7672 (m-80) REVERT: J 167 PHE cc_start: 0.8025 (m-10) cc_final: 0.7792 (m-10) REVERT: J 389 MET cc_start: 0.7953 (tmm) cc_final: 0.7355 (tmm) REVERT: J 592 ARG cc_start: 0.8272 (ttt-90) cc_final: 0.7568 (tmt170) REVERT: K 65 MET cc_start: 0.2613 (mmt) cc_final: 0.2364 (mtt) REVERT: L 55 ARG cc_start: 0.6702 (tpt170) cc_final: 0.6134 (tpp-160) REVERT: E 88 LYS cc_start: 0.7804 (tptm) cc_final: 0.7163 (ttpp) REVERT: E 108 VAL cc_start: 0.8545 (t) cc_final: 0.8286 (m) REVERT: E 139 ASP cc_start: 0.7305 (m-30) cc_final: 0.7031 (m-30) REVERT: E 320 ASP cc_start: 0.8048 (t70) cc_final: 0.7605 (t0) REVERT: F 150 TYR cc_start: 0.8237 (m-80) cc_final: 0.7941 (m-80) REVERT: F 415 MET cc_start: 0.7791 (mmt) cc_final: 0.7298 (mtp) REVERT: F 586 ASP cc_start: 0.8232 (p0) cc_final: 0.7943 (p0) REVERT: F 592 ARG cc_start: 0.8404 (ttt-90) cc_final: 0.8171 (ttt-90) REVERT: F 643 ILE cc_start: 0.8263 (mm) cc_final: 0.7914 (mm) REVERT: F 703 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: H 29 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7853 (mp) REVERT: H 47 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8007 (tm-30) REVERT: H 55 ARG cc_start: 0.6744 (tpt170) cc_final: 0.6303 (tpp-160) outliers start: 90 outliers final: 61 residues processed: 538 average time/residue: 0.1667 time to fit residues: 151.2956 Evaluate side-chains 498 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 434 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 442 THR 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 702 TYR Chi-restraints excluded: chain B residue 703 GLN 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 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 245 SER Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 442 THR 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 86 LEU Chi-restraints excluded: chain E residue 180 ASP 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 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 424 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 535 LEU 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 29 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: 0.7980 chunk 90 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 390 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 348 optimal weight: 0.9990 chunk 263 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 228 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3865 r_free = 0.3865 target = 0.152619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122710 restraints weight = 46239.587| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.49 r_work: 0.3385 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2172 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= 0.124 Angle : 0.528 11.414 45204 Z= 0.266 Chirality : 0.041 0.203 5334 Planarity : 0.003 0.048 5640 Dihedral : 4.310 48.762 4458 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.21 % Allowed : 15.12 % Favored : 82.67 % 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: 1.22 (0.13), residues: 4071 helix: 1.82 (0.10), residues: 2559 sheet: -0.05 (0.31), residues: 276 loop : -1.16 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 256 TYR 0.019 0.001 TYR E 12 PHE 0.020 0.001 PHE I 84 TRP 0.010 0.001 TRP A 394 HIS 0.003 0.001 HIS J 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (33297) covalent geometry : angle 0.52831 / 0.27 (45204) hydrogen bonds : bond 0.03815 / 2.51 ( 2031) hydrogen bonds : angle 3.70694 / 2.68 ( 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 547 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 469 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6851 (t80) cc_final: 0.6634 (t80) REVERT: A 139 ASP cc_start: 0.7366 (m-30) cc_final: 0.6906 (m-30) REVERT: A 204 PHE cc_start: 0.7578 (m-80) cc_final: 0.7158 (t80) REVERT: A 263 ASN cc_start: 0.8777 (t0) cc_final: 0.8568 (t0) REVERT: A 320 ASP cc_start: 0.8399 (t70) cc_final: 0.7942 (t0) REVERT: A 384 ILE cc_start: 0.8068 (mm) cc_final: 0.7844 (mt) REVERT: A 471 ARG cc_start: 0.7397 (mtm-85) cc_final: 0.7161 (mtt90) REVERT: A 541 LEU cc_start: 0.7956 (tt) cc_final: 0.7613 (tt) REVERT: B 150 TYR cc_start: 0.8467 (m-80) cc_final: 0.7995 (m-10) REVERT: B 205 GLU cc_start: 0.8014 (tp30) cc_final: 0.7618 (tp30) REVERT: B 286 MET cc_start: 0.7749 (mmt) cc_final: 0.7479 (mmt) REVERT: B 592 ARG cc_start: 0.8181 (ttt-90) cc_final: 0.7797 (tmt170) REVERT: B 643 ILE cc_start: 0.8107 (mm) cc_final: 0.7711 (mm) REVERT: C 65 MET cc_start: 0.2572 (mmt) cc_final: 0.2065 (mtt) REVERT: D 24 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8093 (mtmm) REVERT: D 50 