Starting phenix.real_space_refine on Sat May 24 07:35:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz3_41732/05_2025/8tz3_41732_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz3_41732/05_2025/8tz3_41732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz3_41732/05_2025/8tz3_41732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz3_41732/05_2025/8tz3_41732.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz3_41732/05_2025/8tz3_41732_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz3_41732/05_2025/8tz3_41732_trim.cif" } resolution = 2.31 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= 0.004 sd= 0.153 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 87 5.16 5 Na 6 4.78 5 C 8412 2.51 5 N 1926 2.21 5 O 2202 1.98 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24810 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Unusual residues: {' NA': 2, 'LBN': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Unusual residues: {' NA': 2, 'LBN': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Unusual residues: {' NA': 2, 'LBN': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7934 SG CYS A 608 49.354 32.824 38.169 1.00 20.21 S ATOM 16063 SG CYS C 608 87.685 68.096 38.146 1.00 20.07 S ATOM 24192 SG CYS B 608 37.946 83.694 38.152 1.00 20.18 S Time building chain proxies: 10.79, per 1000 atoms: 0.43 Number of scatterers: 24810 At special positions: 0 Unit cell: (129.6, 127.44, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 12 15.00 Na 6 11.00 O 2202 8.00 N 1926 7.00 C 8412 6.00 H 12165 1.00 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: 6.15 Conformation dependent library (CDL) restraints added in 2.0 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 3 sheets defined 89.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 removed outlier: 3.619A pdb=" N ILE A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 157 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 157 through 198 Proline residue: A 167 - end of helix removed outlier: 5.006A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 203 through 223 Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.557A pdb=" N THR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.173A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 294 through 311 removed outlier: 3.505A pdb=" N VAL A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.524A pdb=" N TRP A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 320 " --> pdb=" O TRP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.579A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 removed outlier: 3.557A pdb=" N ARG A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.598A pdb=" N GLY A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.529A pdb=" N TYR A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 3.917A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 479 removed outlier: 3.713A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.675A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 3.920A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.523A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 removed outlier: 3.619A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 157 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 157 through 198 Proline residue: C 167 - end of helix removed outlier: 5.006A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 203 through 223 Processing helix chain 'C' and resid 232 through 252 removed outlier: 3.557A pdb=" N THR C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 270 Processing helix chain 'C' and resid 272 through 281 removed outlier: 4.173A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.505A pdb=" N VAL C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.524A pdb=" N TRP C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 320 " --> pdb=" O TRP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.580A pdb=" N ILE C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 361 removed outlier: 3.557A pdb=" N ARG C 355 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 376 removed outlier: 3.599A pdb=" N GLY C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.528A