Starting phenix.real_space_refine on Thu May 29 21:22:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dck_27326/05_2025/8dck_27326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dck_27326/05_2025/8dck_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_27326/05_2025/8dck_27326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dck_27326/05_2025/8dck_27326.map" model { file = "/net/cci-nas-00/data/ceres_data/8dck_27326/05_2025/8dck_27326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dck_27326/05_2025/8dck_27326.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG: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, 'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG: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, 'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG: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: 17.21, per 1000 atoms: 0.53 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: 8.93 Conformation dependent library (CDL) restraints added in 4.4 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: 4.02 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: 13.42 Time building geometry restraints manager: 10.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7427 1.33 - 1.45: 6756 1.45 - 1.57: 18937 1.57 - 1.70: 33 1.70 - 1.82: 144 Bond restraints: 33297 Sorted by residual: bond pdb=" CA ARG A 246 " pdb=" C ARG A 246 " ideal model delta sigma weight residual 1.531 1.492 0.040 1.32e-02 5.74e+03 8.97e+00 bond pdb=" CA ARG I 246 " pdb=" C ARG I 246 " ideal model delta sigma weight residual 1.531 1.492 0.039 1.32e-02 5.74e+03 8.93e+00 bond pdb=" CA ARG E 246 " pdb=" C ARG E 246 " ideal model delta sigma weight residual 1.531 1.492 0.039 1.32e-02 5.74e+03 8.87e+00 bond pdb=" CA TYR A 9 " pdb=" C TYR A 9 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.16e-02 7.43e+03 8.80e+00 bond pdb=" CA TYR I 9 " pdb=" C TYR I 9 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.16e-02 7.43e+03 8.78e+00 ... (remaining 33292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 44787 3.13 - 6.25: 375 6.25 - 9.38: 36 9.38 - 12.51: 3 12.51 - 15.63: 3 Bond angle restraints: 45204 Sorted by residual: angle pdb=" CA GLU I 573 " pdb=" CB GLU I 573 " pdb=" CG GLU I 573 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.47e+01 angle pdb=" CA GLU A 573 " pdb=" CB GLU A 573 " pdb=" CG GLU A 573 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.47e+01 angle pdb=" CA GLU E 573 " pdb=" CB GLU E 573 " pdb=" CG GLU E 573 " ideal model delta sigma weight residual 114.10 125.88 -11.78 2.00e+00 2.50e-01 3.47e+01 angle pdb=" C LEU L 42 " pdb=" N PRO L 43 " pdb=" CA PRO L 43 " ideal model delta sigma weight residual 119.92 114.25 5.67 1.07e+00 8.73e-01 2.81e+01 angle pdb=" C LEU H 42 " pdb=" N PRO H 43 " pdb=" CA PRO H 43 " ideal model delta sigma weight residual 119.92 114.27 5.65 1.07e+00 8.73e-01 2.79e+01 ... (remaining 45199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 17924 17.45 - 34.89: 1662 34.89 - 52.34: 344 52.34 - 69.79: 74 69.79 - 87.23: 39 Dihedral angle restraints: 20043 sinusoidal: 8118 harmonic: 11925 Sorted by residual: dihedral pdb=" CA PHE A 264 " pdb=" C PHE A 264 " pdb=" N LEU A 265 " pdb=" CA LEU A 265 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE E 264 " pdb=" C PHE E 264 " pdb=" N LEU E 265 " pdb=" CA LEU E 265 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE I 264 " pdb=" C PHE I 264 " pdb=" N LEU I 265 " pdb=" CA LEU I 265 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 20040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4018 0.049 - 0.098: 1038 0.098 - 0.148: 266 0.148 - 0.197: 6 0.197 - 0.246: 6 Chirality restraints: 5334 Sorted by residual: chirality pdb=" CA VAL B 526 " pdb=" N VAL B 526 " pdb=" C VAL B 526 " pdb=" CB VAL B 526 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL J 526 " pdb=" N VAL J 526 " pdb=" C VAL J 526 " pdb=" CB VAL J 526 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL F 526 " pdb=" N VAL F 526 " pdb=" C VAL F 526 " pdb=" CB VAL F 526 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5331 not shown) Planarity restraints: 5640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 245 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C SER E 245 " -0.042 2.00e-02 2.50e+03 pdb=" O SER E 245 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG E 246 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 245 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C SER I 245 " 0.042 2.00e-02 2.50e+03 pdb=" O SER I 245 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG I 246 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 245 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C SER A 245 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 245 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 246 " 0.014 2.00e-02 2.50e+03 ... (remaining 5637 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 249 2.59 - 3.17: 27423 3.17 - 3.74: 53028 3.74 - 4.32: 68472 4.32 - 4.90: 114100 Nonbonded interactions: 263272 Sorted by model distance: nonbonded pdb=" OE1 GLN J 550 " pdb="MG MG J 802 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLN B 550 " pdb="MG MG B 802 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLN F 550 " pdb="MG MG F 802 " model vdw 2.013 2.170 nonbonded pdb=" O2B ATP F 801 " pdb="MG MG F 802 " model vdw 2.031 2.170 nonbonded pdb=" O2B ATP B 801 " pdb="MG MG B 802 " model vdw 2.031 2.170 ... (remaining 263267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.21 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.220 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: 1.160 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 70.810 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33297 Z= 0.200 Angle : 0.743 15.632 45204 Z= 0.415 Chirality : 0.045 0.246 5334 Planarity : 0.004 0.055 5640 Dihedral : 14.840 87.232 12315 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP E 394 HIS 0.002 0.000 HIS I 398 PHE 0.025 0.002 PHE B 188 TYR 0.022 0.002 TYR J 477 ARG 0.016 0.001 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.12997 ( 2031) hydrogen bonds : angle 5.46982 ( 5949) covalent geometry : bond 0.00358 (33297) covalent geometry : angle 0.74296 (45204) *********************** 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 : 3.592 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: 0.7578 (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: 0.4005 time to fit residues: 389.1453 Evaluate side-chains 412 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 207 optimal weight: 0.4980 chunk 163 optimal weight: 0.9990 chunk 317 optimal weight: 0.3980 chunk 122 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 367 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN ** I 516 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 