GLU cc_start: 0.7981 (tt0) cc_final: 0.7533 (tp30) REVERT: D 55 ARG cc_start: 0.7125 (tpt170) cc_final: 0.6388 (tpp-160) REVERT: D 65 MET cc_start: 0.6784 (ttt) cc_final: 0.6165 (ttp) REVERT: I 72 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7963 (mm) REVERT: I 77 TRP cc_start: 0.8703 (t-100) cc_final: 0.8380 (t-100) REVERT: I 88 LYS cc_start: 0.7909 (tptm) cc_final: 0.7445 (ttpp) REVERT: I 140 PHE cc_start: 0.7721 (m-10) cc_final: 0.7361 (m-10) REVERT: I 246 ARG cc_start: 0.7403 (mtt90) cc_final: 0.7037 (mtt90) REVERT: I 263 ASN cc_start: 0.9067 (t0) cc_final: 0.8602 (t0) REVERT: J 150 TYR cc_start: 0.8146 (m-80) cc_final: 0.7682 (m-80) REVERT: J 155 ILE cc_start: 0.8793 (mt) cc_final: 0.8466 (mm) REVERT: J 262 ARG cc_start: 0.7338 (ttp-110) cc_final: 0.7018 (ttm110) REVERT: J 389 MET cc_start: 0.7995 (tmm) cc_final: 0.7401 (tmm) REVERT: J 549 LEU cc_start: 0.7801 (mt) cc_final: 0.7570 (mp) REVERT: J 592 ARG cc_start: 0.8312 (ttt-90) cc_final: 0.8065 (ttt-90) REVERT: K 65 MET cc_start: 0.2543 (mmt) cc_final: 0.2323 (mtt) REVERT: L 55 ARG cc_start: 0.6801 (tpt170) cc_final: 0.6197 (tpp-160) REVERT: E 72 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7983 (mm) REVERT: E 88 LYS cc_start: 0.7924 (tptm) cc_final: 0.7287 (ttpp) REVERT: E 108 VAL cc_start: 0.8580 (t) cc_final: 0.8318 (m) REVERT: E 139 ASP cc_start: 0.7338 (m-30) cc_final: 0.7084 (m-30) REVERT: E 320 ASP cc_start: 0.8065 (t70) cc_final: 0.7626 (t0) REVERT: E 415 MET cc_start: 0.6743 (ptp) cc_final: 0.6334 (ptp) REVERT: E 541 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7164 (tt) REVERT: F 150 TYR cc_start: 0.8299 (m-80) cc_final: 0.7962 (m-80) REVERT: F 205 GLU cc_start: 0.8317 (tp30) cc_final: 0.7766 (tp30) REVERT: F 415 MET cc_start: 0.8005 (mmt) cc_final: 0.7490 (mtp) REVERT: F 477 TYR cc_start: 0.8466 (m-80) cc_final: 0.8218 (m-10) REVERT: F 586 ASP cc_start: 0.8326 (p0) cc_final: 0.8021 (p0) REVERT: F 643 ILE cc_start: 0.8270 (mm) cc_final: 0.7922 (mm) REVERT: F 703 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: H 29 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7914 (mp) REVERT: H 47 GLU cc_start: 0.8540 (tm-30) cc_final: 0.7962 (tm-30) REVERT: H 55 ARG cc_start: 0.6947 (tpt170) cc_final: 0.6392 (tpp-160) outliers start: 78 outliers final: 56 residues processed: 522 average time/residue: 0.1706 time to fit residues: 149.7653 Evaluate side-chains 499 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 438 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 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 C residue 37 ASP Chi-restraints excluded: chain D residue 53 VAL 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 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 209 SER 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 535 LEU 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 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 F residue 140 PHE 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 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 14 optimal weight: 0.6980 chunk 393 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 376 optimal weight: 1.9990 chunk 284 optimal weight: 0.5980 chunk 375 optimal weight: 4.9990 chunk 305 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 552 ASN ** 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 = 0.3847 r_free = 0.3847 target = 0.151035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120620 restraints weight = 47285.378| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.54 r_work: 0.3362 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33297 Z= 0.137 Angle : 0.542 11.223 45204 Z= 0.274 Chirality : 0.041 0.201 5334 Planarity : 0.003 0.053 5640 Dihedral : 4.325 49.718 4458 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.55 % Allowed : 16.11 % Favored : 81.34 % 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: 1.19 (0.13), residues: 4071 helix: 1.79 (0.10), residues: 2559 sheet: -0.10 (0.31), residues: 279 loop : -1.15 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 58 TYR 0.016 0.001 TYR E 12 PHE 0.033 0.001 PHE A 475 TRP 0.010 0.001 TRP A 431 HIS 0.005 0.001 HIS I 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (33297) covalent geometry : angle 0.54175 / 0.27 (45204) hydrogen bonds : bond 0.03908 / 2.57 ( 2031) hydrogen bonds : angle 3.72625 / 2.69 ( 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 542 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 452 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7347 (m-30) cc_final: 0.6905 (m-30) REVERT: A 204 PHE cc_start: 0.7595 (m-80) cc_final: 0.7062 (t80) REVERT: A 263 ASN cc_start: 0.8887 (t0) cc_final: 0.8685 (t0) REVERT: A 320 ASP cc_start: 0.8466 (t70) cc_final: 0.8013 (t0) REVERT: A 472 ASN cc_start: 0.7927 (t0) cc_final: 0.7633 (t0) REVERT: A 475 PHE cc_start: 0.8874 (t80) cc_final: 0.8641 (t80) REVERT: A 541 LEU cc_start: 0.7922 (tt) cc_final: 0.7534 (tt) REVERT: B 150 TYR cc_start: 0.8463 (m-80) cc_final: 0.8020 (m-10) REVERT: B 205 GLU cc_start: 0.8025 (tp30) cc_final: 0.7637 (tp30) REVERT: B 286 MET cc_start: 0.7802 (mmt) cc_final: 0.7395 (mmt) REVERT: B 592 ARG cc_start: 0.8212 (ttt-90) cc_final: 0.7990 (ttt-90) REVERT: B 643 ILE cc_start: 0.8160 (mm) cc_final: 0.7761 (mm) REVERT: C 65 MET cc_start: 0.3009 (mmt) cc_final: 0.2728 (mtt) REVERT: D 24 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8154 (mtmm) REVERT: D 50 GLU cc_start: 0.8043 (tt0) cc_final: 0.7581 (tp30) REVERT: D 55 ARG cc_start: 0.6980 (tpt170) cc_final: 0.6280 (tpp-160) REVERT: D 65 MET cc_start: 0.6772 (ttt) cc_final: 0.6145 (ttp) REVERT: I 72 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8077 (mm) REVERT: I 77 TRP cc_start: 0.8675 (t-100) cc_final: 0.8299 (t-100) REVERT: I 88 LYS cc_start: 0.7991 (tptm) cc_final: 0.7552 (ttpp) REVERT: I 140 PHE cc_start: 0.7772 (m-10) cc_final: 0.7389 (m-80) REVERT: I 570 MET cc_start: 0.7964 (ppp) cc_final: 0.6982 (ppp) REVERT: J 150 TYR cc_start: 0.8245 (m-80) cc_final: 0.7721 (m-80) REVERT: J 286 MET cc_start: 0.7670 (mmt) cc_final: 0.7319 (mmt) REVERT: J 389 MET cc_start: 0.8014 (tmm) cc_final: 0.7413 (tmm) REVERT: J 549 LEU cc_start: 0.7861 (mt) cc_final: 0.7577 (mp) REVERT: L 47 GLU cc_start: 0.8603 (tm-30) cc_final: 0.7988 (tm-30) REVERT: L 55 ARG cc_start: 0.6803 (tpt170) cc_final: 0.6176 (tpp-160) REVERT: E 72 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8037 (mm) REVERT: E 88 LYS cc_start: 0.7917 (tptm) cc_final: 0.7346 (ttpp) REVERT: E 108 VAL cc_start: 0.8577 (t) cc_final: 0.8323 (m) REVERT: E 139 ASP cc_start: 0.7445 (m-30) cc_final: 0.7174 (m-30) REVERT: E 175 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6914 (t80) REVERT: E 320 ASP cc_start: 0.8083 (t70) cc_final: 0.7641 (t0) REVERT: E 415 MET cc_start: 0.6795 (ptp) cc_final: 0.6349 (ptp) REVERT: E 541 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7154 (tt) REVERT: F 150 TYR cc_start: 0.8321 (m-80) cc_final: 0.8003 (m-80) REVERT: F 205 GLU cc_start: 0.8294 (tp30) cc_final: 0.7743 (tp30) REVERT: F 286 MET cc_start: 0.7335 (mmt) cc_final: 0.6953 (mmt) REVERT: F 415 MET cc_start: 0.8075 (mmt) cc_final: 0.7541 (mtp) REVERT: F 586 ASP cc_start: 0.8314 (p0) cc_final: 0.7995 (p0) REVERT: F 643 ILE cc_start: 0.8343 (mm) cc_final: 0.8003 (mm) REVERT: F 703 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: G 34 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7243 (mtm-85) REVERT: H 29 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7941 (mp) REVERT: H 47 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8317 (tm-30) REVERT: H 55 ARG cc_start: 0.6964 (tpt170) cc_final: 0.6410 (tpp-160) outliers start: 90 outliers final: 71 residues processed: 516 average time/residue: 0.1877 time to fit residues: 162.6748 Evaluate side-chains 504 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 427 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 330 GLN 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 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 371 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 442 THR 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 D residue 29 LEU Chi-restraints excluded: chain D residue 53 VAL 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 388 VAL 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 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 447 VAL Chi-restraints excluded: chain J residue 501 VAL 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 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 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 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain F residue 140 PHE 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 13 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 165 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 392 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 374 optimal weight: 7.9990 chunk 302 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 GLN ** 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 = 0.3820 r_free = 0.3820 target = 0.148564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118839 restraints weight = 46706.007| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.47 r_work: 0.3341 