pdb=" N TYR C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 3.917A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 479 removed outlier: 3.712A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.675A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 3.920A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.523A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 removed outlier: 3.619A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 157 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 157 through 198 Proline residue: B 167 - end of helix removed outlier: 5.006A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 223 Processing helix chain 'B' and resid 232 through 252 removed outlier: 3.558A pdb=" N THR B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 270 Processing helix chain 'B' and resid 272 through 281 removed outlier: 4.172A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 294 through 311 removed outlier: 3.505A pdb=" N VAL B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.525A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 320 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.579A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 361 removed outlier: 3.558A pdb=" N ARG B 355 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.599A pdb=" N GLY B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.528A pdb=" N TYR B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 3.916A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 479 removed outlier: 3.713A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.675A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 3.920A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.524A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA2, first strand: chain 'C' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 547 967 hydrogen bonds defined for protein. 2856 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: 9.24 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 12147 1.02 - 1.22: 42 1.22 - 1.42: 5401 1.42 - 1.61: 7343 1.61 - 1.81: 180 Bond restraints: 25113 Sorted by residual: bond pdb=" O4 LBN C 804 " pdb=" P1 LBN C 804 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" O4 LBN A 804 " pdb=" P1 LBN A 804 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" O4 LBN A 805 " pdb=" P1 LBN A 805 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O4 LBN B 804 " pdb=" P1 LBN B 804 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" O4 LBN C 805 " pdb=" P1 LBN C 805 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.48e+01 ... (remaining 25108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 44843 3.34 - 6.68: 171 6.68 - 10.03: 37 10.03 - 13.37: 6 13.37 - 16.71: 12 Bond angle restraints: 45069 Sorted by residual: angle pdb=" O1 LBN C 803 " pdb=" P1 LBN C 803 " pdb=" O2 LBN C 803 " ideal model delta sigma weight residual 93.45 110.16 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 110.16 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 110.14 -16.69 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O1 LBN C 806 " pdb=" P1 LBN C 806 " pdb=" O2 LBN C 806 " ideal model delta sigma weight residual 93.45 110.10 -16.65 3.00e+00 1.11e-01 3.08e+01 angle pdb=" O1 LBN A 806 " pdb=" P1 LBN A 806 " pdb=" O2 LBN A 806 " ideal model delta sigma weight residual 93.45 110.06 -16.61 3.00e+00 1.11e-01 3.07e+01 ... (remaining 45064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 11584 35.64 - 71.29: 431 71.29 - 106.93: 18 106.93 - 142.57: 3 142.57 - 178.21: 6 Dihedral angle restraints: 12042 sinusoidal: 6312 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN A 803 " pdb=" C2 LBN A 803 " pdb=" C3 LBN A 803 " pdb=" O7 LBN A 803 " ideal model delta sinusoidal sigma weight residual 62.67 -119.12 -178.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN B 803 " pdb=" C2 LBN B 803 " pdb=" C3 LBN B 803 " pdb=" O7 LBN B 803 " ideal model delta sinusoidal sigma weight residual 62.67 -119.14 -178.