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3904 r_free = 0.3904 target = 0.156144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126517 restraints weight = 45861.800| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.49 r_work: 0.3444 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1224 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= 0.133 Angle : 0.552 9.248 45204 Z= 0.286 Chirality : 0.041 0.201 5334 Planarity : 0.004 0.046 5640 Dihedral : 7.238 72.772 4644 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.30 % Allowed : 9.35 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.13), residues: 4071 helix: 1.37 (0.10), residues: 2529 sheet: -0.10 (0.32), residues: 276 loop : -1.20 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 394 HIS 0.003 0.001 HIS A 398 PHE 0.017 0.001 PHE F 475 TYR 0.022 0.001 TYR J 477 ARG 0.005 0.000 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 2031) hydrogen bonds : angle 4.12844 ( 5949) covalent geometry : bond 0.00299 (33297) covalent geometry : angle 0.55181 (45204) *********************** 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 510 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 464 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7043 (t80) cc_final: 0.6813 (t80) REVERT: A 139 ASP cc_start: 0.7257 (m-30) cc_final: 0.6857 (m-30) REVERT: A 246 ARG cc_start: 0.7408 (mmt90) cc_final: 0.7160 (mtp85) REVERT: A 263 ASN cc_start: 0.8816 (t0) cc_final: 0.8536 (t0) REVERT: A 320 ASP cc_start: 0.8290 (t70) cc_final: 0.7882 (t0) REVERT: A 471 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.6981 (mtt90) REVERT: A 648 MET cc_start: 0.8439 (mmt) cc_final: 0.8211 (mmt) REVERT: B 150 TYR cc_start: 0.8114 (m-80) cc_final: 0.7908 (m-10) REVERT: B 398 HIS cc_start: 0.5947 (t-90) cc_final: 0.5558 (t-170) REVERT: C 56 ARG cc_start: 0.5212 (mtt-85) cc_final: 0.4869 (ptp90) REVERT: D 65 MET cc_start: 0.6814 (ttt) cc_final: 0.6288 (ttp) REVERT: I 77 TRP cc_start: 0.8596 (t-100) cc_final: 0.8178 (t-100) REVERT: I 224 ASP cc_start: 0.8135 (t70) cc_final: 0.7753 (t0) REVERT: I 246 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7177 (mtt90) REVERT: I 263 ASN cc_start: 0.8837 (t0) cc_final: 0.8389 (t0) REVERT: I 475 PHE cc_start: 0.8807 (t80) cc_final: 0.8103 (t80) REVERT: I 645 MET cc_start: 0.8887 (mmp) cc_final: 0.8635 (mmm) REVERT: J 150 TYR cc_start: 0.7985 (m-80) cc_final: 0.7659 (m-80) REVERT: J 155 ILE cc_start: 0.8631 (mt) cc_final: 0.8396 (mm) REVERT: E 108 VAL cc_start: 0.8219 (t) cc_final: 0.7943 (m) REVERT: E 139 ASP cc_start: 0.7082 (m-30) cc_final: 0.6713 (m-30) REVERT: E 263 ASN cc_start: 0.8995 (t0) cc_final: 0.8588 (t0) REVERT: E 320 ASP cc_start: 0.7988 (t70) cc_final: 0.7601 (t0) REVERT: E 415 MET cc_start: 0.6674 (ptp) cc_final: 0.6190 (ptp) REVERT: E 648 MET cc_start: 0.8517 (tpt) cc_final: 0.8204 (mmt) REVERT: F 150 TYR cc_start: 0.8220 (m-80) cc_final: 0.7731 (m-80) REVERT: F 385 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8002 (tm-30) REVERT: F 598 ILE cc_start: 0.7427 (mm) cc_final: 0.7201 (mm) REVERT: H 47 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8104 (tm-30) REVERT: H 55 ARG cc_start: 0.6601 (tpt170) cc_final: 0.6310 (tpp-160) REVERT: H 65 MET cc_start: 0.6605 (ttt) cc_final: 0.6070 (ttp) outliers start: 46 outliers final: 38 residues processed: 491 average time/residue: 0.3957 time to fit residues: 326.4903 Evaluate side-chains 460 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 422 time to evaluate : 3.639 ------------------------------------------------------------------------------- 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 390 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 702 TYR 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 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 E residue 702 TYR 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 390 ILE 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 39 optimal weight: 9.9990 chunk 9 optimal weight: 0.0570 chunk 382 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 370 optimal weight: 0.6980 chunk 278 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 516 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 119 GLN E 330 GLN ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.155018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125585 restraints weight = 47347.699| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.52 r_work: 0.3424 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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= 0.112 Angle : 0.514 11.793 45204 Z= 0.261 Chirality : 0.040 0.164 5334 Planarity : 0.003 0.043 5640 Dihedral : 6.861 66.083 4644 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.07 % Allowed : 11.21 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.13), residues: 4071 helix: 1.63 (0.10), residues: 2547 sheet: -0.12 (0.32), residues: 276 loop : -1.17 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 394 HIS 0.002 0.000 HIS A 398 PHE 0.017 0.001 PHE E 84 TYR 0.016 0.001 TYR J 477 ARG 0.005 0.000 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 2031) hydrogen bonds : angle 3.84015 ( 5949) covalent geometry : bond 0.00246 (33297) covalent geometry : angle 0.51365 (45204) *********************** 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 551 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 478 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6697 (t80) cc_final: 0.6471 (t80) REVERT: A 139 ASP cc_start: 0.7339 (m-30) cc_final: 0.6942 (m-30) REVERT: A 320 ASP cc_start: 0.8337 (t70) cc_final: 0.7932 (t0) REVERT: A 471 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.7025 (mtt90) REVERT: B 150 TYR cc_start: 0.8206 (m-80) cc_final: 0.7911 (m-10) REVERT: B 167 PHE cc_start: 0.8120 (m-10) cc_final: 0.7798 (m-10) REVERT: B 205 GLU cc_start: 0.8002 (tp30) cc_final: 0.7601 (tp30) REVERT: B 286 MET cc_start: 0.7605 (mmt) cc_final: 0.7259 (mmt) REVERT: D 24 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8132 (mtmm) REVERT: D 65 MET cc_start: 0.6936 (ttt) cc_final: 0.6386 (ttp) REVERT: I 12 TYR cc_start: 0.7000 (t80) cc_final: 0.6797 (t80) REVERT: I 77 TRP cc_start: 0.8662 (t-100) cc_final: 0.8292 (t-100) REVERT: I 246 ARG cc_start: 0.7539 (mtt90) cc_final: 0.7162 (mtt90) REVERT: I 263 ASN cc_start: 0.8854 (t0) cc_final: 0.8413 (t0) REVERT: I 645 MET cc_start: 0.8936 (mmp) cc_final: 0.8678 (mmm) REVERT: J 150 TYR cc_start: 0.7952 (m-80) cc_final: 0.7633 (m-80) REVERT: J 155 ILE cc_start: 0.8744 (mt) cc_final: 0.8461 (mm) REVERT: J 156 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8211 (tp30) REVERT: J 549 LEU cc_start: 0.7855 (mt) cc_final: 0.7630 (mp) REVERT: J 592 ARG cc_start: 0.8195 (ttt-90) cc_final: 0.7947 (tmt170) REVERT: K 65 MET cc_start: 0.2702 (mmt) cc_final: 0.2452 (mtt) REVERT: E 108 VAL cc_start: 0.8462 (t) cc_final: 