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33297 Z= 0.148 Angle : 0.552 9.830 45204 Z= 0.281 Chirality : 0.042 0.206 5334 Planarity : 0.003 0.050 5640 Dihedral : 4.365 49.343 4458 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.69 % Allowed : 16.96 % Favored : 80.35 % 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 (0.13), residues: 4071 helix: 1.78 (0.10), residues: 2556 sheet: -0.18 (0.31), residues: 279 loop : -1.16 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 592 TYR 0.020 0.001 TYR B 288 PHE 0.022 0.001 PHE A 475 TRP 0.013 0.001 TRP A 431 HIS 0.008 0.001 HIS E 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (33297) covalent geometry : angle 0.55160 / 0.28 (45204) hydrogen bonds : bond 0.04010 / 2.65 ( 2031) hydrogen bonds : angle 3.77762 / 2.74 ( 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 547 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 452 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7767 (mm) REVERT: A 139 ASP cc_start: 0.7456 (m-30) cc_final: 0.7063 (m-30) REVERT: A 263 ASN cc_start: 0.8903 (t0) cc_final: 0.8700 (t0) REVERT: A 320 ASP cc_start: 0.8461 (t70) cc_final: 0.8002 (t0) REVERT: A 471 ARG cc_start: 0.7346 (mtm-85) cc_final: 0.7094 (mtt90) REVERT: A 541 LEU cc_start: 0.7950 (tt) cc_final: 0.7541 (tt) REVERT: B 150 TYR cc_start: 0.8529 (m-80) cc_final: 0.8114 (m-10) REVERT: B 205 GLU cc_start: 0.8030 (tp30) cc_final: 0.7617 (tp30) REVERT: B 592 ARG cc_start: 0.8240 (ttt-90) cc_final: 0.7976 (ttt-90) REVERT: B 643 ILE cc_start: 0.8260 (mm) cc_final: 0.7874 (mm) REVERT: C 42 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6591 (mp) REVERT: D 24 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8250 (mtmm) REVERT: D 47 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8328 (tm-30) REVERT: D 50 GLU cc_start: 0.8197 (tt0) cc_final: 0.7877 (tp30) REVERT: D 55 ARG cc_start: 0.7199 (tpt170) cc_final: 0.6458 (tpp-160) REVERT: D 65 MET cc_start: 0.6772 (ttt) cc_final: 0.6158 (ttp) REVERT: I 72 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8182 (mm) REVERT: I 77 TRP cc_start: 0.8685 (t-100) cc_final: 0.8178 (t-100) REVERT: I 88 LYS cc_start: 0.8061 (tptm) cc_final: 0.7635 (ttpp) REVERT: I 140 PHE cc_start: 0.7828 (m-10) cc_final: 0.7487 (m-80) REVERT: I 246 ARG cc_start: 0.7519 (mtt90) cc_final: 0.7211 (mtt90) REVERT: I 389 MET cc_start: 0.7289 (tmm) cc_final: 0.7029 (tmm) REVERT: J 150 TYR cc_start: 0.8312 (m-80) cc_final: 0.7746 (m-80) REVERT: J 276 LEU cc_start: 0.7537 (tt) cc_final: 0.7314 (tt) REVERT: J 286 MET cc_start: 0.7694 (mmt) cc_final: 0.7382 (mmt) REVERT: J 308 SER cc_start: 0.8840 (t) cc_final: 0.8223 (p) REVERT: J 389 MET cc_start: 0.8060 (tmm) cc_final: 0.7450 (tmm) REVERT: J 549 LEU cc_start: 0.7910 (mt) cc_final: 0.7626 (mp) REVERT: L 55 ARG cc_start: 0.6645 (tpt170) cc_final: 0.6221 (tpp-160) REVERT: E 72 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8158 (mm) REVERT: E 88 LYS cc_start: 0.8233 (tptm) cc_final: 0.7640 (ttpp) REVERT: E 108 VAL cc_start: 0.8388 (t) cc_final: 0.8137 (m) REVERT: E 139 ASP cc_start: 0.7533 (m-30) cc_final: 0.7252 (m-30) REVERT: E 175 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6876 (t80) REVERT: E 320 ASP cc_start: 0.8089 (t70) cc_final: 0.7642 (t0) REVERT: E 541 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7086 (tt) REVERT: F 150 TYR cc_start: 0.8344 (m-80) cc_final: 0.8106 (m-80) REVERT: F 205 GLU cc_start: 0.8300 (tp30) cc_final: 0.7760 (tp30) REVERT: F 286 MET cc_start: 0.7400 (mmt) cc_final: 0.7010 (mmt) REVERT: F 415 MET cc_start: 0.8111 (mmt) cc_final: 0.7530 (mtp) REVERT: F 475 PHE cc_start: 0.8544 (t80) cc_final: 0.8290 (t80) REVERT: F 586 ASP cc_start: 0.8263 (p0) cc_final: 0.7919 (p0) REVERT: F 703 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: H 55 ARG cc_start: 0.7196 (tpt170) cc_final: 0.6630 (tpp-160) outliers start: 95 outliers final: 72 residues processed: 527 average time/residue: 0.1780 time to fit residues: 158.2405 Evaluate side-chains 500 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 421 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 330 GLN 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 371 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 442 THR 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 621 VAL 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 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 388 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 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 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 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 