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN C 803 " pdb=" C2 LBN C 803 " pdb=" C3 LBN C 803 " pdb=" O7 LBN C 803 " ideal model delta sinusoidal sigma weight residual 62.67 -119.15 -178.18 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1183 0.039 - 0.078: 636 0.078 - 0.117: 147 0.117 - 0.156: 26 0.156 - 0.195: 3 Chirality restraints: 1995 Sorted by residual: chirality pdb=" C2 LBN A 805 " pdb=" C1 LBN A 805 " pdb=" C3 LBN A 805 " pdb=" O7 LBN A 805 " both_signs ideal model delta sigma weight residual False -2.36 -2.56 0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" C2 LBN C 805 " pdb=" C1 LBN C 805 " pdb=" C3 LBN C 805 " pdb=" O7 LBN C 805 " both_signs ideal model delta sigma weight residual False -2.36 -2.56 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C2 LBN B 805 " pdb=" C1 LBN B 805 " pdb=" C3 LBN B 805 " pdb=" O7 LBN B 805 " both_signs ideal model delta sigma weight residual False -2.36 -2.56 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1992 not shown) Planarity restraints: 3657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 295 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO A 296 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 295 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO C 296 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 295 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO B 296 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.035 5.00e-02 4.00e+02 ... (remaining 3654 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 694 2.14 - 2.76: 44243 2.76 - 3.37: 68493 3.37 - 3.99: 90622 3.99 - 4.60: 143127 Nonbonded interactions: 347179 Sorted by model distance: nonbonded pdb=" O PHE C 223 " pdb="HH22 ARG C 599 " model vdw 1.530 2.450 nonbonded pdb=" O PHE B 223 " pdb="HH22 ARG B 599 " model vdw 1.532 2.450 nonbonded pdb=" O PHE A 223 " pdb="HH22 ARG A 599 " model vdw 1.532 2.450 nonbonded pdb=" O VAL C 298 " pdb=" HG SER C 302 " model vdw 1.540 2.450 nonbonded pdb=" O VAL B 298 " pdb=" HG SER B 302 " model vdw 1.564 2.450 ... (remaining 347174 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.800 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: 0.420 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 50.280 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.011 0.149 12948 Z= 0.499 Angle : 0.991 16.712 17547 Z= 0.438 Chirality : 0.048 0.195 1995 Planarity : 0.006 0.062 2115 Dihedral : 16.560 178.214 4548 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.82 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.08 (0.17), residues: 1593 helix: -1.96 (0.11), residues: 1323 sheet: None (None), residues: 0 loop : -1.07 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 476 HIS 0.004 0.001 HIS B 367 PHE 0.022 0.002 PHE C 279 TYR 0.012 0.002 TYR A 285 ARG 0.002 0.001 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.25785 ( 967) hydrogen bonds : angle 8.08470 ( 2856) covalent geometry : bond 0.01135 (12948) covalent geometry : angle 0.99096 (17547) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.7105 (mtp) cc_final: 0.6829 (mtp) REVERT: A 228 THR cc_start: 0.8253 (p) cc_final: 0.8035 (p) REVERT: A 248 LEU cc_start: 0.8141 (tp) cc_final: 0.7831 (mp) REVERT: A 421 LYS cc_start: 0.7891 (mttt) cc_final: 0.7514 (mmtt) REVERT: A 483 TYR cc_start: 0.8200 (t80) cc_final: 0.7737 (t80) REVERT: A 508 GLN cc_start: 0.7509 (mt0) cc_final: 0.7051 (mp10) REVERT: A 590 LYS cc_start: 0.8215 (tttt) cc_final: 0.8007 (ttmt) REVERT: C 129 MET cc_start: 0.6650 (mtp) cc_final: 0.6326 (mtp) REVERT: C 231 TYR cc_start: 0.7955 (t80) cc_final: 0.7543 (t80) REVERT: C 248 LEU cc_start: 0.7823 (tp) cc_final: 0.7592 (mp) REVERT: C 317 ILE cc_start: 0.8435 (mt) cc_final: 0.8159 (tp) REVERT: C 325 MET cc_start: 0.8319 (mtm) cc_final: 0.8106 (mtm) REVERT: C 355 ARG cc_start: 0.7716 (ttt180) cc_final: 0.7341 (ttp80) REVERT: C 370 MET cc_start: 0.8699 (mtm) cc_final: 0.8373 (mtm) REVERT: C 421 LYS cc_start: 0.7873 (mttt) cc_final: 0.7668 (mmtp) REVERT: B 129 MET cc_start: 0.6740 (mtp) cc_final: 0.6533 (mtp) REVERT: B 151 ASP cc_start: 0.7696 (m-30) cc_final: 0.7422 (m-30) REVERT: B 231 TYR cc_start: 0.8021 (t80) cc_final: 0.7588 (t80) REVERT: B 248 LEU cc_start: 0.7926 (tp) cc_final: 0.7718 (mp) REVERT: B 325 MET cc_start: 0.8169 (mtm) cc_final: 0.7925 (mtm) REVERT: B 421 LYS cc_start: 0.7846 (mttt) cc_final: 0.7392 (mmtt) REVERT: B 440 GLU cc_start: 0.8230 (tt0) cc_final: 0.7934 (tt0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 1.9884 time to fit residues: 507.3361 Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 144 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 426 ASN C 204 GLN C 426 ASN B 423 ASN B 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116765 restraints weight = 29731.608| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.10 r_work: 0.3180 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12948 Z= 0.130 Angle : 0.525 4.492 17547 Z= 0.288 Chirality : 0.036 0.126 1995 Planarity : 0.005 0.048 2115 Dihedral : 14.765 146.961 1998 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.16 % Allowed : 7.68 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.20), residues: 1593 helix: 1.20 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : -0.50 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.004 0.001 HIS C 288 PHE 0.016 0.001 PHE B 279 TYR 0.010 0.001 TYR B 519 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.05900 ( 967) hydrogen bonds : angle 4.21099 ( 2856) covalent geometry : bond 0.00248 (12948) covalent geometry : angle 0.52495 (17547) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 1.832 Fit side-chains REVERT: A 129 MET cc_start: 0.6484 (mtp) cc_final: 0.6228 (mtp) REVERT: A 189 LEU cc_start: 0.6965 (tp) cc_final: 0.6460 (tm) REVERT: A 231 TYR cc_start: 0.7979 (t80) cc_final: 0.7628 (t80) REVERT: A 248 LEU cc_start: 0.8129 (tp) cc_final: 0.7701 (mp) REVERT: A 317 ILE cc_start: 0.8683 (mt) cc_final: 0.8401 (tp) REVERT: A 325 MET cc_start: 0.8549 (mtm) cc_final: 0.8175 (mtm) REVERT: A 421 LYS cc_start: 0.7887 (mttt) cc_final: 0.7686 (mttp) REVERT: A 483 TYR cc_start: 0.8252 (t80) cc_final: 0.7803 (t80) REVERT: C 129 MET cc_start: 0.6528 (mtp) cc_final: 0.6279 (mtp) REVERT: C 151 ASP cc_start: 0.7950 (m-30) cc_final: 0.7685 (m-30) REVERT: C 231 TYR cc_start: 0.7861 (t80) cc_final: 0.7650 (t80) REVERT: C 317 ILE cc_start: 0.8646 (mt) cc_final: 0.8283 (tp) REVERT: C 355 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7071 (ttp80) REVERT: C 421 LYS cc_start: 0.7857 (mttt) cc_final: 0.7553 (mmtp) REVERT: B 142 VAL cc_start: 0.7731 (t) cc_final: 0.7350 (p) REVERT: B 154 MET cc_start: 0.6747 (mmt) cc_final: 0.6469 (mmm) REVERT: B 231 TYR cc_start: 0.7903 (t80) cc_final: 0.7568 (t80) REVERT: B 248 LEU cc_start: 0.8004 (tp) cc_final: 0.7695 (mp) REVERT: B 325 MET cc_start: 0.8589 (mtm) cc_final: 0.8064 (mtm) REVERT: B 421 LYS cc_start: 0.7833 (mttt) cc_final: 0.7140 (mmtp) REVERT: B 440 GLU cc_start: 0.8347 (tt0) cc_final: 0.8133 (tt0) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 1.8235 time to fit residues: 378.5770 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 65 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN B 426 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106684 restraints weight = 29066.867| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.06 r_work: 0.3019 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12948 Z= 0.194 Angle : 0.593 6.360 17547 Z= 0.322 Chirality : 0.040 0.126 1995 Planarity : 0.005 0.047 2115 Dihedral : 14.417 146.705 1998 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.03 % Allowed : 7.05 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.12 (0.21), residues: 1593 helix: 1.80 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -0.47 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 323 HIS 0.006 0.001 HIS C 288 PHE 0.030 0.002 PHE A 279 TYR 0.010 0.002 TYR C 310 ARG 0.005 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.07421 ( 967) hydrogen bonds : angle 4.19248 ( 2856) covalent geometry : bond 0.00433 (12948) covalent geometry : angle 0.59259 (17547) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 1.716 Fit side-chains REVERT: A 129 MET cc_start: 0.6461 (mtp) cc_final: 0.6203 (mtp) REVERT: A 193 LEU cc_start: 0.7991 (mt) cc_final: 0.7667 (mm) REVERT: A 248 LEU cc_start: 0.8330 (tp) cc_final: 0.7819 (mp) REVERT: A 483 TYR cc_start: 0.8258 (t80) cc_final: 0.7738 (t80) REVERT: A 497 MET cc_start: 0.8813 (tmm) cc_final: 0.8553 (tmm) REVERT: C 129 MET cc_start: 0.6517 (mtp) cc_final: 0.6286 (mtp) REVERT: C 231 TYR cc_start: 0.8156 (t80) cc_final: 0.7738 (t80) REVERT: C 253 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6880 (tp30) REVERT: C 355 ARG cc_start: 0.7952 (ttt180) cc_final: 0.7119 (ttp80) REVERT: C 421 LYS cc_start: 0.7814 (mttt) cc_final: 0.7585 (mmtp) REVERT: B 142 VAL cc_start: 0.7741 (t) cc_final: 0.7355 (p) REVERT: B 231 TYR cc_start: 0.7996 (t80) cc_final: 0.7596 (t80) REVERT: B 248 LEU cc_start: 0.8315 (tp) cc_final: 0.7897 (mp) REVERT: B 305 MET cc_start: 0.8872 (mmm) cc_final: 0.8613 (mmm) REVERT: B 325 MET cc_start: 0.8675 (mtm) cc_final: 0.8012 (mtm) REVERT: B 421 LYS cc_start: 0.7875 (mttt) cc_final: 0.7215 (mmtp) REVERT: B 440 GLU cc_start: 0.8611 (tt0) cc_final: 0.8394 (tt0) REVERT: B 448 SER cc_start: 0.8965 (m) cc_final: 0.8762 (p) outliers start: 13 outliers final: 6 residues processed: 186 average time/residue: 1.7284 time to fit residues: 365.0745 Evaluate side-chains 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 127 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.153225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107622 restraints weight = 29501.564| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.06 r_work: 0.3032 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12948 Z= 0.167 Angle : 0.550 5.522 17547 Z= 0.298 Chirality : 0.038 0.123 1995 Planarity : 0.004 0.046 2115 Dihedral : 13.970 147.508 1998 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.11 % Allowed : 7.36 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.51 (0.21), residues: 1593 helix: 2.09 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 323 HIS 0.005 0.001 HIS C 288 PHE 0.026 0.002 PHE C 279 TYR 0.010 0.002 TYR C 310 ARG 0.004 0.001 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.06570 ( 967) hydrogen bonds : angle 4.05521 ( 2856) covalent geometry : bond 0.00365 (12948) covalent geometry : angle 0.55019 (17547) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 1.829 Fit side-chains REVERT: A 193 LEU cc_start: 0.8118 (mt) cc_final: 0.7809 (mm) REVERT: A 248 LEU cc_start: 0.8332 (tp) cc_final: 0.7826 (mp) REVERT: A 483 TYR cc_start: 0.8259 (t80) cc_final: 0.7787 (t80) REVERT: C 129 MET cc_start: 0.6727 (mtp) cc_final: 0.6477 (mtp) REVERT: C 253 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6885 (tp30) REVERT: C 355 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7186 (ttp80) REVERT: C 421 LYS cc_start: 0.7839 (mttt) cc_final: 0.7617 (mmtp) REVERT: B 142 VAL cc_start: 0.7765 (t) cc_final: 0.7419 (p) REVERT: B 231 TYR cc_start: 0.7998 (t80) cc_final: 0.7633 (t80) REVERT: B 248 LEU cc_start: 0.8294 (tp) cc_final: 0.7845 (mp) REVERT: B 325 MET cc_start: 0.8757 (mtm) cc_final: 0.8013 (mtm) REVERT: B 421 LYS cc_start: 0.7890 (mttt) cc_final: 0.7173 (mmtp) REVERT: B 440 GLU cc_start: 0.8570 (tt0) cc_final: 0.8363 (tt0) REVERT: B 448 SER cc_start: 0.8986 (m) cc_final: 0.8762 (p) outliers start: 14 outliers final: 10 residues processed: 177 average time/residue: 1.8567 time to fit residues: 370.8409 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.108687 restraints weight = 29522.801| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.12 r_work: 0.3024 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12948 Z= 0.159 Angle : 0.540 5.797 17547 Z= 0.292 Chirality : 0.038 0.123 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.613 147.680 1998 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.27 % Allowed : 7.28 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.66 (0.21), residues: 1593 helix: 2.20 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.005 0.001 HIS C 288 PHE 0.024 0.002 PHE A 279 TYR 0.009 0.002 TYR C 310 ARG 0.003 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.06446 ( 967) hydrogen bonds : angle 3.99218 ( 2856) covalent geometry : bond 0.00341 (12948) covalent geometry : angle 0.54000 (17547) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.720 Fit side-chains REVERT: A 193 LEU cc_start: 0.8022 (mt) cc_final: 0.7713 (mm) REVERT: A 231 TYR cc_start: 0.8073 (t80) cc_final: 0.7694 (t80) REVERT: A 248 LEU cc_start: 0.8336 (tp) cc_final: 0.7887 (mm) REVERT: A 483 TYR cc_start: 0.8231 (t80) cc_final: 0.7772 (t80) REVERT: C 129 MET cc_start: 0.6640 (mtp) cc_final: 0.6382 (mtp) REVERT: C 231 TYR cc_start: 0.8124 (t80) cc_final: 0.7789 (t80) REVERT: C 253 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6860 (tp30) REVERT: C 355 ARG cc_start: 0.7929 (ttt180) cc_final: 0.7151 (ttp80) REVERT: C 421 LYS cc_start: 0.7821 (mttt) cc_final: 0.7593 (mmtp) REVERT: B 142 VAL cc_start: 0.7687 (t) cc_final: 0.7338 (p) REVERT: B 231 TYR cc_start: 0.7963 (t80) cc_final: 0.7521 (t80) REVERT: B 248 LEU cc_start: 0.8241 (tp) cc_final: 0.7841 (mm) REVERT: B 325 MET cc_start: 0.8741 (mtm) cc_final: 0.7929 (mtm) REVERT: B 421 LYS cc_start: 0.7821 (mttt) cc_final: 0.7195 (mmtt) REVERT: B 448 SER cc_start: 0.8971 (m) cc_final: 0.8744 (p) outliers start: 16 outliers final: 14 residues processed: 181 average time/residue: 1.7737 time to fit residues: 363.3447 Evaluate side-chains 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.152966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108358 restraints weight = 29358.469| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.03 r_work: 0.3041 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12948 Z= 0.154 Angle : 0.533 7.060 17547 Z= 0.287 Chirality : 0.037 0.121 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.540 148.878 1998 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.35 % Allowed : 7.68 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.78 (0.21), residues: 1593 helix: 2.29 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.34 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 PHE 0.024 0.002 PHE A 279 TYR 0.009 0.002 TYR C 310 ARG 0.003 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.06279 ( 967) hydrogen bonds : angle 3.96008 ( 2856) covalent geometry : bond 0.00329 (12948) covalent geometry : angle 0.53303 (17547) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 2.057 Fit side-chains REVERT: A 193 LEU cc_start: 0.8011 (mt) cc_final: 0.7706 (mm) REVERT: A 231 TYR cc_start: 0.8062 (t80) cc_final: 0.7713 (t80) REVERT: A 248 LEU cc_start: 0.8331 (tp) cc_final: 0.7887 (mm) REVERT: A 483 TYR cc_start: 0.8235 (t80) cc_final: 0.7682 (t80) REVERT: C 129 MET cc_start: 0.6616 (mtp) cc_final: 0.6359 (mtp) REVERT: C 253 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6879 (tp30) REVERT: C 355 ARG cc_start: 0.7931 (ttt180) cc_final: 0.7164 (ttp80) REVERT: C 421 LYS cc_start: 0.7831 (mttt) cc_final: 0.7605 (mmtp) REVERT: B 142 VAL cc_start: 0.7748 (t) cc_final: 0.7373 (p) REVERT: B 231 TYR cc_start: 0.7940 (t80) cc_final: 0.7514 (t80) REVERT: B 248 LEU cc_start: 0.8225 (tp) cc_final: 0.7829 (mm) REVERT: B 325 MET cc_start: 0.8738 (mtm) cc_final: 0.7996 (mtm) REVERT: B 421 LYS cc_start: 0.7824 (mttt) cc_final: 0.7207 (mmtt) REVERT: B 448 SER cc_start: 0.8969 (m) cc_final: 0.8741 (p) outliers start: 17 outliers final: 15 residues processed: 176 average time/residue: 1.8027 time to fit residues: 360.6041 Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.152576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107184 restraints weight = 29265.484| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.05 r_work: 0.3026 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12948 Z= 0.179 Angle : 0.571 6.822 17547 Z= 0.308 Chirality : 0.039 0.129 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.828 149.955 1998 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.43 % Allowed : 7.76 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.61 (0.21), residues: 1593 helix: 2.14 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -0.29 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.005 0.001 HIS C 288 PHE 0.027 0.002 PHE A 279 TYR 0.010 0.002 TYR C 310 ARG 0.005 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.06804 ( 967) hydrogen bonds : angle 4.04650 ( 2856) covalent geometry : bond 0.00395 (12948) covalent geometry : angle 0.57121 (17547) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.951 Fit side-chains REVERT: A 193 LEU cc_start: 0.7934 (mt) cc_final: 0.7616 (mm) REVERT: A 231 TYR cc_start: 0.8090 (t80) cc_final: 0.7736 (t80) REVERT: A 248 LEU cc_start: 0.8364 (tp) cc_final: 0.7918 (mm) REVERT: A 421 LYS cc_start: 0.8010 (mttp) cc_final: 