Starting phenix.real_space_refine on Sat Jun 28 05:10:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dck_27326/06_2025/8dck_27326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dck_27326/06_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_27326/06_2025/8dck_27326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dck_27326/06_2025/8dck_27326.map" model { file = "/net/cci-nas-00/data/ceres_data/8dck_27326/06_2025/8dck_27326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dck_27326/06_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-5710/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: 18.95, per 1000 atoms: 0.58 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: 9.02 Conformation dependent library (CDL) restraints added in 4.5 seconds 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 21 sheets defined 67.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.14 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: 13.77 Time building geometry restraints manager: 10.68 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: 0.22 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: 2.200 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: 1.430 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 76.690 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.200 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.880 ------------------------------------------------------------------------------- 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 : 3.710 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: 0.4062 time to fit residues: 394.8016 Evaluate side-chains 413 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 3.595 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN 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 119 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 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 = 0.3895 r_free = 0.3895 target = 0.155310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125725 restraints weight = 45830.117| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.47 r_work: 0.3431 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.137 Angle : 0.556 8.921 45204 Z= 0.288 Chirality : 0.041 0.197 5334 Planarity : 0.004 0.046 5640 Dihedral : 7.193 71.539 4644 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.44 % Allowed : 9.43 % Favored : 89.12 % 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: 0.67 (0.13), residues: 4071 helix: 1.33 (0.10), residues: 2541 sheet: -0.11 (0.32), residues: 276 loop : -1.22 (0.18), residues: 1254 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 0.023 0.001 TYR J 477 ARG 0.005 0.000 ARG B 426 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 2031) hydrogen bonds : angle 4.11338 ( 5949) covalent geometry : bond 0.00313 (33297) covalent geometry : angle 0.55598 (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 521 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 470 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7040 (t80) cc_final: 0.6814 (t80) REVERT: A 139 ASP cc_start: 0.7267 (m-30) cc_final: 0.6876 (m-30) REVERT: A 263 ASN cc_start: 0.8925 (t0) cc_final: 0.8653 (t0) REVERT: A 320 ASP cc_start: 0.8330 (t70) cc_final: 0.7914 (t0) REVERT: A 471 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.6907 (mtt90) REVERT: A 648 MET cc_start: 0.8445 (mmt) cc_final: 0.8225 (mmt) REVERT: B 150 TYR cc_start: 0.8033 (m-80) cc_final: 0.7816 (m-10) REVERT: B 398 HIS cc_start: 0.5955 (t-90) cc_final: 0.5558 (t-170) REVERT: C 56 ARG cc_start: 0.5229 (mtt-85) cc_final: 0.4884 (ptp90) REVERT: D 65 MET cc_start: 0.6820 (ttt) cc_final: 0.6279 (ttp) REVERT: I 77 TRP cc_start: 0.8617 (t-100) cc_final: 0.8189 (t-100) REVERT: I 224 ASP cc_start: 0.8164 (t70) cc_final: 0.7781 (t0) REVERT: I 246 ARG cc_start: 0.7531 (mtt90) cc_final: 0.7130 (mtt90) REVERT: I 263 ASN cc_start: 0.8843 (t0) cc_final: 0.8392 (t0) REVERT: I 475 PHE cc_start: 0.8826 (t80) cc_final: 0.8132 (t80) REVERT: I 645 MET cc_start: 0.8906 (mmp) cc_final: 0.8661 (mmm) REVERT: J 150 TYR cc_start: 0.7875 (m-80) cc_final: 0.7600 (m-80) REVERT: J 155 ILE cc_start: 0.8637 (mt) cc_final: 0.8393 (mm) REVERT: J 549 LEU cc_start: 0.7741 (mt) cc_final: 0.7508 (mp) REVERT: J 592 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7834 (tmt170) REVERT: E 108 VAL cc_start: 0.8261 (t) cc_final: 0.8006 (m) REVERT: E 139 ASP cc_start: 0.7102 (m-30) cc_final: 0.6724 (m-30) REVERT: E 263 ASN cc_start: 0.9015 (t0) cc_final: 0.8596 (t0) REVERT: E 320 ASP cc_start: 0.7997 (t70) cc_final: 0.7606 (t0) REVERT: E 648 MET cc_start: 0.8534 (tpt) cc_final: 0.8269 (mmt) REVERT: F 150 TYR cc_start: 0.8204 (m-80) cc_final: 0.7659 (m-80) REVERT: F 586 ASP cc_start: 0.8182 (p0) cc_final: 0.7822 (p0) REVERT: F 598 ILE cc_start: 0.7428 (mm) cc_final: 0.7200 (mm) REVERT: H 47 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8062 (tm-30) REVERT: H 55 ARG cc_start: 0.6628 (tpt170) cc_final: 0.6320 (tpp-160) REVERT: H 65 MET cc_start: 0.6596 (ttt) cc_final: 0.6061 (ttp) outliers start: 51 outliers final: 41 residues processed: 501 average time/residue: 0.4125 time to fit residues: 344.8903 Evaluate side-chains 466 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 425 time to evaluate : 4.057 ------------------------------------------------------------------------------- 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 371 THR Chi-restraints excluded: chain B residue 375 THR 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 442 THR 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 390 ILE 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 48 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: 4.9990 chunk 9 optimal weight: 0.8980 chunk 382 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 370 optimal weight: 0.5980 chunk 278 optimal weight: 6.9990 chunk 90 optimal weight: 0.0870 chunk 145 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** A 539 ASN ** 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 ** 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 = 0.3878 r_free = 0.3878 