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 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain F residue 140 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 357 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 251 optimal weight: 0.6980 chunk 372 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 221 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3838 r_free = 0.3838 target = 0.150205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120639 restraints weight = 46328.291| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.47 r_work: 0.3359 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33297 Z= 0.125 Angle : 0.541 11.272 45204 Z= 0.273 Chirality : 0.041 0.242 5334 Planarity : 0.003 0.050 5640 Dihedral : 4.327 48.774 4458 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.69 % Allowed : 18.07 % Favored : 79.24 % 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: 1.27 (0.14), residues: 4071 helix: 1.87 (0.10), residues: 2553 sheet: -0.13 (0.31), residues: 279 loop : -1.11 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 592 TYR 0.022 0.001 TYR A 12 PHE 0.027 0.001 PHE I 99 TRP 0.009 0.001 TRP E 431 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (33297) covalent geometry : angle 0.54134 / 0.27 (45204) hydrogen bonds : bond 0.03853 / 2.54 ( 2031) hydrogen bonds : angle 3.71731 / 2.69 ( 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 556 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 461 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8091 (tptm) cc_final: 0.7552 (ttpp) REVERT: A 139 ASP cc_start: 0.7453 (m-30) cc_final: 0.7062 (m-30) REVERT: A 204 PHE cc_start: 0.7619 (m-80) cc_final: 0.7182 (t80) REVERT: A 263 ASN cc_start: 0.8896 (t0) cc_final: 0.8669 (t0) REVERT: A 320 ASP cc_start: 0.8442 (t70) cc_final: 0.7981 (t0) REVERT: A 471 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7087 (mtt180) REVERT: A 472 ASN cc_start: 0.7933 (t0) cc_final: 0.7710 (t0) REVERT: B 150 TYR cc_start: 0.8485 (m-80) cc_final: 0.8067 (m-10) REVERT: B 286 MET cc_start: 0.7874 (mmt) cc_final: 0.7461 (mmt) REVERT: B 592 ARG cc_start: 0.8252 (ttt-90) cc_final: 0.7971 (ttt-90) REVERT: B 643 ILE cc_start: 0.8246 (mm) cc_final: 0.7864 (mm) REVERT: C 42 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6501 (mp) REVERT: D 24 LYS cc_start: 0.8335 (mtmm) cc_final: 0.8060 (mtmm) REVERT: D 47 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8300 (tm-30) REVERT: D 50 GLU cc_start: 0.8232 (tt0) cc_final: 0.7839 (tp30) REVERT: D 55 ARG cc_start: 0.7168 (tpt170) cc_final: 0.6444 (tpp-160) REVERT: D 65 MET cc_start: 0.6681 (ttt) cc_final: 0.6095 (ttp) REVERT: I 72 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8154 (mm) REVERT: I 77 TRP cc_start: 0.8665 (t-100) cc_final: 0.8186 (t-100) REVERT: I 88 LYS cc_start: 0.8022 (tptm) cc_final: 0.7593 (ttpp) REVERT: I 140 PHE cc_start: 0.7805 (m-10) cc_final: 0.7470 (m-80) REVERT: I 246 ARG cc_start: 0.7359 (mtt90) cc_final: 0.7106 (mtt90) REVERT: I 268 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8020 (mt0) REVERT: I 384 ILE cc_start: 0.7877 (mm) cc_final: 0.7646 (mt) REVERT: I 389 MET cc_start: 0.7268 (tmm) cc_final: 0.7014 (tmm) REVERT: I 471 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.7132 (mtt90) REVERT: J 150 TYR cc_start: 0.8315 (m-80) cc_final: 0.7816 (m-80) REVERT: J 276 LEU cc_start: 0.7499 (tt) cc_final: 0.7269 (tt) REVERT: J 286 MET cc_start: 0.7722 (mmt) cc_final: 0.7387 (mmt) REVERT: J 308 SER cc_start: 0.8833 (t) cc_final: 0.8251 (p) REVERT: J 389 MET cc_start: 0.8059 (tmm) cc_final: 0.7456 (tmm) REVERT: J 549 LEU cc_start: 0.7887 (mt) cc_final: 0.7612 (mp) REVERT: J 683 GLU cc_start: 0.7013 (mp0) cc_final: 0.6245 (mp0) REVERT: L 55 ARG cc_start: 0.6619 (tpt170) cc_final: 0.6189 (tpp-160) REVERT: E 72 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8140 (mm) REVERT: E 88 LYS cc_start: 0.8232 (tptm) cc_final: 0.7631 (ttpp) REVERT: E 108 VAL cc_start: 0.8389 (t) cc_final: 0.8138 (m) REVERT: E 139 ASP cc_start: 0.7572 (m-30) cc_final: 0.7300 (m-30) REVERT: E 320 ASP cc_start: 0.8069 (t70) cc_final: 0.7619 (t0) REVERT: F 205 GLU cc_start: 0.8283 (tp30) cc_final: 0.7721 (tp30) REVERT: F 286 MET cc_start: 0.7373 (mmt) cc_final: 0.7003 (mmt) REVERT: F 415 MET cc_start: 0.8107 (mmt) cc_final: 0.7524 (mtp) REVERT: F 586 ASP cc_start: 0.8338 (p0) cc_final: 0.8010 (p0) REVERT: F 703 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: H 55 ARG cc_start: 0.7053 (tpt170) cc_final: 0.6475 (tpp-160) outliers start: 95 outliers final: 76 residues processed: 535 average time/residue: 0.1838 time to fit residues: 