0.7798 (mttt) REVERT: A 483 TYR cc_start: 0.8264 (t80) cc_final: 0.7717 (t80) REVERT: C 129 MET cc_start: 0.6679 (mtp) cc_final: 0.6470 (mtp) REVERT: C 253 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6914 (tp30) REVERT: C 355 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7177 (ttp80) REVERT: C 421 LYS cc_start: 0.7832 (mttt) cc_final: 0.7620 (mmtp) REVERT: B 142 VAL cc_start: 0.7704 (t) cc_final: 0.7323 (p) REVERT: B 231 TYR cc_start: 0.7979 (t80) cc_final: 0.7579 (t80) REVERT: B 248 LEU cc_start: 0.8292 (tp) cc_final: 0.7896 (mm) REVERT: B 325 MET cc_start: 0.8757 (mtm) cc_final: 0.7939 (mtm) REVERT: B 421 LYS cc_start: 0.7898 (mttt) cc_final: 0.7204 (mmtt) REVERT: B 448 SER cc_start: 0.8984 (m) cc_final: 0.8755 (p) outliers start: 18 outliers final: 15 residues processed: 179 average time/residue: 1.7393 time to fit residues: 354.8355 Evaluate side-chains 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 129 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.153497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109112 restraints weight = 29290.175| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.03 r_work: 0.3053 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12948 Z= 0.141 Angle : 0.512 6.274 17547 Z= 0.276 Chirality : 0.037 0.121 1995 Planarity : 0.004 0.044 2115 Dihedral : 13.360 150.583 1998 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.27 % Allowed : 8.08 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.93 (0.21), residues: 1593 helix: 2.35 (0.14), residues: 1332 sheet: None (None), residues: 0 loop : -0.27 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 PHE 0.023 0.001 PHE C 279 TYR 0.008 0.001 TYR C 310 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05952 ( 967) hydrogen bonds : angle 3.89221 ( 2856) covalent geometry : bond 0.00295 (12948) covalent geometry : angle 0.51206 (17547) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7898 (mt) cc_final: 0.7577 (mm) REVERT: A 231 TYR cc_start: 0.8037 (t80) cc_final: 0.7688 (t80) REVERT: A 248 LEU cc_start: 0.8288 (tp) cc_final: 0.7851 (mm) REVERT: A 483 TYR cc_start: 0.8293 (t80) cc_final: 0.7799 (t80) REVERT: C 129 MET cc_start: 0.6653 (mtp) cc_final: 0.6443 (mtp) REVERT: C 253 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6798 (tp30) REVERT: C 355 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7082 (ttp80) REVERT: C 421 LYS cc_start: 0.7840 (mttt) cc_final: 0.7605 (mmtp) REVERT: C 506 ASP cc_start: 0.8286 (p0) cc_final: 0.8080 (p0) REVERT: B 142 VAL cc_start: 0.7738 (t) cc_final: 0.7406 (p) REVERT: B 231 TYR cc_start: 0.7916 (t80) cc_final: 0.7499 (t80) REVERT: B 248 LEU cc_start: 0.8205 (tp) cc_final: 0.7822 (mm) REVERT: B 325 MET cc_start: 0.8745 (mtm) cc_final: 0.8000 (mtm) REVERT: B 421 LYS cc_start: 0.7832 (mttt) cc_final: 0.7216 (mmtt) REVERT: B 448 SER cc_start: 0.8969 (m) cc_final: 0.8739 (p) outliers start: 16 outliers final: 13 residues processed: 175 average time/residue: 1.7877 time to fit residues: 354.8095 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 79 optimal weight: 0.0570 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.156001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110974 restraints weight = 29365.052| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.06 r_work: 0.3078 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12948 Z= 0.118 Angle : 0.471 6.231 17547 Z= 0.254 Chirality : 0.035 0.118 1995 Planarity : 0.003 0.043 2115 Dihedral : 12.660 148.508 1998 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.79 % Allowed : 8.55 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.25 (0.21), residues: 1593 helix: 2.56 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -0.13 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.003 0.001 HIS C 288 PHE 0.019 0.001 PHE C 279 TYR 0.007 0.001 TYR C 231 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 967) hydrogen bonds : angle 3.72101 ( 2856) covalent geometry : bond 0.00236 (12948) covalent geometry : angle 0.47145 (17547) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7857 (mt) cc_final: 0.7547 (mm) REVERT: A 248 LEU cc_start: 0.8170 (tp) cc_final: 0.7722 (mm) REVERT: A 483 TYR