target = 0.153476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123894 restraints weight = 47320.732| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.54 r_work: 0.3414 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.114 Angle : 0.517 12.297 45204 Z= 0.263 Chirality : 0.040 0.164 5334 Planarity : 0.003 0.044 5640 Dihedral : 6.899 65.930 4644 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.04 % Allowed : 11.36 % Favored : 86.60 % 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 (0.14), residues: 4071 helix: 1.62 (0.10), residues: 2535 sheet: -0.12 (0.32), residues: 276 loop : -1.14 (0.18), residues: 1260 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 0.016 0.001 PHE E 84 TYR 0.015 0.001 TYR J 477 ARG 0.007 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 2031) hydrogen bonds : angle 3.86526 ( 5949) covalent geometry : bond 0.00251 (33297) covalent geometry : angle 0.51706 (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 540 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 468 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6765 (t80) cc_final: 0.6510 (t80) REVERT: A 139 ASP cc_start: 0.7391 (m-30) cc_final: 0.6982 (m-30) REVERT: A 320 ASP cc_start: 0.8335 (t70) cc_final: 0.7930 (t0) REVERT: A 471 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.6984 (mtt90) REVERT: B 150 TYR cc_start: 0.8202 (m-80) cc_final: 0.7963 (m-10) REVERT: B 167 PHE cc_start: 0.8058 (m-10) cc_final: 0.7742 (m-10) REVERT: B 205 GLU cc_start: 0.7997 (tp30) cc_final: 0.7596 (tp30) REVERT: B 286 MET cc_start: 0.7799 (mmt) cc_final: 0.7434 (mmt) REVERT: B 385 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 703 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8327 (mp10) REVERT: D 24 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8062 (mtmm) REVERT: D 65 MET cc_start: 0.6819 (ttt) cc_final: 0.6280 (ttp) REVERT: I 77 TRP cc_start: 0.8669 (t-100) cc_final: 0.8323 (t-100) REVERT: I 140 PHE cc_start: 0.7554 (m-10) cc_final: 0.7264 (m-10) REVERT: I 246 ARG cc_start: 0.7516 (mtt90) cc_final: 0.7100 (mtt90) REVERT: I 263 ASN cc_start: 0.8838 (t0) cc_final: 0.8382 (t0) REVERT: I 645 MET cc_start: 0.8973 (mmp) cc_final: 0.8679 (mmm) REVERT: J 150 TYR cc_start: 0.7966 (m-80) cc_final: 0.7643 (m-80) REVERT: J 155 ILE cc_start: 0.8659 (mt) cc_final: 0.8381 (mm) REVERT: J 156 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: J 205 GLU cc_start: 0.7929 (tp30) cc_final: 0.7677 (tp30) REVERT: J 549 LEU cc_start: 0.7807 (mt) cc_final: 0.7564 (mp) REVERT: J 592 ARG cc_start: 0.8216 (ttt-90) cc_final: 0.7930 (tmt170) REVERT: K 65 MET cc_start: 0.2677 (mmt) cc_final: 0.2403 (mtt) REVERT: E 108 VAL cc_start: 0.8491 (t) cc_final: 0.8231 (m) REVERT: E 139 ASP cc_start: 0.7298 (m-30) cc_final: 0.7039 (m-30) REVERT: E 320 ASP cc_start: 0.8077 (t70) cc_final: 0.7671 (t0) REVERT: E 415 MET cc_start: 0.6817 (ptp) cc_final: 0.6365 (ptp) REVERT: E 648 MET cc_start: 0.8534 (tpt) cc_final: 0.8286 (mmt) REVERT: F 150 TYR cc_start: 0.8200 (m-80) cc_final: 0.7608 (m-80) REVERT: F 156 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8256 (tp30) REVERT: F 586 ASP cc_start: 0.8126 (p0) cc_final: 0.7847 (p0) REVERT: F 598 ILE cc_start: 0.7454 (mm) cc_final: 0.7235 (mm) REVERT: F 703 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8224 (mp10) REVERT: H 55 ARG cc_start: 0.6737 (tpt170) cc_final: 0.6337 (tpp-160) REVERT: H 65 MET cc_start: 0.6545 (ttt) cc_final: 0.6068 (ttp) outliers start: 72 outliers final: 51 residues processed: 517 average time/residue: 0.4747 time to fit residues: 418.4858 Evaluate side-chains 487 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 432 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 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 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 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 29 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 220 THR 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 I residue 620 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 702 TYR 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 220 THR 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 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 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: 1.9990 chunk 324 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 393 optimal weight: 0.0170 chunk 129 optimal weight: 0.6980 chunk 362 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 379 optimal weight: 4.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 330 GLN ** E 516 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 = 0.3882 r_free = 0.3882 target = 0.154238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124642 restraints weight = 46144.968| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.48 r_work: 0.3409 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.117 Angle : 0.516 10.558 45204 Z= 0.262 Chirality : 0.041 0.168 5334 Planarity : 0.003 0.042 5640 Dihedral : 6.752 67.285 4644 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.27 % Allowed : 13.31 % Favored : 84.42 % 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: 1.16 (0.14), residues: 4071 helix: 1.77 (0.10), residues: 2538 sheet: -0.08 (0.31), residues: 276 loop : -1.13 (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 0.021 0.001 PHE A 84 TYR 0.015 0.001 TYR J 477 ARG 0.006 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 2031) hydrogen bonds : angle 3.74414 ( 5949) covalent geometry : bond 0.00258 (33297) covalent geometry : angle 0.51628 (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 548 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 468 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6719 (t80) cc_final: 0.6506 (t80) REVERT: A 139 ASP cc_start: 0.7290 (m-30) cc_final: 0.6863 (m-30) REVERT: A 320 ASP cc_start: 0.8355 (t70) cc_final: 0.7924 (t0) REVERT: A 471 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.7046 (mtt90) REVERT: B 150 TYR cc_start: 0.8249 (m-80) cc_final: 0.7691 (m-10) REVERT: B 167 PHE cc_start: 0.8061 (m-10) cc_final: 0.7857 (m-10) REVERT: B 205 GLU cc_start: 0.7945 (tp30) cc_final: 0.7557 (tp30) REVERT: B 286 MET cc_start: 0.7709 (mmt) cc_final: 0.7355 (mmt) REVERT: B 385 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 643 ILE cc_start: 0.8058 (mm) cc_final: 0.7661 (mm) REVERT: B 703 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8313 (mp10) REVERT: C 65 MET cc_start: 0.3016 (mmt) cc_final: 0.2646 (mtt) REVERT: D 24 LYS cc_start: 0.8337 (mtmm) cc_final: 0.8060 (mtmm) REVERT: D 55 ARG cc_start: 0.7057 (tpt170) cc_final: 0.6340 (tpp-160) REVERT: D 65 MET cc_start: 0.6817 (ttt) cc_final: 0.6301 (ttp) REVERT: I 72 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7950 (mm) REVERT: I 77 TRP cc_start: 0.8666 (t-100) cc_final: 0.8321 (t-100) REVERT: I 246 ARG cc_start: 0.7414 (mtt90) cc_final: 0.7040 (mtt90) REVERT: I 263 ASN cc_start: 0.8962 (t0) cc_final: 0.8485 (t0) REVERT: I 268 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7702 (mt0) REVERT: I 645 MET cc_start: 0.9022 (mmp) cc_final: 0.8800 (mmm) REVERT: J 150 TYR cc_start: 0.8009 (m-80) cc_final: 0.7595 (m-80) REVERT: J 155 ILE cc_start: 0.8775 (mt) cc_final: 0.8460 (mm) REVERT: J 167 PHE cc_start: 0.8081 (m-10) cc_final: 0.7827 (m-10) REVERT: J 205 GLU cc_start: 0.8076 (tp30) cc_final: 0.7863 (tm-30) REVERT: J 549 LEU cc_start: 0.7822 (mt) cc_final: 0.7535 (mp) REVERT: J 592 ARG cc_start: 0.8228 (ttt-90) cc_final: 0.7570 (tmt170) REVERT: K 65 MET cc_start: 0.2651 (mmt) cc_final: 0.2379 (mtt) REVERT: L 55 ARG cc_start: 0.6721 (tpt170) cc_final: 0.6172 (tpp-160) REVERT: E 72 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7973 (mm) REVERT: E 108 VAL cc_start: 0.8546 (t) cc_final: 0.8288 (m) REVERT: E 139 ASP cc_start: 0.7278 (m-30) cc_final: 0.7037 (m-30) REVERT: E 320 ASP cc_start: 0.8026 (t70) cc_final: 0.7596 (t0) REVERT: E 415 MET cc_start: 0.6766 (ptp) cc_final: 0.6322 (ptp) REVERT: E 541 LEU cc_start: 0.7907 (tt) cc_final: 0.7420 (tt) REVERT: F 150 TYR cc_start: 0.8247 (m-80) cc_final: 0.7843 (m-80) REVERT: F 156 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8264 (tp30) REVERT: F 415 MET cc_start: 0.7926 (mmt) cc_final: 0.7450 (mtp) REVERT: F 586 ASP cc_start: 0.8126 (p0) cc_final: 0.7862 (p0) REVERT: F 592 ARG cc_start: 0.8389 (ttt-90) cc_final: 0.7633 (tmt170) REVERT: F 598 ILE cc_start: 0.7451 (mm) cc_final: 0.7236 (mm) REVERT: F 703 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: H 29 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7892 (mp) REVERT: H 55 ARG cc_start: 0.6727 (tpt170) cc_final: 0.6340 (tpp-160) outliers start: 80 outliers final: 57 residues processed: 523 average time/residue: 0.4079 time to fit residues: 357.2627 Evaluate side-chains 495 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 432 time to evaluate : 3.654 ------------------------------------------------------------------------------- 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 220 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 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 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 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 220 THR 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 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 156 GLU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 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 29 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 116 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 369 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 397 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 356 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** I 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 472 ASN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3860 r_free = 0.3860 target = 0.151967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122265 restraints weight = 46301.387| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.48 r_work: 0.3399 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.127 Angle : 0.530 10.767 45204 Z= 0.268 Chirality : 0.041 0.228 5334 Planarity : 0.003 0.041 5640 Dihedral : 6.710 69.226 4644 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.49 % Allowed : 14.81 % Favored : 82.70 % 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: 1.23 (0.14), residues: 4071 helix: 1.82 (0.10), residues: 2553 sheet: -0.08 (0.31), residues: 276 loop : -1.12 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 394 HIS 0.003 0.001 HIS J 662 PHE 0.027 0.001 PHE A 475 TYR 0.016 0.001 TYR B 477 ARG 0.004 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 2031) hydrogen bonds : angle 3.73216 ( 5949) covalent geometry : bond 0.00293 (33297) covalent geometry : angle 0.52963 (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 547 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 459 time to evaluate : 4.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6802 (t80) cc_final: 0.6586 (t80) REVERT: A 139 ASP cc_start: 0.7344 (m-30) cc_final: 0.6906 (m-30) REVERT: A 204 PHE cc_start: 0.7500 (m-80) cc_final: 0.7016 (t80) REVERT: A 320 ASP cc_start: 0.8384 (t70) cc_final: 0.7931 (t0) REVERT: A 471 ARG cc_start: 0.7383 (mtm-85) cc_final: 0.7123 (mtt90) REVERT: A 475 PHE cc_start: 0.8809 (t80) cc_final: 0.8515 (t80) REVERT: B 150 TYR cc_start: 0.8368 (m-80) cc_final: 0.7887 (m-10) REVERT: B 205 GLU cc_start: 0.7967 (tp30) cc_final: 0.7543 (tp30) REVERT: B 286 MET cc_start: 0.7726 (mmt) cc_final: 0.7476 (mmt) REVERT: B 385 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7859 (tm-30) REVERT: B 643 ILE cc_start: 0.8076 (mm) cc_final: 0.7678 (mm) REVERT: B 703 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: C 65 MET cc_start: 0.2909 (mmt) cc_final: 0.2629 (mtt) REVERT: D 24 LYS cc_start: 0.8318 (mtmm) cc_final: 0.8061 (mtmm) REVERT: D 50 GLU cc_start: 0.7905 (tt0) cc_final: 0.7453 (tp30) REVERT: D 55 ARG cc_start: 0.7158 (tpt170) cc_final: 0.6390 (tpp-160) REVERT: D 65 MET cc_start: 0.6609 (ttt) cc_final: 0.6061 (ttp) REVERT: I 72 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7993 (mm) REVERT: I 77 TRP cc_start: 0.8654 (t-100) cc_final: 0.8300 (t-100) REVERT: I 88 LYS cc_start: 0.7883 (tptm) cc_final: 0.7389 (ttpp) REVERT: I 246 ARG cc_start: 0.7363 (mtt90) cc_final: 0.6963 (mtt90) REVERT: I 263 ASN cc_start: 0.9003 (t0) cc_final: 0.8518 (t0) REVERT: I 268 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7820 (mt0) REVERT: I 570 MET cc_start: 0.8036 (ppp) cc_final: 0.6476 (ppp) REVERT: J 150 TYR cc_start: 0.8118 (m-80) cc_final: 0.7668 (m-80) REVERT: J 167 PHE cc_start: 0.8066 (m-10) cc_final: 0.7850 (m-10) REVERT: J 205 GLU cc_start: 0.8027 (tp30) cc_final: 0.7804 (tm-30) REVERT: J 262 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.6979 (ttm110) REVERT: J 286 MET cc_start: 0.7610 (mmt) cc_final: 0.7247 (mmt) REVERT: J 389 MET cc_start: 0.7960 (tmm) cc_final: 0.7368 (tmm) REVERT: J 592 ARG cc_start: 0.8308 (ttt-90) cc_final: 0.8050 (ttt-90) REVERT: J 703 GLN cc_start: 0.8609 (mp10) cc_final: 0.8352 (mp10) REVERT: K 65 MET cc_start: 0.2591 (mmt) cc_final: 0.2354 (mtt) REVERT: L 55 ARG cc_start: 0.6791 (tpt170) cc_final: 0.6180 (tpp-160) REVERT: E 72 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7954 (mm) REVERT: E 108 VAL cc_start: 0.8597 (t) cc_final: 0.8348 (m) REVERT: E 139 ASP cc_start: 0.7312 (m-30) cc_final: 0.7058 (m-30) REVERT: E 320 ASP cc_start: 0.8014 (t70) cc_final: 0.7577 (t0) REVERT: E 415 MET cc_start: 0.6734 (ptp) cc_final: 0.6289 (ptp) REVERT: E 541 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7153 (tt) REVERT: F 150 TYR cc_start: 0.8286 (m-80) cc_final: 0.7898 (m-80) REVERT: F 156 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: F 205 GLU cc_start: 0.8308 (tp30) cc_final: 0.7774 (tp30) REVERT: F 415 MET cc_start: 0.7978 (mmt) cc_final: 0.7473 (mtp) REVERT: F 477 TYR cc_start: 0.8430 (m-80) cc_final: 0.8186 (m-10) REVERT: F 586 ASP cc_start: 0.8282 (p0) cc_final: 0.7988 (p0) REVERT: F 598 ILE cc_start: 0.7460 (mm) cc_final: 0.7247 (mm) REVERT: G 34 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7252 (mtm-85) REVERT: H 29 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7903 (mp) REVERT: H 47 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7984 (tm-30) REVERT: H 55 ARG cc_start: 0.6782 (tpt170) cc_final: 0.6332 (tpp-160) outliers start: 88 outliers final: 62 residues processed: 514 average time/residue: 0.3946 time to fit residues: 340.5899 Evaluate side-chains 508 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 440 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 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 209 SER Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 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 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 156 GLU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 254 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 337 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 262 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 388 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** ** I 516 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** F 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122789 restraints weight = 46359.839| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.49 r_work: 0.3389 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33297 Z= 0.118 Angle : 0.519 10.022 45204 Z= 0.264 Chirality : 0.041 0.200 5334 Planarity : 0.003 0.041 5640 Dihedral : 6.645 71.972 4644 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.58 % Allowed : 16.09 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.14), residues: 4071 helix: 1.89 (0.10), residues: 2556 sheet: -0.06 (0.31), residues: 276 loop : -1.14 (0.18), 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 0.020 0.001 PHE J 475 TYR 0.014 0.001 TYR E 289 ARG 0.006 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 2031) hydrogen bonds : angle 3.67368 ( 5949) covalent geometry : bond 0.00269 (33297) covalent geometry : angle 0.51907 (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 557 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 466 time to evaluate : 9.343 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7388 (m-30) cc_final: 0.6933 (m-30) REVERT: A 320 ASP cc_start: 0.8405 (t70) cc_final: 0.7945 (t0) REVERT: A 384 ILE cc_start: 0.8061 (mm) cc_final: 0.7848 (mt) REVERT: A 472 ASN cc_start: 0.8057 (t0) cc_final: 0.7778 (t0) REVERT: A 475 PHE cc_start: 0.8774 (t80) cc_final: 0.8572 (t80) REVERT: A 528 ILE cc_start: 0.8475 (mm) cc_final: 0.8257 (tt) REVERT: B 150 TYR cc_start: 0.8353 (m-80) cc_final: 0.7901 (m-10) REVERT: B 205 GLU cc_start: 0.7992 (tp30) cc_final: 0.7610 (tp30) REVERT: B 286 MET cc_start: 0.7749 (mmt) cc_final: 0.7451 (mmt) REVERT: B 385 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 592 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7784 (tmt170) REVERT: B 643 ILE cc_start: 0.8115 (mm) cc_final: 0.7716 (mm) REVERT: B 703 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: C 65 MET cc_start: 0.2682 (mmt) cc_final: 0.2366 (mtt) REVERT: D 24 LYS cc_start: 0.8345 (mtmm) cc_final: 0.8142 (mtmm) REVERT: D 50 GLU cc_start: 0.8016 (tt0) cc_final: 0.7558 (tp30) REVERT: D 55 ARG cc_start: 0.6932 (tpt170) cc_final: 0.6183 (tpp-160) REVERT: D 65 MET cc_start: 0.6657 (ttt) cc_final: 0.6149 (ttp) REVERT: I 72 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8021 (mm) REVERT: I 77 TRP cc_start: 0.8646 (t-100) cc_final: 0.8274 (t-100) REVERT: I 88 LYS cc_start: 0.7890 (tptm) cc_final: 0.7366 (ttpp) REVERT: I 246 ARG cc_start: 0.7366 (mtt90) cc_final: 0.7136 (mtt90) REVERT: I 261 ILE cc_start: 0.7916 (mt) cc_final: 0.7627 (tt) REVERT: I 263 ASN cc_start: 0.8879 (t0) cc_final: 0.8384 (t0) REVERT: I 268 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7840 (mt0) REVERT: I 384 ILE cc_start: 0.7897 (mm) cc_final: 0.7653 (mt) REVERT: I 389 MET cc_start: 0.7259 (tmm) cc_final: 0.7024 (tmm) REVERT: I 570 MET cc_start: 0.7736 (ppp) cc_final: 0.6938 (ppp) REVERT: J 150 TYR cc_start: 0.8168 (m-80) cc_final: 0.7634 (m-80) REVERT: J 276 LEU cc_start: 0.7571 (tt) cc_final: 0.7350 (tt) REVERT: J 286 MET cc_start: 0.7641 (mmt) cc_final: 0.7290 (mmt) REVERT: J 389 MET cc_start: 0.8008 (tmm) cc_final: 0.7418 (tmm) REVERT: J 549 LEU cc_start: 0.7783 (mt) cc_final: 0.7576 (mp) REVERT: J 592 ARG cc_start: 0.8299 (ttt-90) cc_final: 0.8076 (ttt-90) REVERT: J 703 GLN cc_start: 0.8502 (mp10) cc_final: 0.8012 (mp10) REVERT: L 47 GLU cc_start: 0.8592 (tm-30) cc_final: 0.7989 (tm-30) REVERT: L 55 ARG cc_start: 0.6788 (tpt170) cc_final: 0.6174 (tpp-160) REVERT: E 72 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7980 (mm) REVERT: E 108 VAL cc_start: 0.8566 (t) cc_final: 0.8310 (m) REVERT: E 139 ASP cc_start: 0.7397 (m-30) cc_final: 0.7132 (m-30) REVERT: E 320 ASP cc_start: 0.8008 (t70) cc_final: 0.7579 (t0) REVERT: E 415 MET cc_start: 0.6784 (ptp) cc_final: 0.6335 (ptp) REVERT: E 541 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7116 (tt) REVERT: F 150 TYR cc_start: 0.8257 (m-80) cc_final: 0.7914 (m-80) REVERT: F 156 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8284 (tp30) REVERT: F 205 GLU cc_start: 0.8283 (tp30) cc_final: 0.7739 (tp30) REVERT: F 415 MET cc_start: 0.8092 (mmt) cc_final: 0.7592 (mtp) REVERT: F 477 TYR cc_start: 0.8396 (m-80) cc_final: 0.8163 (m-10) REVERT: F 586 ASP cc_start: 0.8272 (p0) cc_final: 0.7981 (p0) REVERT: F 598 ILE cc_start: 0.7445 (mm) cc_final: 0.7232 (mm) REVERT: F 703 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8001 (mp10) REVERT: G 34 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7332 (mtm-85) REVERT: H 11 PHE cc_start: 0.6223 (p90) cc_final: 0.6015 (p90) REVERT: H 47 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7955 (tm-30) REVERT: H 55 ARG cc_start: 0.6907 (tpt170) cc_final: 0.6375 (tpp-160) outliers start: 91 outliers final: 67 residues processed: 531 average time/residue: 0.5208 time to fit residues: 463.8796 Evaluate side-chains 510 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 437 time to evaluate : 5.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 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 421 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 570 MET 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 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 245 SER Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 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: 5.9990 chunk 287 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 331 optimal weight: 0.7980 chunk 284 optimal weight: 0.6980 chunk 387 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 361 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3856 r_free = 0.3856 target = 0.151872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122316 restraints weight = 46253.679| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.47 r_work: 0.3389 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2385 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= 0.121 Angle : 0.527 9.535 45204 Z= 0.268 Chirality : 0.041 0.206 5334 Planarity : 0.003 0.050 5640 Dihedral : 6.602 74.401 4644 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.46 % Allowed : 17.05 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.14), residues: 4071 helix: 1.93 (0.10), residues: 2556 sheet: 0.00 (0.31), residues: 276 loop : -1.12 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 431 HIS 0.002 0.001 HIS J 662 PHE 0.018 0.001 PHE J 475 TYR 0.019 0.001 TYR B 288 ARG 0.007 0.000 ARG J 256 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 2031) hydrogen bonds : angle 3.65867 ( 5949) covalent geometry : bond 0.00278 (33297) covalent geometry : angle 0.52746 (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 546 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 459 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7449 (m-30) cc_final: 0.7067 (m-30) REVERT: A 320 ASP cc_start: 0.8452 (t70) cc_final: 0.7994 (t0) REVERT: A 384 ILE cc_start: 0.8124 (mm) cc_final: 0.7923 (mt) REVERT: A 471 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.7156 (mtt180) REVERT: A 472 ASN cc_start: 0.7942 (t0) cc_final: 0.7551 (t0) REVERT: A 475 PHE cc_start: 0.8786 (t80) cc_final: 0.8580 (t80) REVERT: B 150 TYR cc_start: 0.8393 (m-80) cc_final: 0.7970 (m-10) REVERT: B 286 MET cc_start: 0.7783 (mmt) cc_final: 0.7396 (mmt) REVERT: B 385 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 475 PHE cc_start: 0.8547 (t80) cc_final: 0.8167 (t80) REVERT: B 643 ILE cc_start: 0.8154 (mm) cc_final: 0.7757 (mm) REVERT: B 703 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: C 65 MET cc_start: 0.2650 (mmt) cc_final: 0.2348 (mtt) REVERT: D 24 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8132 (mtmm) REVERT: D 50 GLU cc_start: 0.8125 (tt0) cc_final: 0.7686 (tp30) REVERT: D 55 ARG cc_start: 0.6979 (tpt170) cc_final: 0.6232 (tpp-160) REVERT: D 65 MET cc_start: 0.6577 (ttt) cc_final: 0.6026 (ttp) REVERT: I 72 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.8003 (mm) REVERT: I 77 TRP cc_start: 0.8631 (t-100) cc_final: 0.8222 (t-100) REVERT: I 88 LYS cc_start: 0.7952 (tptm) cc_final: 0.7433 (ttpp) REVERT: I 261 ILE cc_start: 0.7946 (mt) cc_final: 0.7659 (tt) REVERT: I 268 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7917 (mt0) REVERT: I 384 ILE cc_start: 0.7884 (mm) cc_final: 0.7651 (mt) REVERT: I 389 MET cc_start: 0.7279 (tmm) cc_final: 0.7022 (tmm) REVERT: I 570 MET cc_start: 0.7790 (ppp) cc_final: 0.6721 (ppp) REVERT: J 150 TYR cc_start: 0.8197 (m-80) cc_final: 0.7731 (m-80) REVERT: J 276 LEU cc_start: 0.7561 (tt) cc_final: 0.7342 (tt) REVERT: J 286 MET cc_start: 0.7674 (mmt) cc_final: 0.7346 (mmt) REVERT: J 389 MET cc_start: 0.8012 (tmm) cc_final: 0.7415 (tmm) REVERT: J 549 LEU cc_start: 0.7839 (mt) cc_final: 0.7574 (mp) REVERT: J 703 GLN cc_start: 0.8506 (mp10) cc_final: 0.8118 (mp10) REVERT: L 47 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8021 (tm-30) REVERT: L 55 ARG cc_start: 0.6725 (tpt170) cc_final: 0.6238 (tpp-160) REVERT: E 72 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8024 (mm) REVERT: E 108 VAL cc_start: 0.8354 (t) cc_final: 0.8107 (m) REVERT: E 139 ASP cc_start: 0.7454 (m-30) cc_final: 0.7179 (m-30) REVERT: E 175 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6921 (t80) REVERT: E 320 ASP cc_start: 0.8047 (t70) cc_final: 0.7618 (t0) REVERT: E 415 MET cc_start: 0.6830 (ptp) cc_final: 0.6382 (ptp) REVERT: E 541 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7134 (tt) REVERT: F 156 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8365 (tp30) REVERT: F 205 GLU cc_start: 0.8295 (tp30) cc_final: 0.7763 (tp30) REVERT: F 415 MET cc_start: 0.8095 (mmt) cc_final: 0.7582 (mtp) REVERT: F 586 ASP cc_start: 0.8239 (p0) cc_final: 0.7935 (p0) REVERT: F 598 ILE cc_start: 0.7440 (mm) cc_final: 0.7229 (mm) REVERT: F 703 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: H 47 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8278 (tm-30) REVERT: H 55 ARG cc_start: 0.6999 (tpt170) cc_final: 0.6438 (tpp-160) outliers start: 87 outliers final: 69 residues processed: 523 average time/residue: 0.4106 time to fit residues: 362.5970 Evaluate side-chains 512 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 436 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 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 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 535 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 490 LEU Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 245 SER Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 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 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 344 optimal weight: 3.9990 chunk 391 optimal weight: 7.9990 chunk 333 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 284 optimal weight: 0.4980 chunk 348 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 334 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.151317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121750 restraints weight = 46531.167| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.48 r_work: 0.3374 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2510 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 : 0.536 10.753 45204 Z= 0.270 Chirality : 0.041 0.232 5334 Planarity : 0.003 0.052 5640 Dihedral : 6.557 76.972 4644 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.41 % Allowed : 17.70 % Favored : 79.89 % 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: 1.36 (0.14), residues: 4071 helix: 1.95 (0.10), residues: 2553 sheet: -0.05 (0.31), residues: 279 loop : -1.12 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 23 HIS 0.003 0.001 HIS J 662 PHE 0.021 0.001 PHE B 413 TYR 0.014 0.001 TYR B 288 ARG 0.010 0.000 ARG J 592 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 2031) hydrogen bonds : angle 3.65140 ( 5949) covalent geometry : bond 0.00287 (33297) covalent geometry : angle 0.53616 (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 540 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 455 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7425 (m-30) cc_final: 0.7030 (m-30) REVERT: A 204 PHE cc_start: 0.7588 (m-80) cc_final: 0.7191 (t80) REVERT: A 320 ASP cc_start: 0.8445 (t70) cc_final: 0.7980 (t0) REVERT: A 471 ARG cc_start: 0.7479 (mtm-85) cc_final: 0.7153 (mtt180) REVERT: B 150 TYR cc_start: 0.8410 (m-80) cc_final: 0.7997 (m-10) REVERT: B 205 GLU cc_start: 0.8078 (tp30) cc_final: 0.7664 (tp30) REVERT: B 385 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 486 ASP cc_start: 0.8050 (t0) cc_final: 0.7777 (t0) REVERT: B 592 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.7924 (ttt-90) REVERT: B 643 ILE cc_start: 0.8166 (mm) cc_final: 0.7773 (mm) REVERT: B 703 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: C 65 MET cc_start: 0.2473 (mmt) cc_final: 0.2168 (mtt) REVERT: D 24 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8171 (mtmm) REVERT: D 50 GLU cc_start: 0.8183 (tt0) cc_final: 0.7894 (tp30) REVERT: D 55 ARG cc_start: 0.7042 (tpt170) cc_final: 0.6298 (tpp-160) REVERT: D 65 MET cc_start: 0.6741 (ttt) cc_final: 0.6207 (ttp) REVERT: I 72 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7967 (mm) REVERT: I 77 TRP cc_start: 0.8625 (t-100) cc_final: 0.8098 (t-100) REVERT: I 88 LYS cc_start: 0.7991 (tptm) cc_final: 0.7469 (ttpp) REVERT: I 261 ILE cc_start: 0.7930 (mt) cc_final: 0.7641 (tt) REVERT: I 268 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7964 (mt0) REVERT: I 384 ILE cc_start: 0.7902 (mm) cc_final: 0.7677 (mt) REVERT: I 389 MET cc_start: 0.7322 (tmm) cc_final: 0.7058 (tmm) REVERT: I 570 MET cc_start: 0.7869 (ppp) cc_final: 0.6787 (ppp) REVERT: J 150 TYR cc_start: 0.8305 (m-80) cc_final: 0.7808 (m-80) REVERT: J 276 LEU cc_start: 0.7552 (tt) cc_final: 0.7327 (tt) REVERT: J 286 MET cc_start: 0.7709 (mmt) cc_final: 0.7373 (mmt) REVERT: J 308 SER cc_start: 0.8896 (t) cc_final: 0.8334 (p) REVERT: J 389 MET cc_start: 0.8014 (tmm) cc_final: 0.7417 (tmm) REVERT: J 549 LEU cc_start: 0.7853 (mt) cc_final: 0.7585 (mp) REVERT: J 683 GLU cc_start: 0.7090 (mp0) cc_final: 0.6300 (mp0) REVERT: J 703 GLN cc_start: 0.8518 (mp10) cc_final: 0.8028 (mp10) REVERT: L 47 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7842 (tm-30) REVERT: L 55 ARG cc_start: 0.6597 (tpt170) cc_final: 0.6193 (tpp-160) REVERT: E 72 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8009 (mm) REVERT: E 108 VAL cc_start: 0.8392 (t) cc_final: 0.8148 (m) REVERT: E 139 ASP cc_start: 0.7477 (m-30) cc_final: 0.7199 (m-30) REVERT: E 175 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6834 (t80) REVERT: E 180 ASP cc_start: 0.6542 (t70) cc_final: 0.6336 (t70) REVERT: E 320 ASP cc_start: 0.8057 (t70) cc_final: 0.7612 (t0) REVERT: E 415 MET cc_start: 0.6838 (ptp) cc_final: 0.6427 (ptp) REVERT: F 156 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8371 (tp30) REVERT: F 205 GLU cc_start: 0.8291 (tp30) cc_final: 0.7732 (tp30) REVERT: F 415 MET cc_start: 0.8163 (mmt) cc_final: 0.7632 (mtp) REVERT: F 586 ASP cc_start: 0.8240 (p0) cc_final: 0.7938 (p0) REVERT: F 598 ILE cc_start: 0.7409 (mm) cc_final: 0.7200 (mm) REVERT: F 703 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: H 55 ARG cc_start: 0.6986 (tpt170) cc_final: 0.6423 (tpp-160) outliers start: 85 outliers final: 71 residues processed: 519 average time/residue: 0.5023 time