165.3538 Evaluate side-chains 515 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 435 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 330 GLN 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 179 MET 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 442 THR 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 621 VAL 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 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 388 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 147 ILE 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 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 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 180 ASP 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 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain F residue 140 PHE 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 535 LEU Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 682 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 9 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 290 optimal weight: 0.5980 chunk 348 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 243 optimal weight: 0.0770 chunk 229 optimal weight: 0.7980 chunk 395 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 360 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 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 = 0.3828 r_free = 0.3828 target = 0.149363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119654 restraints weight = 46364.469| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.48 r_work: 0.3345 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2793 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= 0.139 Angle : 0.563 10.423 45204 Z= 0.284 Chirality : 0.042 0.228 5334 Planarity : 0.003 0.050 5640 Dihedral : 4.353 49.165 4458 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.55 % Allowed : 18.55 % Favored : 78.90 % 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: 1.24 (0.13), residues: 4071 helix: 1.85 (0.10), residues: 2550 sheet: -0.18 (0.31), residues: 279 loop : -1.12 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 592 TYR 0.021 0.001 TYR B 288 PHE 0.024 0.001 PHE I 99 TRP 0.011 0.001 TRP A 431 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (33297) covalent geometry : angle 0.56284 / 0.28 (45204) hydrogen bonds : bond 0.03924 / 2.59 ( 2031) hydrogen bonds : angle 3.74098 / 2.71 ( 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 538 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 448 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8118 (tptm) cc_final: 0.7586 (ttpp) REVERT: A 139 ASP cc_start: 0.7526 (m-30) cc_final: 0.7123 (m-30) REVERT: A 204 PHE cc_start: 0.7626 (m-80) cc_final: 0.7120 (t80) REVERT: A 263 ASN cc_start: 0.8922 (t0) cc_final: 0.8717 (t0) REVERT: A 320 ASP cc_start: 0.8438 (t70) cc_final: 0.7976 (t0) REVERT: A 471 ARG cc_start: 0.7298 (mtm-85) cc_final: 0.6879 (mtt180) REVERT: A 472 ASN cc_start: 0.7902 (t0) cc_final: 0.7647 (t0) REVERT: B 150 TYR cc_start: 0.8533 (m-80) cc_final: 0.8140 (m-10) REVERT: B 205 GLU cc_start: 0.8097 (tp30) cc_final: 0.7704 (tp30) REVERT: B 286 MET cc_start: 0.8021 (mmt) cc_final: 0.7664 (mmt) REVERT: B 592 ARG cc_start: 0.8314 (ttt-90) cc_final: 0.8022 (ttt-90) REVERT: B 643 ILE cc_start: 0.8272 (mm) cc_final: 0.7895 (mm) REVERT: C 42 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6444 (mp) REVERT: D 24 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8064 (mtmm) REVERT: D 47 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8318 (tm-30) REVERT: D 50 GLU cc_start: 0.8218 (tt0) cc_final: 0.7858 (tp30) REVERT: D 55 ARG cc_start: 0.7031 (tpt170) cc_final: 0.5624 (ttp-170) REVERT: D 65 MET cc_start: 0.6715 (ttt) cc_final: 0.6113 (ttp) REVERT: I 72 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8173 (mm) REVERT: I 77 TRP cc_start: 0.8636 (t-100) cc_final: 0.8154 (t-100) REVERT: I 88 LYS cc_start: 0.8050 (tptm) cc_final: 0.7517 (ttpp) REVERT: I 140 PHE cc_start: 0.7841 (m-10) cc_final: 0.7505 (m-80) REVERT: I 175 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6503 (t80) REVERT: I 246 ARG cc_start: 0.7454 (mtt90) cc_final: 0.7194 (mtt90) REVERT: I 268 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8038 (mt0) REVERT: I 389 MET cc_start: 0.7303 (tmm) cc_final: 0.7060 (tmm) REVERT: I 472 ASN cc_start: 0.7778 (m-40) cc_final: 0.6829 (t160) REVERT: J 150 TYR cc_start: 0.8363 (m-80) cc_final: 0.7786 (m-80) REVERT: J 276 LEU cc_start: 0.7515 (tt) cc_final: 0.7281 (tt) REVERT: J 286 MET cc_start: 0.7745 (mmt) cc_final: 0.7406 (mmt) REVERT: J 308 SER cc_start: 0.8862 (t) cc_final: 