cc_start: 0.8385 (t80) cc_final: 0.7903 (t80) REVERT: A 506 ASP cc_start: 0.7833 (p0) cc_final: 0.7579 (p0) REVERT: C 129 MET cc_start: 0.6643 (mtp) cc_final: 0.6430 (mtp) REVERT: C 253 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6746 (tp30) REVERT: C 317 ILE cc_start: 0.8614 (mt) cc_final: 0.8186 (tp) REVERT: C 355 ARG cc_start: 0.7879 (ttt180) cc_final: 0.7065 (ttp80) REVERT: C 421 LYS cc_start: 0.7885 (mttt) cc_final: 0.7605 (mmtp) REVERT: C 472 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8441 (t) REVERT: B 142 VAL cc_start: 0.7741 (t) cc_final: 0.7377 (p) REVERT: B 231 TYR cc_start: 0.7849 (t80) cc_final: 0.7560 (t80) REVERT: B 248 LEU cc_start: 0.8099 (tp) cc_final: 0.7700 (mm) REVERT: B 325 MET cc_start: 0.8753 (mtm) cc_final: 0.7877 (mtm) REVERT: B 421 LYS cc_start: 0.7886 (mttt) cc_final: 0.7204 (mmtp) REVERT: B 448 SER cc_start: 0.8973 (m) cc_final: 0.8756 (p) outliers start: 10 outliers final: 5 residues processed: 175 average time/residue: 1.7413 time to fit residues: 345.3022 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.153554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109101 restraints weight = 29259.729| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.03 r_work: 0.3051 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12948 Z= 0.145 Angle : 0.519 6.942 17547 Z= 0.280 Chirality : 0.037 0.122 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.210 148.576 1998 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.48 % Allowed : 9.74 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.06 (0.21), residues: 1593 helix: 2.44 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 323 HIS 0.004 0.001 HIS C 288 PHE 0.024 0.002 PHE A 279 TYR 0.009 0.001 TYR C 310 ARG 0.002 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.06030 ( 967) hydrogen bonds : angle 3.86072 ( 2856) covalent geometry : bond 0.00305 (12948) covalent geometry : angle 0.51921 (17547) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 1.839 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7867 (mt) cc_final: 0.7549 (mm) REVERT: A 231 TYR cc_start: 0.8043 (t80) cc_final: 0.7611 (t80) REVERT: A 248 LEU cc_start: 0.8295 (tp) cc_final: 0.7840 (mm) REVERT: A 483 TYR cc_start: 0.8390 (t80) cc_final: 0.7902 (t80) REVERT: C 129 MET cc_start: 0.6612 (mtp) cc_final: 0.6399 (mtp) REVERT: C 253 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6809 (tp30) REVERT: C 355 ARG cc_start: 0.7921 (ttt180) cc_final: 0.7157 (ttp80) REVERT: C 421 LYS cc_start: 0.7844 (mttt) cc_final: 0.7586 (mmtp) REVERT: B 142 VAL cc_start: 0.7765 (t) cc_final: 0.7394 (p) REVERT: B 231 TYR cc_start: 0.7927 (t80) cc_final: 0.7529 (t80) REVERT: B 248 LEU cc_start: 0.8164 (tp) cc_final: 0.7765 (mm) REVERT: B 325 MET cc_start: 0.8773 (mtm) cc_final: 0.7922 (mtm) REVERT: B 421 LYS cc_start: 0.7847 (mttt) cc_final: 0.7174 (mmtp) REVERT: B 448 SER cc_start: 0.8978 (m) cc_final: 0.8765 (p) outliers start: 6 outliers final: 6 residues processed: 170 average time/residue: 1.8404 time to fit residues: 353.4270 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 49 optimal weight: 4.9990 chunk 151 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108796 restraints weight = 29139.224| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.12 r_work: 0.3030 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12948 Z= 0.164 Angle : 0.546 6.720 17547 Z= 0.294 Chirality : 0.038 0.129 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.459 150.722 1998 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.87 % Allowed : 9.58 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.89 (0.21), residues: 1593 helix: 2.32 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -0.30 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 323 HIS 0.005 0.001 HIS C 288 PHE 0.024 0.002 PHE A 279 TYR 0.010 0.002 TYR C 310 ARG 0.004 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.06401 ( 967) hydrogen bonds : angle 3.94194 ( 2856) covalent geometry : bond 0.00356 (12948) covalent geometry : angle 0.54641 (17547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17564.77 seconds wall clock time: 300 minutes 24.14 seconds (18024.14 seconds total)