to fit residues: 440.9388 Evaluate side-chains 512 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 435 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 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 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 535 LEU Chi-restraints excluded: chain B residue 570 MET 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 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 108 VAL Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 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 407 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain E residue 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 388 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 676 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 57 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 273 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 256 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS B 596 ASN I 489 ASN I 531 HIS ** I 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 687 HIS ** J 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 622 ASN ** J 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 622 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108779 restraints weight = 48250.714| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.52 r_work: 0.3206 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 33297 Z= 0.355 Angle : 0.782 10.406 45204 Z= 0.405 Chirality : 0.050 0.248 5334 Planarity : 0.005 0.067 5640 Dihedral : 7.279 88.578 4644 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.44 % Allowed : 18.01 % 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: 0.03 (0.13), residues: 4071 helix: 0.87 (0.10), residues: 2532 sheet: -0.49 (0.34), residues: 240 loop : -1.51 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 431 HIS 0.006 0.001 HIS A 531 PHE 0.030 0.003 PHE B 475 TYR 0.022 0.002 TYR J 477 ARG 0.008 0.001 ARG J 592 Details of bonding type rmsd hydrogen bonds : bond 0.05639 ( 2031) hydrogen bonds : angle 4.50976 ( 5949) covalent geometry : bond 0.00858 (33297) covalent geometry : angle 0.78157 (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 538 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 452 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8153 (tptm) cc_final: 0.7654 (ttpp) REVERT: A 139 ASP cc_start: 0.7720 (m-30) cc_final: 0.7337 (m-30) REVERT: A 287 TRP cc_start: 0.6922 (t60) cc_final: 0.6691 (t60) REVERT: A 320 ASP cc_start: 0.8455 (t70) cc_final: 0.7980 (t0) REVERT: A 471 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7264 (mtt180) REVERT: A 496 GLU cc_start: 0.7525 (tt0) cc_final: 0.6815 (mm-30) REVERT: B 150 TYR cc_start: 0.8755 (m-80) cc_final: 0.8395 (m-10) REVERT: B 286 MET cc_start: 0.8142 (mmt) cc_final: 0.7817 (mmt) REVERT: B 308 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.7901 (p) REVERT: B 535 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8116 (pp) REVERT: B 592 ARG cc_start: 0.8488 (ttt-90) cc_final: 0.7931 (ttt-90) REVERT: B 703 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8188 (mp10) REVERT: C 65 MET cc_start: 0.2617 (mmt) cc_final: 0.2320 (mtt) REVERT: D 24 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8315 (mtmm) REVERT: D 40 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7645 (mt-10) REVERT: D 47 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8452 (tm-30) REVERT: D 50 GLU cc_start: 0.8086 (tt0) cc_final: 0.7759 (tp30) REVERT: D 55 ARG cc_start: 0.7204 (tpt170) cc_final: 0.6367 (tpp-160) REVERT: I 88 LYS cc_start: 0.8129 (tptm) cc_final: 0.7679 (ttpp) REVERT: I 316 ARG cc_start: 0.7667 (tpp80) cc_final: 0.7197 (tpp80) REVERT: I 320 ASP cc_start: 0.8542 (t70) cc_final: 0.8060 (t70) REVERT: I 389 MET cc_start: 0.7436 (tmm) cc_final: 0.7180 (tmm) REVERT: I 587 PHE cc_start: 0.6396 (m-10) cc_final: 0.6165 (m-10) REVERT: J 150 TYR cc_start: 0.8555 (m-80) cc_final: 0.8218 (m-80) REVERT: J 286 MET cc_start: 0.7918 (mmt) cc_final: 0.7575 (mmt) REVERT: J 389 MET cc_start: 0.8244 (tmm) cc_final: 0.7397 (tmm) REVERT: J 703 GLN cc_start: 0.8643 (mp10) cc_final: 0.8164 (mp10) REVERT: L 55 ARG cc_start: 0.7197 (tpt170) cc_final: 0.6661 (tpp-160) REVERT: L 65 MET cc_start: 0.6294 (ttt) cc_final: 0.5755 (ttp) REVERT: E 139 ASP cc_start: 0.7663 (m-30) cc_final: 0.7428 (m-30) REVERT: E 320 ASP cc_start: 0.8214 (t70) cc_final: 0.7975 (t0) REVERT: E 354 ASN cc_start: 0.7992 (t0) cc_final: 0.7712 (t0) REVERT: E 471 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.7036 (mtm-85) REVERT: E 587 PHE cc_start: 0.6267 (m-10) cc_final: 0.6054 (m-10) REVERT: F 156 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8373 (tp30) REVERT: F 586 ASP cc_start: 0.8366 (p0) cc_final: 0.8004 (p0) REVERT: F 703 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: H 47 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7691 (tt0) REVERT: H 55 ARG cc_start: 0.7596 (tpt170) cc_final: 0.6920 (tpp-160) outliers start: 86 outliers final: 62 residues processed: 513 average time/residue: 0.4613 time to fit residues: 389.9302 Evaluate side-chains 485 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 418 time to evaluate : 5.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 THR 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 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 308 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 675 VAL 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 D residue 54 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 469 THR 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 390 ILE 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 L residue 53 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 65 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 42 optimal weight: 0.5980 chunk 251 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 270 optimal weight: 8.9990 chunk 330 optimal weight: 0.9980 chunk 359 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 313 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116470 restraints weight = 