0.8171 (m) REVERT: E 139 ASP cc_start: 0.7249 (m-30) cc_final: 0.7015 (m-30) REVERT: E 263 ASN cc_start: 0.9025 (t0) cc_final: 0.8577 (t0) REVERT: E 320 ASP cc_start: 0.8110 (t70) cc_final: 0.7713 (t0) REVERT: E 415 MET cc_start: 0.6836 (ptp) cc_final: 0.6516 (ptp) REVERT: E 648 MET cc_start: 0.8533 (tpt) cc_final: 0.8281 (mmt) REVERT: E 676 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7836 (mtp) REVERT: F 150 TYR cc_start: 0.8163 (m-80) cc_final: 0.7594 (m-80) REVERT: F 156 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8290 (tp30) REVERT: F 385 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7936 (tm-30) REVERT: F 586 ASP cc_start: 0.8096 (p0) cc_final: 0.7815 (p0) REVERT: F 598 ILE cc_start: 0.7497 (mm) cc_final: 0.7286 (mm) REVERT: G 34 ARG cc_start: 0.7364 (mtm110) cc_final: 0.7138 (mtm110) REVERT: H 55 ARG cc_start: 0.6756 (tpt170) cc_final: 0.6390 (tpp-160) REVERT: H 65 MET cc_start: 0.6623 (ttt) cc_final: 0.6144 (ttp) outliers start: 73 outliers final: 49 residues processed: 529 average time/residue: 0.3858 time to fit residues: 339.9144 Evaluate side-chains 479 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 427 time to evaluate : 3.416 ------------------------------------------------------------------------------- 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 245 SER 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 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 B residue 703 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS 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 156 GLU Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 702 TYR Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 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 E residue 398 HIS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 99 optimal weight: 2.9990 chunk 324 optimal weight: 0.0870 chunk 168 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 275 optimal weight: 0.0070 chunk 393 optimal weight: 0.0470 chunk 129 optimal weight: 0.7980 chunk 362 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 379 optimal weight: 4.9990 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 516 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 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127628 restraints weight = 45841.128| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.48 r_work: 0.3444 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1815 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 : 0.507 10.716 45204 Z= 0.255 Chirality : 0.040 0.169 5334 Planarity : 0.003 0.040 5640 Dihedral : 6.724 66.109 4644 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.07 % Allowed : 12.86 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.14), residues: 4071 helix: 1.86 (0.10), residues: 2538 sheet: -0.04 (0.31), residues: 276 loop : -1.16 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 394 HIS 0.003 0.000 HIS A 398 PHE 0.017 0.001 PHE A 84 TYR 0.016 0.001 TYR B 477 ARG 0.006 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 2031) hydrogen bonds : angle 3.69287 ( 5949) covalent geometry : bond 0.00216 (33297) covalent geometry : angle 0.50654 (45204) *********************** 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 535 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 462 time to evaluate : 3.714 Fit side-chains revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6715 (t80) cc_final: 0.6488 (t80) REVERT: A 139 ASP cc_start: 0.7225 (m-30) cc_final: 0.6777 (m-30) REVERT: A 175 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6715 (t80) REVERT: A 204 PHE cc_start: 0.7692 (m-80) cc_final: 0.7102 (t80) REVERT: A 320 ASP cc_start: 0.8366 (t70) cc_final: 0.7921 (t0) REVERT: A 471 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7127 (mtt90) REVERT: B 150 TYR cc_start: 0.8150 (m-80) cc_final: 0.7867 (m-10) REVERT: B 167 PHE cc_start: 0.8042 (m-10) cc_final: 0.7832 (m-10) REVERT: B 205 GLU cc_start: 0.7908 (tp30) cc_final: 0.7546 (tp30) REVERT: B 286 MET cc_start: 0.7579 (mmt) cc_final: 0.7321 (mmt) REVERT: B 308 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 385 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 643 ILE cc_start: 0.7995 (mm) cc_final: 0.7600 (mm) REVERT: B 703 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: C 65 MET cc_start: 0.2712 (mmt) cc_final: 0.2335 (mtt) REVERT: D 24 LYS cc_start: 0.8340 (mtmm) cc_final: 0.8069 (mtmm) REVERT: D 65 MET cc_start: 0.6789 (ttt) cc_final: 0.6279 (ttp) REVERT: I 12 TYR cc_start: 0.6939 (t80) cc_final: 0.6728 (t80) REVERT: I 77 TRP cc_start: 0.8659 (t-100) cc_final: 0.8309 (t-100) REVERT: I 88 LYS cc_start: 0.7770 (tptm) cc_final: 0.7266 (ttpp) REVERT: I 246 ARG cc_start: 0.7338 (mtt90) cc_final: 0.7017 (mtt90) REVERT: I 261 ILE cc_start: 0.7764 (mt) cc_final: 0.7526 (tt) REVERT: I 263 ASN cc_start: 0.8848 (t0) cc_final: 0.8347 (t0) REVERT: I 268 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7670 (mt0) REVERT: J 150 TYR cc_start: 0.8015 (m-80) cc_final: 0.7670 (m-80) REVERT: J 155 ILE cc_start: 0.8759 (mt) cc_final: 0.8426 (mm) REVERT: J 167 PHE cc_start: 0.8053 (m-10) cc_final: 0.7805 (m-10) REVERT: J 262 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6958 (ttm110) REVERT: J 549 LEU cc_start: 0.7785 (mt) cc_final: 0.7514 (mp) REVERT: J 592 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.8005 (ttt-90) REVERT: J 648 MET cc_start: 0.7483 (tpp) cc_final: 0.6722 (tpp) REVERT: J 703 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8266 (mp10) REVERT: K 65 MET cc_start: 0.2624 (mmt) cc_final: 0.2376 (mtt) REVERT: E 72 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7847 (mm) REVERT: E 108 VAL cc_start: 0.8488 (t) cc_final: 0.8230 (m) REVERT: E 139 ASP cc_start: 0.7201 (m-30) cc_final: 0.6974 (m-30) REVERT: E 320 ASP cc_start: 0.7970 (t70) cc_final: 0.7564 (t0) REVERT: E 415 MET cc_start: 0.6568 (ptp) cc_final: 0.6359 (ptp) REVERT: E 541 LEU cc_start: 0.7739 (tt) cc_final: 0.7217 (tt) REVERT: F 150 TYR cc_start: 0.8090 (m-80) cc_final: 0.7673 (m-80) REVERT: F 385 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7835 (tm-30) REVERT: F 415 MET cc_start: 0.7789 (mmt) cc_final: 0.7341 (mtp) REVERT: F 477 TYR cc_start: 0.8400 (m-80) cc_final: 0.8162 (m-10) REVERT: F 586 ASP cc_start: 0.8104 (p0) cc_final: 0.7852 (p0) REVERT: F 703 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: H 55 ARG cc_start: 0.6671 (tpt170) cc_final: 0.6310 (tpp-160) outliers start: 73 outliers final: 50 residues processed: 514 average time/residue: 0.3911 time to fit residues: 337.1209 Evaluate side-chains 490 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 434 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain B residue 308 SER 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 535 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 398 HIS 