0.8357 (p) REVERT: J 389 MET cc_start: 0.8073 (tmm) cc_final: 0.7470 (tmm) REVERT: L 55 ARG cc_start: 0.6680 (tpt170) cc_final: 0.6245 (tpp-160) REVERT: E 72 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8169 (mm) REVERT: E 88 LYS cc_start: 0.8267 (tptm) cc_final: 0.7676 (ttpp) REVERT: E 108 VAL cc_start: 0.8422 (t) cc_final: 0.8167 (m) REVERT: E 139 ASP cc_start: 0.7594 (m-30) cc_final: 0.7330 (m-30) REVERT: E 175 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6866 (t80) REVERT: E 180 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6737 (m-30) REVERT: E 320 ASP cc_start: 0.8077 (t70) cc_final: 0.7636 (t0) REVERT: F 205 GLU cc_start: 0.8277 (tp30) cc_final: 0.7746 (tp30) REVERT: F 415 MET cc_start: 0.8102 (mmt) cc_final: 0.7502 (mtp) REVERT: F 586 ASP cc_start: 0.8331 (p0) cc_final: 0.8004 (p0) REVERT: F 703 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: H 55 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6658 (tpp-160) outliers start: 90 outliers final: 76 residues processed: 515 average time/residue: 0.1904 time to fit residues: 163.8916 Evaluate side-chains 517 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 434 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 330 GLN 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 179 MET Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 209 SER 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 442 THR 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 621 VAL Chi-restraints excluded: chain B residue 666 THR 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 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 388 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 147 ILE 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 535 LEU 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 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 180 ASP 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 F residue 140 PHE 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 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 13 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 353 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 367 optimal weight: 0.9990 chunk 286 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 133 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3843 r_free = 0.3843 target = 0.150619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120991 restraints weight = 46372.316| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.48 r_work: 0.3365 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33297 Z= 0.123 Angle : 0.553 10.094 45204 Z= 0.278 Chirality : 0.041 0.221 5334 Planarity : 0.003 0.050 5640 Dihedral : 4.308 48.395 4458 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.29 % Allowed : 18.89 % Favored : 78.82 % 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: 1.93 (0.10), residues: 2550 sheet: -0.08 (0.32), residues: 276 loop : -1.09 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 246 TYR 0.020 0.001 TYR A 12 PHE 0.030 0.001 PHE I 99 TRP 0.009 0.001 TRP L 23 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (33297) covalent geometry : angle 0.55338 / 0.28 (45204) hydrogen bonds : bond 0.03761 / 2.49 ( 2031) hydrogen bonds : angle 3.68438 / 2.66 ( 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 539 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 458 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8148 (tptm) cc_final: 0.7591 (ttpp) REVERT: A 139 ASP cc_start: 0.7520 (m-30) cc_final: 0.7241 (m-30) REVERT: A 204 PHE cc_start: 0.7612 (m-80) cc_final: 0.7081 (t80) REVERT: A 263 ASN cc_start: 0.8927 (t0) cc_final: 0.8717 (t0) REVERT: A 320 ASP cc_start: 0.8434 (t70) cc_final: 0.7961 (t0) REVERT: A 471 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.7029 (mtt180) REVERT: A 472 ASN cc_start: 0.7902 (t0) cc_final: 0.7660 (t0) REVERT: B 150 TYR cc_start: 0.8450 (m-80) cc_final: 0.8042 (m-10) REVERT: B 205 GLU cc_start: 0.8114 (tp30) cc_final: 0.7684 (tp30) REVERT: B 286 MET cc_start: 0.8194 (mmt) cc_final: 0.7856 (mmt) REVERT: B 592 ARG cc_start: 0.8302 (ttt-90) cc_final: 0.8006 (ttt-90) REVERT: B 643 ILE cc_start: 0.8256 (mm) cc_final: 0.7881 (mm) REVERT: C 42 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6356 (mp) REVERT: D 24 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8041 (mtmm) REVERT: D 47 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8297 (tm-30) REVERT: D 50 GLU cc_start: 0.8100 (tt0) cc_final: 0.7749 (tp30) REVERT: D 55 ARG cc_start: 0.6897 (tpt170) cc_final: 0.5752 (ttp-170) REVERT: D 65 MET cc_start: 0.6691 (ttt) cc_final: 0.6094 (ttp) REVERT: I 72 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8107 (mm) REVERT: I 77 TRP cc_start: 0.8608 (t-100) cc_final: 0.8079 (t-100) REVERT: I 88 LYS cc_start: 0.8044 (tptm) cc_final: 0.7484 (ttpp) REVERT: I 140 PHE cc_start: 0.7804 (m-10) cc_final: 0.7477 (m-80) REVERT: I 175 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6500 (t80) REVERT: I 246 ARG cc_start: 0.7375 (mtt90) cc_final: 0.7148 (mtt90) REVERT: I 268 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8076 (mt0) REVERT: I 384 ILE cc_start: 0.7866 (mm) cc_final: 0.7637 (mt) REVERT: I 389 MET cc_start: 0.7293 (tmm) cc_final: 0.7064 (tmm) REVERT: I 472 ASN cc_start: 0.7682 (m-40) cc_final: 0.6701 (t160) REVERT: J 150 TYR cc_start: 0.8301 (m-80) cc_final: 0.7790 (m-80) REVERT: J 276 LEU cc_start: 0.7518 (tt) cc_final: 0.7280 (tt) REVERT: J 286 MET cc_start: 0.7734 (mmt) cc_final: 0.7395 (mmt) REVERT: J 308 SER cc_start: 0.8934 (t) cc_final: 0.8363 (p) REVERT: J 389 MET cc_start: 0.8023 (tmm) cc_final: 0.7422 (tmm) REVERT: J 549 LEU cc_start: 0.7952 (mt) cc_final: 0.7739 (mp) REVERT: L 55 ARG cc_start: 0.6699 (tpt170) cc_final: 0.6236 (tpp-160) REVERT: E 72 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8136 (mm) REVERT: E 88 LYS cc_start: 0.8268 (tptm) cc_final: 0.7694 (ttpp) REVERT: E 108 VAL cc_start: 0.8421 (t) cc_final: 0.8162 (m) REVERT: E 139 ASP cc_start: 0.7610 (m-30) cc_final: 0.7343 (m-30) REVERT: E 180 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: E 186 ARG cc_start: 0.6184 (mmm160) cc_final: 0.5880 (mmm160) REVERT: E 320 ASP cc_start: 0.8068 (t70) cc_final: 0.7617 (t0) REVERT: F 205 GLU cc_start: 0.8326 (tp30) cc_final: 0.7824 (tp30) REVERT: F 286 MET cc_start: 0.7545 (mmt) cc_final: 0.7094 (mmt) REVERT: F 570 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7083 (ptt) REVERT: F 586 ASP cc_start: 0.8316 (p0) cc_final: 0.8001 (p0) REVERT: F 643 ILE cc_start: 0.8365 (mm) cc_final: 0.8015 (mm) REVERT: F 703 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: H 55 ARG cc_start: 0.7124 (tpt170) cc_final: 0.6544 (tpp-160) outliers start: 81 outliers final: 69 residues processed: 519 average time/residue: 0.1860 time to fit residues: 161.2394 Evaluate side-chains 520 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 444 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 330 GLN 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 179 MET Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 209 SER 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 442 THR 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 621 VAL 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 147 ILE 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 535 LEU 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 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 180 ASP 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 F residue 140 PHE 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 447 VAL Chi-restraints excluded: chain F residue 535 LEU 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 13 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 139 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 402 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 389 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 271 optimal weight: 0.0770 chunk 294 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 369 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 703 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.151125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121507 restraints weight = 46308.191| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.49 r_work: 0.3368 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2867 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 : 0.551 9.908 45204 Z= 0.277 Chirality : 0.041 0.220 5334 Planarity : 0.003 0.049 5640 Dihedral : 4.282 48.663 4458 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.27 % Allowed : 19.09 % Favored : 78.65 % 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: 1.39 (0.14), residues: 4071 helix: 1.97 (0.10), residues: 2550 sheet: -0.08 (0.32), residues: 276 loop : -1.07 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 256 TYR 0.024 0.001 TYR A 12 PHE 0.032 0.001 PHE I 99 TRP 0.008 0.001 TRP L 23 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (33297) covalent geometry : angle 0.55130 / 0.28 (45204) hydrogen bonds : bond 0.03708 / 2.45 ( 2031) hydrogen bonds : angle 3.65393 / 2.64 ( 5949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6086.94 seconds wall clock time: 105 minutes 50.71 seconds (6350.71 seconds total)