46656.488| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.44 r_work: 0.3303 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33297 Z= 0.142 Angle : 0.592 10.521 45204 Z= 0.305 Chirality : 0.042 0.226 5334 Planarity : 0.004 0.051 5640 Dihedral : 6.767 76.686 4644 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.98 % Allowed : 19.29 % Favored : 78.73 % 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: 0.77 (0.13), residues: 4071 helix: 1.49 (0.10), residues: 2529 sheet: -0.52 (0.32), residues: 276 loop : -1.25 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 431 HIS 0.011 0.001 HIS I 185 PHE 0.022 0.002 PHE E 323 TYR 0.019 0.001 TYR B 288 ARG 0.008 0.000 ARG J 592 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 2031) hydrogen bonds : angle 3.98733 ( 5949) covalent geometry : bond 0.00323 (33297) covalent geometry : angle 0.59216 (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 528 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 458 time to evaluate : 3.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8079 (tptm) cc_final: 0.7597 (ttpp) REVERT: A 139 ASP cc_start: 0.7646 (m-30) cc_final: 0.7297 (m-30) REVERT: A 173 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6375 (mp) REVERT: A 175 PHE cc_start: 0.6806 (m-80) cc_final: 0.6361 (m-80) REVERT: A 204 PHE cc_start: 0.7616 (m-80) cc_final: 0.7067 (t80) REVERT: A 320 ASP cc_start: 0.8433 (t70) cc_final: 0.7959 (t0) REVERT: A 471 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7274 (mtt90) REVERT: B 150 TYR cc_start: 0.8553 (m-80) cc_final: 0.8281 (m-10) REVERT: B 308 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8143 (p) REVERT: B 592 ARG cc_start: 0.8425 (ttt-90) cc_final: 0.8104 (ttt-90) REVERT: C 65 MET cc_start: 0.2539 (mmt) cc_final: 0.2258 (mtt) REVERT: D 24 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8131 (mtmm) REVERT: D 40 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7498 (mt-10) REVERT: D 50 GLU cc_start: 0.8223 (tt0) cc_final: 0.7805 (tp30) REVERT: D 55 ARG cc_start: 0.7168 (tpt170) cc_final: 0.5861 (ttp-170) REVERT: D 65 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6092 (ttp) REVERT: I 77 TRP cc_start: 0.8613 (t-100) cc_final: 0.7856 (t-100) REVERT: I 88 LYS cc_start: 0.8065 (tptm) cc_final: 0.7574 (ttpp) REVERT: I 316 ARG cc_start: 0.7518 (tpp80) cc_final: 0.7046 (tpp80) REVERT: I 389 MET cc_start: 0.7264 (tmm) cc_final: 0.7013 (tmm) REVERT: I 472 ASN cc_start: 0.7814 (m-40) cc_final: 0.6749 (t0) REVERT: I 570 MET cc_start: 0.7682 (ppp) cc_final: 0.7248 (ppp) REVERT: I 587 PHE cc_start: 0.6387 (m-10) cc_final: 0.6177 (m-10) REVERT: J 150 TYR cc_start: 0.8269 (m-80) cc_final: 0.7768 (m-80) REVERT: J 276 LEU cc_start: 0.7334 (tt) cc_final: 0.7132 (tt) REVERT: J 286 MET cc_start: 0.7864 (mmt) cc_final: 0.7509 (mmt) REVERT: J 308 SER cc_start: 0.9001 (t) cc_final: 0.8389 (p) REVERT: J 389 MET cc_start: 0.8146 (tmm) cc_final: 0.7388 (tmm) REVERT: J 703 GLN cc_start: 0.8634 (mp10) cc_final: 0.8138 (mp10) REVERT: L 50 GLU cc_start: 0.8114 (tp30) cc_final: 0.7735 (tp30) REVERT: L 55 ARG cc_start: 0.6641 (tpt170) cc_final: 0.6199 (tpp-160) REVERT: E 48 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7822 (mm) REVERT: E 139 ASP cc_start: 0.7561 (m-30) cc_final: 0.7328 (m-30) REVERT: E 320 ASP cc_start: 0.8099 (t70) cc_final: 0.7650 (t0) REVERT: E 354 ASN cc_start: 0.7839 (t0) cc_final: 0.7505 (t0) REVERT: E 429 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8522 (mt0) REVERT: E 471 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.7100 (mtm-85) REVERT: E 587 PHE cc_start: 0.6199 (m-10) cc_final: 0.5978 (m-10) REVERT: F 156 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8422 (tp30) REVERT: F 415 MET cc_start: 0.8072 (mmt) cc_final: 0.7569 (mtp) REVERT: F 586 ASP cc_start: 0.8215 (p0) cc_final: 0.7881 (p0) REVERT: F 598 ILE cc_start: 0.7402 (mm) cc_final: 0.7197 (mm) REVERT: F 703 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: H 55 ARG cc_start: 0.7224 (tpt170) cc_final: 0.6652 (tpp-160) outliers start: 70 outliers final: 56 residues processed: 509 average time/residue: 0.4191 time to fit residues: 354.7480 Evaluate side-chains 494 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 432 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 173 LEU 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 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 308 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 248 VAL Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 469 THR 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 L residue 53 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 308 SER 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 441 VAL Chi-restraints excluded: chain F residue 597 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 65 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 121 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 221 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 311 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 371 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118134 restraints weight = 46557.068| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.46 r_work: 0.3328 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33297 Z= 0.134 Angle : 0.569 10.094 45204 Z= 0.290 Chirality : 0.042 0.222 5334 Planarity : 0.004 0.049 5640 Dihedral : 6.693 82.253 4644 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.87 % Allowed : 19.63 % Favored : 78.50 % 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: 0.99 (0.13), residues: 4071 helix: 1.66 (0.10), residues: 2547 sheet: -0.47 (0.32), residues: 276 loop : -1.17 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 287 HIS 0.004 0.001 HIS A 185 PHE 0.023 0.001 PHE D 67 TYR 0.022 0.001 TYR B 288 ARG 0.007 0.000 ARG J 592 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 2031) hydrogen bonds : angle 3.83080 ( 5949) covalent geometry : bond 0.00311 (33297) covalent geometry : angle 0.56920 (45204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14954.64 seconds wall clock time: 263 minutes 20.09 seconds (15800.09 seconds total)