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 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 702 TYR Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 13 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 220 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 676 MET 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 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 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 116 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 369 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 397 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 229 optimal weight: 0.9980 chunk 356 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 472 ASN ** E 516 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 = 0.3845 r_free = 0.3845 target = 0.150787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120873 restraints weight = 46389.603| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.49 r_work: 0.3361 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33297 Z= 0.153 Angle : 0.555 11.259 45204 Z= 0.282 Chirality : 0.042 0.190 5334 Planarity : 0.003 0.042 5640 Dihedral : 6.725 73.601 4644 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.52 % Allowed : 14.42 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.13), residues: 4071 helix: 1.74 (0.10), residues: 2550 sheet: -0.08 (0.31), residues: 276 loop : -1.16 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 431 HIS 0.004 0.001 HIS A 398 PHE 0.032 0.002 PHE A 475 TYR 0.015 0.001 TYR B 477 ARG 0.006 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 2031) hydrogen bonds : angle 3.78166 ( 5949) covalent geometry : bond 0.00362 (33297) covalent geometry : angle 0.55523 (45204) *********************** 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 560 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 471 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6755 (t80) cc_final: 0.6526 (t80) REVERT: A 139 ASP cc_start: 0.7320 (m-30) cc_final: 0.6884 (m-30) REVERT: A 175 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6691 (t80) REVERT: A 320 ASP cc_start: 0.8460 (t70) cc_final: 0.8015 (t0) REVERT: A 471 ARG cc_start: 0.7365 (mtm-85) cc_final: 0.7120 (mtt90) REVERT: A 475 PHE cc_start: 0.8799 (t80) cc_final: 0.8597 (t80) REVERT: A 570 MET cc_start: 0.7798 (ppp) cc_final: 0.6759 (ppp) REVERT: B 150 TYR cc_start: 0.8482 (m-80) cc_final: 0.8079 (m-10) REVERT: B 205 GLU cc_start: 0.7973 (tp30) cc_final: 0.7568 (tp30) REVERT: B 286 MET cc_start: 0.7675 (mmt) cc_final: 0.7413 (mmt) REVERT: B 385 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 475 PHE cc_start: 0.8527 (t80) cc_final: 0.8134 (t80) REVERT: B 592 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.7785 (tmt170) REVERT: B 643 ILE cc_start: 0.8134 (mm) cc_final: 0.7736 (mm) REVERT: B 703 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8139 (mp10) REVERT: C 42 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6578 (mp) REVERT: C 65 MET cc_start: 0.2566 (mmt) cc_final: 0.2139 (mtt) REVERT: D 24 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8166 (mtmm) REVERT: D 50 GLU cc_start: 0.7947 (tt0) cc_final: 0.7562 (tp30) REVERT: D 55 ARG cc_start: 0.7190 (tpt170) cc_final: 0.6445 (tpp-160) REVERT: D 65 MET cc_start: 0.6671 (ttt) cc_final: 0.6106 (ttp) REVERT: I 72 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8097 (mm) REVERT: I 77 TRP cc_start: 0.8703 (t-100) cc_final: 0.8199 (t-100) REVERT: I 88 LYS cc_start: 0.7924 (tptm) cc_final: 0.7461 (ttpp) REVERT: I 140 PHE cc_start: 0.7762 (m-10) cc_final: 0.7410 (m-10) REVERT: I 263 ASN cc_start: 0.9055 (t0) cc_final: 0.8571 (t0) REVERT: I 570 MET cc_start: 0.7925 (ppp) cc_final: 0.6729 (ppp) REVERT: J 150 TYR cc_start: 0.8268 (m-80) cc_final: 0.7744 (m-80) REVERT: J 167 PHE cc_start: 0.8200 (m-10) cc_final: 0.7911 (m-10) REVERT: J 286 MET cc_start: 0.7662 (mmt) cc_final: 0.7450 (mmt) REVERT: J 389 MET cc_start: 0.8019 (tmm) cc_final: 0.7417 (tmm) REVERT: J 592 ARG cc_start: 0.8330 (ttt-90) cc_final: 0.8054 (ttt-90) REVERT: J 648 MET cc_start: 0.7571 (tpp) cc_final: 0.7222 (tpt) REVERT: J 703 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8351 (mp10) REVERT: K 65 MET cc_start: 0.2594 (mmt) cc_final: 0.2353 (mtt) REVERT: L 55 ARG cc_start: 0.6740 (tpt170) cc_final: 0.6221 (tpp-160) REVERT: E 72 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8026 (mm) REVERT: E 108 VAL cc_start: 0.8591 (t) cc_final: 0.8321 (m) REVERT: E 139 ASP cc_start: 0.7414 (m-30) cc_final: 0.7158 (m-30) REVERT: E 320 ASP cc_start: 0.8052 (t70) cc_final: 0.7614 (t0) REVERT: E 541 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7378 (tt) REVERT: F 150 TYR cc_start: 0.8355 (m-80) cc_final: 0.8016 (m-80) REVERT: F 205 GLU cc_start: 0.8322 (tp30) cc_final: 0.7802 (tp30) REVERT: F 415 MET cc_start: 0.8013 (mmt) cc_final: 0.7499 (mtp) REVERT: F 586 ASP cc_start: 0.8321 (p0) cc_final: 0.8001 (p0) REVERT: G 34 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7164 (mtm-85) REVERT: H 47 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7852 (tm-30) REVERT: H 55 ARG cc_start: 0.6957 (tpt170) cc_final: 0.6506 (tpp-160) outliers start: 89 outliers final: 58 residues processed: 531 average time/residue: 0.3974 time to fit residues: 351.2028 Evaluate side-chains 505 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 440 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 245 SER 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 371 THR 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 C residue 42 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 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 441 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 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 501 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET 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 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 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 254 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 337 optimal weight: 0.9990 chunk 121 optimal weight: 0.0070 chunk 262 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 202 optimal weight: 0.0670 chunk 82 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 516 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.152186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122619 restraints weight = 46427.406| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.49 r_work: 0.3391 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2290 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= 0.113 Angle : 0.520 12.192 45204 Z= 0.264 Chirality : 0.041 0.206 5334 Planarity : 0.003 0.043 5640 Dihedral : 6.609 73.252 4644 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.24 % Allowed : 16.23 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.13), residues: 4071 helix: 1.89 (0.10), residues: 2556 sheet: -0.07 (0.31), residues: 276 loop : -1.17 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 394 HIS 0.005 0.001 HIS E 185 PHE 0.018 0.001 PHE I 84 TYR 0.012 0.001 TYR B 477 ARG 0.010 0.000 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 2031) hydrogen bonds : angle 3.65944 ( 5949) covalent geometry : bond 0.00254 (33297) covalent geometry : angle 0.52036 (45204) *********************** 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 551 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 472 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7389 (m-30) cc_final: 0.6928 (m-30) REVERT: A 175 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6706 (t80) REVERT: A 204 PHE cc_start: 0.7620 (m-80) cc_final: 0.7187 (t80) REVERT: A 320 ASP cc_start: 0.8381 (t70) cc_final: 0.7920 (t0) REVERT: A 384 ILE cc_start: 0.8061 (mm) cc_final: 0.7848 (mt) REVERT: A 471 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.7135 (mtt180) REVERT: A 472 ASN cc_start: 0.7873 (t0) cc_final: 0.7573 (t0) REVERT: A 475 PHE cc_start: 0.8737 (t80) cc_final: 0.8505 (t80) REVERT: A 570 MET cc_start: 0.7884 (ppp) cc_final: 0.7201 (ppp) REVERT: B 286 MET cc_start: 0.7678 (mmt) cc_final: 0.7361 (mmt) REVERT: B 385 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7904 (tm-30) REVERT: B 643 ILE cc_start: 0.8121 (mm) cc_final: 0.7718 (mm) REVERT: C 42 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6410 (mp) REVERT: C 65 MET cc_start: 0.2694 (mmt) cc_final: 0.2358 (mtt) REVERT: D 24 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8134 (mtmm) REVERT: D 50 GLU cc_start: 0.8084 (tt0) cc_final: 0.7747 (tp30) REVERT: D 55 ARG cc_start: 0.6938 (tpt170) cc_final: 0.6188 (tpp-160) REVERT: D 65 MET cc_start: 0.6786 (ttt) cc_final: 0.6213 (ttp) REVERT: I 72 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7981 (mm) REVERT: I 77 TRP cc_start: 0.8677 (t-100) cc_final: 0.8296 (t-100) REVERT: I 88 LYS cc_start: 0.7911 (tptm) cc_final: 0.7428 (ttpp) REVERT: I 140 PHE cc_start: 0.7718 (m-10) cc_final: 0.7340 (m-80) REVERT: I 246 ARG cc_start: 0.7396 (mtt90) cc_final: 0.7119 (mtt90) REVERT: I 261 ILE cc_start: 0.7908 (mt) cc_final: 0.7634 (tt) REVERT: I 263 ASN cc_start: 0.8926 (t0) cc_final: 0.8443 (t0) REVERT: I 268 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7855 (mt0) REVERT: I 389 MET cc_start: 0.7255 (tmm) cc_final: 0.7020 (tmm) REVERT: I 443 ARG cc_start: 0.8206 (mmp80) cc_final: 0.7787 (mmm160) REVERT: I 570 MET cc_start: 0.7892 (ppp) cc_final: 0.7039 (ppp) REVERT: J 150 TYR cc_start: 0.8171 (m-80) cc_final: 0.7672 (m-80) REVERT: J 167 PHE cc_start: 0.8211 (m-10) cc_final: 0.7920 (m-10) REVERT: J 276 LEU cc_start: 0.7559 (tt) cc_final: 0.7330 (tt) REVERT: J 286 MET cc_start: 0.7619 (mmt) cc_final: 0.7374 (mmt) REVERT: J 389 MET cc_start: 0.7984 (tmm) cc_final: 0.7386 (tmm) REVERT: J 549 LEU cc_start: 0.7791 (mt) cc_final: 0.7577 (mp) REVERT: J 592 ARG cc_start: 0.8305 (ttt-90) cc_final: 0.8103 (ttt-90) REVERT: J 648 MET cc_start: 0.7473 (tpp) cc_final: 0.7135 (tpt) REVERT: J 683 GLU cc_start: 0.7229 (mp0) cc_final: 0.6356 (mp0) REVERT: J 703 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: L 55 ARG cc_start: 0.6783 (tpt170) cc_final: 0.6167 (tpp-160) REVERT: E 72 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7949 (mm) REVERT: E 108 VAL cc_start: 0.8532 (t) cc_final: 0.8267 (m) REVERT: E 139 ASP cc_start: 0.7395 (m-30) cc_final: 0.7132 (m-30) REVERT: E 263 ASN cc_start: 0.9096 (t0) cc_final: 0.8710 (t0) REVERT: E 320 ASP cc_start: 0.7996 (t70) cc_final: 0.7566 (t0) REVERT: E 415 MET cc_start: 0.6763 (ptp) cc_final: 0.6305 (ptp) REVERT: E 541 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7149 (tt) REVERT: F 150 TYR cc_start: 0.8244 (m-80) cc_final: 0.7908 (m-80) REVERT: F 205 GLU cc_start: 0.8272 (tp30) cc_final: 0.7717 (tp30) REVERT: F 415 MET cc_start: 0.8035 (mmt) cc_final: 0.7510 (mtp) REVERT: F 477 TYR cc_start: 0.8398 (m-80) cc_final: 0.8186 (m-10) REVERT: F 586 ASP cc_start: 0.8299 (p0) cc_final: 0.7981 (p0) REVERT: F 703 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: H 11 PHE cc_start: 0.6249 (p90) cc_final: 0.6037 (p90) REVERT: H 47 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7787 (tm-30) REVERT: H 55 ARG cc_start: 0.6945 (tpt170) cc_final: 0.6401 (tpp-160) outliers start: 79 outliers final: 55 residues processed: 530 average time/residue: 0.4084 time to fit residues: 365.2565 Evaluate side-chains 503 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 441 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 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 B residue 202 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 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 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 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 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 219 optimal weight: 0.9980 chunk 287 optimal weight: 0.0570 chunk 172 optimal weight: 0.7980 chunk 331 optimal weight: 1.9990 chunk 284 optimal weight: 0.7980 chunk 387 optimal weight: 0.0670 chunk 100 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 361 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 GLN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.152887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123454 restraints weight = 46304.511| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.48 r_work: 0.3403 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2371 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= 0.109 Angle : 0.524 11.996 45204 Z= 0.264 Chirality : 0.041 0.229 5334 Planarity : 0.003 0.046 5640 Dihedral : 6.544 75.700 4644 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.21 % Allowed : 17.02 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.14), residues: 4071 helix: 2.00 (0.10), residues: 2553 sheet: 0.02 (0.31), residues: 276 loop : -1.10 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 23 HIS 0.002 0.000 HIS J 662 PHE 0.020 0.001 PHE F 413 TYR 0.018 0.001 TYR B 288 ARG 0.007 0.000 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 2031) hydrogen bonds : angle 3.60439 ( 5949) covalent geometry : bond 0.00240 (33297) covalent geometry : angle 0.52388 (45204) *********************** 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: 78 poor density : 469 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7419 (m-30) cc_final: 0.7029 (m-30) REVERT: A 204 PHE cc_start: 0.7621 (m-80) cc_final: 0.7129 (t80) REVERT: A 320 ASP cc_start: 0.8360 (t70) cc_final: 0.7867 (t0) REVERT: A 384 ILE cc_start: 0.8065 (mm) cc_final: 0.7863 (mt) REVERT: A 471 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.7005 (mtt180) REVERT: A 570 MET cc_start: 0.7851 (ppp) cc_final: 0.7256 (ppp) REVERT: B 205 GLU cc_start: 0.8062 (tp30) cc_final: 0.7644 (tp30) REVERT: B 385 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 643 ILE cc_start: 0.8113 (mm) cc_final: 0.7716 (mm) REVERT: B 703 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: C 42 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6368 (mp) REVERT: C 65 MET cc_start: 0.2655 (mmt) cc_final: 0.2347 (mtt) REVERT: D 24 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8145 (mtmm) REVERT: D 50 GLU cc_start: 0.8106 (tt0) cc_final: 0.7660 (tp30) REVERT: D 55 ARG cc_start: 0.6900 (tpt170) cc_final: 0.6220 (tpp-160) REVERT: D 65 MET cc_start: 0.6766 (ttt) cc_final: 0.6204 (ttp) REVERT: I 72 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7956 (mm) REVERT: I 77 TRP cc_start: 0.8642 (t-100) cc_final: 0.8291 (t-100) REVERT: I 88 LYS cc_start: 0.7925 (tptm) cc_final: 0.7439 (ttpp) REVERT: I 140 PHE cc_start: 0.7674 (m-10) cc_final: 0.7282 (m-80) REVERT: I 261 ILE cc_start: 0.7871 (mt) cc_final: 0.7608 (tt) REVERT: I 263 ASN cc_start: 0.8922 (t0) cc_final: 0.8434 (t0) REVERT: I 268 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7835 (mt0) REVERT: I 384 ILE cc_start: 0.7859 (mm) cc_final: 0.7630 (mt) REVERT: I 389 MET cc_start: 0.7248 (tmm) cc_final: 0.7000 (tmm) REVERT: I 443 ARG cc_start: 0.8156 (mmp80) cc_final: 0.7746 (mmm160) REVERT: I 570 MET cc_start: 0.7751 (ppp) cc_final: 0.7055 (ppp) REVERT: J 150 TYR cc_start: 0.8169 (m-80) cc_final: 0.7639 (m-80) REVERT: J 276 LEU cc_start: 0.7525 (tt) cc_final: 0.7301 (tt) REVERT: J 286 MET cc_start: 0.7612 (mmt) cc_final: 0.7329 (mmt) REVERT: J 549 LEU cc_start: 0.7819 (mt) cc_final: 0.7571 (mp) REVERT: J 592 ARG cc_start: 0.8345 (ttt-90) cc_final: 0.8126 (ttt-90) REVERT: J 648 MET cc_start: 0.7408 (tpp) cc_final: 0.7058 (tpt) REVERT: J 683 GLU cc_start: 0.7182 (mp0) cc_final: 0.6357 (mp0) REVERT: J 703 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: L 47 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7954 (tm-30) REVERT: L 55 ARG cc_start: 0.6724 (tpt170) cc_final: 0.6167 (tpp-160) REVERT: E 72 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8001 (mm) REVERT: E 108 VAL cc_start: 0.8521 (t) cc_final: 0.8240 (m) REVERT: E 139 ASP cc_start: 0.7468 (m-30) cc_final: 0.7193 (m-30) REVERT: E 263 ASN cc_start: 0.9089 (t0) cc_final: 0.8704 (t0) REVERT: E 320 ASP cc_start: 0.7980 (t70) cc_final: 0.7567 (t0) REVERT: E 415 MET cc_start: 0.6717 (ptp) cc_final: 0.6281 (ptp) REVERT: F 150 TYR cc_start: 0.8219 (m-80) cc_final: 0.7945 (m-80) REVERT: F 205 GLU cc_start: 0.8275 (tp30) cc_final: 0.7681 (tp30) REVERT: F 415 MET cc_start: 0.8121 (mmt) cc_final: 0.7603 (mtp) REVERT: F 477 TYR cc_start: 0.8385 (m-80) cc_final: 0.8163 (m-10) REVERT: F 586 ASP cc_start: 0.8266 (p0) cc_final: 0.7954 (p0) REVERT: F 703 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: G 34 ARG cc_start: 0.7581 (mtm110) cc_final: 0.7266 (mtm-85) REVERT: H 55 ARG cc_start: 0.6914 (tpt170) cc_final: 0.6426 (tpp-160) outliers start: 78 outliers final: 58 residues processed: 532 average time/residue: 0.4007 time to fit residues: 359.5111 Evaluate side-chains 503 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 439 time to evaluate : 3.626 ------------------------------------------------------------------------------- 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 180 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain I residue 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 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 147 ILE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 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 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 344 optimal weight: 10.0000 chunk 391 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 284 optimal weight: 0.6980 chunk 348 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 334 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.152118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122449 restraints weight = 46474.156| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.49 r_work: 0.3381 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2499 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= 0.125 Angle : 0.538 11.166 45204 Z= 0.271 Chirality : 0.041 0.223 5334 Planarity : 0.003 0.050 5640 Dihedral : 6.532 79.064 4644 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.46 % Allowed : 17.16 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.14), residues: 4071 helix: 1.96 (0.10), residues: 2553 sheet: -0.02 (0.31), residues: 279 loop : -1.09 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 431 HIS 0.003 0.001 HIS J 662 PHE 0.021 0.001 PHE B 413 TYR 0.018 0.001 TYR B 288 ARG 0.010 0.000 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 2031) hydrogen bonds : angle 3.62924 ( 5949) covalent geometry : bond 0.00289 (33297) covalent geometry : angle 0.53837 (45204) *********************** 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 537 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 450 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8040 (tptm) cc_final: 0.7504 (ttpp) REVERT: A 139 ASP cc_start: 0.7369 (m-30) cc_final: 0.6990 (m-30) REVERT: A 320 ASP cc_start: 0.8365 (t70) cc_final: 0.7886 (t0) REVERT: A 471 ARG cc_start: 0.7259 (mtm-85) cc_final: 0.7046 (mtt180) REVERT: A 472 ASN cc_start: 0.7920 (t0) cc_final: 0.7703 (t0) REVERT: A 570 MET cc_start: 0.7813 (ppp) cc_final: 0.7467 (ppp) REVERT: B 205 GLU cc_start: 0.8086 (tp30) cc_final: 0.7648 (tp30) REVERT: B 286 MET cc_start: 0.7902 (mmt) cc_final: 0.7460 (mmt) REVERT: B 385 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 592 ARG cc_start: 0.8179 (ttt-90) cc_final: 0.7901 (ttt-90) REVERT: B 643 ILE cc_start: 0.8145 (mm) cc_final: 0.7746 (mm) REVERT: B 703 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: C 42 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6394 (mp) REVERT: C 65 MET cc_start: 0.2514 (mmt) cc_final: 0.2253 (mtt) REVERT: D 24 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8157 (mtmm) REVERT: D 50 GLU cc_start: 0.8188 (tt0) cc_final: 0.7783 (tp30) REVERT: D 55 ARG cc_start: 0.6990 (tpt170) cc_final: 0.6318 (tpp-160) REVERT: D 65 MET cc_start: 0.6758 (ttt) cc_final: 0.6226 (ttp) REVERT: I 72 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7980 (mm) REVERT: I 77 TRP cc_start: 0.8645 (t-100) cc_final: 0.8289 (t-100) REVERT: I 88 LYS cc_start: 0.7993 (tptm) cc_final: 0.7528 (ttpp) REVERT: I 140 PHE cc_start: 0.7753 (m-10) cc_final: 0.7501 (m-80) REVERT: I 261 ILE cc_start: 0.7898 (mt) cc_final: 0.7629 (tt) REVERT: I 268 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7892 (mt0) REVERT: I 384 ILE cc_start: 0.7856 (mm) cc_final: 0.7626 (mt) REVERT: I 389 MET cc_start: 0.7253 (tmm) cc_final: 0.6987 (tmm) REVERT: I 443 ARG cc_start: 0.8241 (mmp80) cc_final: 0.7833 (mmm160) REVERT: I 570 MET cc_start: 0.7857 (ppp) cc_final: 0.7227 (ppp) REVERT: J 150 TYR cc_start: 0.8302 (m-80) cc_final: 0.7740 (m-80) REVERT: J 276 LEU cc_start: 0.7537 (tt) cc_final: 0.7311 (tt) REVERT: J 286 MET cc_start: 0.7653 (mmt) cc_final: 0.7372 (mmt) REVERT: J 389 MET cc_start: 0.8005 (tmm) cc_final: 0.7407 (tmm) REVERT: J 549 LEU cc_start: 0.7846 (mt) cc_final: 0.7583 (mp) REVERT: J 648 MET cc_start: 0.7480 (tpp) cc_final: 0.7132 (tpt) REVERT: J 683 GLU cc_start: 0.7068 (mp0) cc_final: 0.6290 (mp0) REVERT: J 703 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: L 47 GLU cc_start: 0.8578 (tm-30) cc_final: 0.7961 (tm-30) REVERT: L 54 SER cc_start: 0.7907 (OUTLIER) cc_final: 0.7624 (m) REVERT: L 55 ARG cc_start: 0.6593 (tpt170) cc_final: 0.6157 (tpp-160) REVERT: E 72 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8056 (mm) REVERT: E 108 VAL cc_start: 0.8549 (t) cc_final: 0.8270 (m) REVERT: E 139 ASP cc_start: 0.7482 (m-30) cc_final: 0.7201 (m-30) REVERT: E 261 ILE cc_start: 0.8143 (tt) cc_final: 0.7871 (pt) REVERT: E 320 ASP cc_start: 0.8056 (t70) cc_final: 0.7617 (t0) REVERT: E 415 MET cc_start: 0.6752 (ptp) cc_final: 0.6336 (ptp) REVERT: F 150 TYR cc_start: 0.8270 (m-80) cc_final: 0.8013 (m-80) REVERT: F 205 GLU cc_start: 0.8292 (tp30) cc_final: 0.7720 (tp30) REVERT: F 415 MET cc_start: 0.8182 (mmt) cc_final: 0.7620 (mtp) REVERT: F 477 TYR cc_start: 0.8343 (m-80) cc_final: 0.8116 (m-10) REVERT: F 586 ASP cc_start: 0.8284 (p0) cc_final: 0.7969 (p0) REVERT: F 703 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: G 34 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7379 (mtm-85) REVERT: H 55 ARG cc_start: 0.7067 (tpt170) cc_final: 0.6590 (tpp-160) outliers start: 87 outliers final: 67 residues processed: 520 average time/residue: 0.3965 time to fit residues: 345.2981 Evaluate side-chains 500 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 426 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 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 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 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 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET 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 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 0.0870 chunk 119 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.148782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118905 restraints weight = 46433.521| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.47 r_work: 0.3331 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33297 Z= 0.154 Angle : 0.571 9.797 45204 Z= 0.290 Chirality : 0.042 0.240 5334 Planarity : 0.004 0.052 5640 Dihedral : 6.598 84.298 4644 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.32 % Allowed : 17.87 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.13), residues: 4071 helix: 1.83 (0.10), residues: 2550 sheet: -0.13 (0.32), residues: 279 loop : -1.11 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 431 HIS 0.003 0.001 HIS A 32 PHE 0.021 0.002 PHE B 413 TYR 0.022 0.001 TYR B 288 ARG 0.011 0.000 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 2031) hydrogen bonds : angle 3.75591 ( 5949) covalent geometry : bond 0.00366 (33297) covalent geometry : angle 0.57141 (45204) *********************** 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 532 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 450 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8122 (tptm) cc_final: 0.7603 (ttpp) REVERT: A 139 ASP cc_start: 0.7493 (m-30) cc_final: 0.7116 (m-30) REVERT: A 204 PHE cc_start: 0.7605 (m-80) cc_final: 0.7361 (t80) REVERT: A 320 ASP cc_start: 0.8390 (t70) cc_final: 0.7958 (t0) REVERT: A 471 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.7118 (mtt180) REVERT: A 472 ASN cc_start: 0.7923 (t0) cc_final: 0.7681 (t0) REVERT: A 570 MET cc_start: 0.8012 (ppp) cc_final: 0.7693 (ppp) REVERT: B 205 GLU cc_start: 0.8120 (tp30) cc_final: 0.7640 (tp30) REVERT: B 286 MET cc_start: 0.8131 (mmt) cc_final: 0.7748 (mmt) REVERT: B 385 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 592 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.8013 (ttt-90) REVERT: B 643 ILE cc_start: 0.8298 (mm) cc_final: 0.7906 (mm) REVERT: B 703 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: C 42 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6644 (mp) REVERT: D 24 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8077 (mtmm) REVERT: D 47 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8336 (tm-30) REVERT: D 50 GLU cc_start: 0.8271 (tt0) cc_final: 0.7949 (tp30) REVERT: D 55 ARG cc_start: 0.7108 (tpt170) cc_final: 0.6357 (tpp-160) REVERT: D 65 MET cc_start: 0.6791 (ttt) cc_final: 0.6211 (ttp) REVERT: I 72 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8209 (mm) REVERT: I 77 TRP cc_start: 0.8629 (t-100) cc_final: 0.8099 (t-100) REVERT: I 88 LYS cc_start: 0.8105 (tptm) cc_final: 0.7689 (ttpp) REVERT: I 246 ARG cc_start: 0.7508 (mtt90) cc_final: 0.7118 (mtt90) REVERT: I 389 MET cc_start: 0.7425 (tmm) cc_final: 0.7147 (tmm) REVERT: I 443 ARG cc_start: 0.8327 (mmp80) cc_final: 0.7627 (mmm160) REVERT: I 472 ASN cc_start: 0.7751 (m-40) cc_final: 0.6775 (t160) REVERT: I 570 MET cc_start: 0.7715 (ppp) cc_final: 0.7241 (ppp) REVERT: J 150 TYR cc_start: 0.8423 (m-80) cc_final: 0.7823 (m-80) REVERT: J 276 LEU cc_start: 0.7585 (tt) cc_final: 0.7353 (tt) REVERT: J 286 MET cc_start: 0.7755 (mmt) cc_final: 0.7504 (mmt) REVERT: J 308 SER cc_start: 0.8871 (t) cc_final: 0.8262 (p) REVERT: J 389 MET cc_start: 0.8146 (tmm) cc_final: 0.7513 (tmm) REVERT: J 648 MET cc_start: 0.7669 (tpp) cc_final: 0.7302 (tpt) REVERT: J 683 GLU cc_start: 0.7031 (mp0) cc_final: 0.6286 (mp0) REVERT: J 703 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8009 (mp10) REVERT: L 47 GLU cc_start: 0.8621 (tm-30) cc_final: 0.7992 (tm-30) REVERT: L 55 ARG cc_start: 0.6693 (tpt170) cc_final: 0.6303 (tpp-160) REVERT: E 72 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8224 (mm) REVERT: E 108 VAL cc_start: 0.8410 (t) cc_final: 0.8137 (m) REVERT: E 139 ASP cc_start: 0.7499 (m-30) cc_final: 0.7266 (m-30) REVERT: E 320 ASP cc_start: 0.8117 (t70) cc_final: 0.7665 (t0) REVERT: F 415 MET cc_start: 0.8238 (mmt) cc_final: 0.7640 (mtp) REVERT: F 477 TYR cc_start: 0.8369 (m-80) cc_final: 0.8097 (m-10) REVERT: F 586 ASP cc_start: 0.8197 (p0) cc_final: 0.7857 (p0) REVERT: F 643 ILE cc_start: 0.8397 (mm) cc_final: 0.8053 (mm) REVERT: F 703 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: H 55 ARG cc_start: 0.7191 (tpt170) cc_final: 0.6639 (tpp-160) outliers start: 82 outliers final: 65 residues processed: 515 average time/residue: 0.4193 time to fit residues: 360.7289 Evaluate side-chains 502 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 431 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 180 ASP 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 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 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 447 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 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 421 VAL Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET 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 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 42 optimal weight: 0.8980 chunk 251 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 270 optimal weight: 8.9990 chunk 330 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 189 optimal weight: 0.0370 chunk 46 optimal weight: 0.5980 chunk 302 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119478 restraints weight = 46581.966| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.47 r_work: 0.3353 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2783 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= 0.130 Angle : 0.550 10.005 45204 Z= 0.279 Chirality : 0.041 0.231 5334 Planarity : 0.003 0.050 5640 Dihedral : 6.520 83.197 4644 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.10 % Allowed : 18.10 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4071 helix: 1.86 (0.10), residues: 2562 sheet: -0.15 (0.32), residues: 279 loop : -1.08 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 431 HIS 0.002 0.001 HIS J 218 PHE 0.020 0.001 PHE B 413 TYR 0.019 0.001 TYR B 288 ARG 0.010 0.000 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 2031) hydrogen bonds : angle 3.69616 ( 5949) covalent geometry : bond 0.00304 (33297) covalent geometry : angle 0.54989 (45204) ********************** 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 520 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 446 time to evaluate : 5.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8143 (tptm) cc_final: 0.7624 (ttpp) REVERT: A 139 ASP cc_start: 0.7574 (m-30) cc_final: 0.7207 (m-30) REVERT: A 204 PHE cc_start: 0.7504 (m-80) cc_final: 0.7148 (t80) REVERT: A 320 ASP cc_start: 0.8375 (t70) cc_final: 0.7929 (t0) REVERT: A 570 MET cc_start: 0.8001 (ppp) cc_final: 0.7657 (ppp) REVERT: B 205 GLU cc_start: 0.8072 (tp30) cc_final: 0.7617 (tp30) REVERT: B 286 MET cc_start: 0.8069 (mmt) cc_final: 0.7680 (mmt) REVERT: B 385 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7820 (tm-30) REVERT: B 592 ARG cc_start: 0.8309 (ttt-90) cc_final: 0.8005 (ttt-90) REVERT: B 643 ILE cc_start: 0.8249 (mm) cc_final: 0.7871 (mm) REVERT: C 42 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6480 (mp) REVERT: D 24 LYS cc_start: 0.8307 (mtmm) cc_final: 0.8041 (mtmm) REVERT: D 50 GLU cc_start: 0.8056 (tt0) cc_final: 0.7769 (tp30) REVERT: D 55 ARG cc_start: 0.7112 (tpt170) cc_final: 0.5765 (ttp-170) REVERT: D 65 MET cc_start: 0.6687 (ttt) cc_final: 0.6128 (ttp) REVERT: I 72 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8162 (mm) REVERT: I 77 TRP cc_start: 0.8640 (t-100) cc_final: 0.8124 (t-100) REVERT: I 88 LYS cc_start: 0.8030 (tptm) cc_final: 0.7558 (ttpp) REVERT: I 389 MET cc_start: 0.7273 (tmm) cc_final: 0.7019 (tmm) REVERT: I 443 ARG cc_start: 0.8281 (mmp80) cc_final: 0.7848 (mmm160) REVERT: I 570 MET cc_start: 0.7890 (ppp) cc_final: 0.7255 (ppp) REVERT: J 150 TYR cc_start: 0.8353 (m-80) cc_final: 0.7804 (m-80) REVERT: J 276 LEU cc_start: 0.7388 (tt) cc_final: 0.7145 (tt) REVERT: J 286 MET cc_start: 0.7741 (mmt) cc_final: 0.7466 (mmt) REVERT: J 308 SER cc_start: 0.8857 (t) cc_final: 0.8351 (p) REVERT: J 389 MET cc_start: 0.8065 (tmm) cc_final: 0.7454 (tmm) REVERT: J 549 LEU cc_start: 0.7942 (mt) cc_final: 0.7720 (mp) REVERT: J 648 MET cc_start: 0.7481 (tpp) cc_final: 0.7098 (tpt) REVERT: J 683 GLU cc_start: 0.7280 (mp0) cc_final: 0.6423 (mp0) REVERT: J 703 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: L 47 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7931 (tm-30) REVERT: L 55 ARG cc_start: 0.6677 (tpt170) cc_final: 0.6223 (tpp-160) REVERT: L 65 MET cc_start: 0.6044 (ttt) cc_final: 0.5565 (ttp) REVERT: E 72 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8147 (mm) REVERT: E 108 VAL cc_start: 0.8425 (t) cc_final: 0.8169 (m) REVERT: E 139 ASP cc_start: 0.7579 (m-30) cc_final: 0.7337 (m-30) REVERT: E 320 ASP cc_start: 0.8058 (t70) cc_final: 0.7609 (t0) REVERT: E 471 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.7069 (mtm-85) REVERT: F 205 GLU cc_start: 0.8351 (tp30) cc_final: 0.7861 (tp30) REVERT: F 415 MET cc_start: 0.8155 (mmt) cc_final: 0.7561 (mtp) REVERT: F 477 TYR cc_start: 0.8369 (m-80) cc_final: 0.8048 (m-10) REVERT: F 586 ASP cc_start: 0.8306 (p0) cc_final: 0.7982 (p0) REVERT: F 643 ILE cc_start: 0.8362 (mm) cc_final: 0.8029 (mm) REVERT: F 703 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: H 55 ARG cc_start: 0.7129 (tpt170) cc_final: 0.6553 (tpp-160) outliers start: 74 outliers final: 66 residues processed: 502 average time/residue: 0.4092 time to fit residues: 343.0937 Evaluate side-chains 503 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 432 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 535 LEU 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 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 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 442 THR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 703 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 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 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET 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 421 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 121 optimal weight: 0.7980 chunk 246 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 221 optimal weight: 0.0980 chunk 106 optimal weight: 0.9980 chunk 311 optimal weight: 0.0970 chunk 308 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 371 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122262 restraints weight = 46129.855| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.48 r_work: 0.3377 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2811 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= 0.116 Angle : 0.542 10.869 45204 Z= 0.274 Chirality : 0.041 0.214 5334 Planarity : 0.003 0.048 5640 Dihedral : 6.440 83.882 4644 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.01 % Allowed : 18.44 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.14), residues: 4071 helix: 1.99 (0.10), residues: 2553 sheet: -0.05 (0.32), residues: 276 loop : -1.05 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 23 HIS 0.002 0.000 HIS A 649 PHE 0.019 0.001 PHE I 99 TYR 0.021 0.001 TYR B 288 ARG 0.010 0.000 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 2031) hydrogen bonds : angle 3.61182 ( 5949) covalent geometry : bond 0.00263 (33297) covalent geometry : angle 0.54171 (45204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13609.98 seconds wall clock time: 237 minutes 10.64 seconds (14230.64 seconds total)