Starting phenix.real_space_refine on Sat Jun 21 20:16:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz3_41732/06_2025/8tz3_41732_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz3_41732/06_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_41732/06_2025/8tz3_41732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz3_41732/06_2025/8tz3_41732.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz3_41732/06_2025/8tz3_41732_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz3_41732/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.28, per 1000 atoms: 0.49 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: 6.44 Conformation dependent library (CDL) restraints added in 2.2 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: 2.09 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: 8.90 Time building geometry restraints manager: 7.88 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: 2.070 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: 0.470 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 53.500 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.850 ------------------------------------------------------------------------------- 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 : 1.833 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: 2.0425 time to fit residues: 521.6936 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 : 1.871 ------------------------------------------------------------------------------- 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 = 71)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116745 restraints weight = 29731.608| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.11 r_work: 0.3179 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 1.804 Fit side-chains REVERT: A 129 MET cc_start: 0.6501 (mtp) cc_final: 0.6247 (mtp) REVERT: A 189 LEU cc_start: 0.6990 (tp) cc_final: 0.6484 (tm) REVERT: A 231 TYR cc_start: 0.7984 (t80) cc_final: 0.7635 (t80) REVERT: A 248 LEU cc_start: 0.8130 (tp) cc_final: 0.7705 (mp) REVERT: A 317 ILE cc_start: 0.8684 (mt) cc_final: 0.8406 (tp) REVERT: A 325 MET cc_start: 0.8551 (mtm) cc_final: 0.8177 (mtm) REVERT: A 483 TYR cc_start: 0.8260 (t80) cc_final: 0.7811 (t80) REVERT: C 129 MET cc_start: 0.6543 (mtp) cc_final: 0.6293 (mtp) REVERT: C 151 ASP cc_start: 0.7955 (m-30) cc_final: 0.7688 (m-30) REVERT: C 231 TYR cc_start: 0.7866 (t80) cc_final: 0.7654 (t80) REVERT: C 317 ILE cc_start: 0.8648 (mt) cc_final: 0.8288 (tp) REVERT: C 355 ARG cc_start: 0.7859 (ttt180) cc_final: 0.7087 (ttp80) REVERT: C 421 LYS cc_start: 0.7864 (mttt) cc_final: 0.7562 (mmtp) REVERT: B 142 VAL cc_start: 0.7737 (t) cc_final: 0.7356 (p) REVERT: B 154 MET cc_start: 0.6757 (mmt) cc_final: 0.6479 (mmm) REVERT: B 231 TYR cc_start: 0.7910 (t80) cc_final: 0.7574 (t80) REVERT: B 248 LEU cc_start: 0.8005 (tp) cc_final: 0.7698 (mp) REVERT: B 325 MET cc_start: 0.8591 (mtm) cc_final: 0.8065 (mtm) REVERT: B 421 LYS cc_start: 0.7839 (mttt) cc_final: 0.7152 (mmtp) REVERT: B 440 GLU cc_start: 0.8348 (tt0) cc_final: 0.8134 (tt0) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 1.8306 time to fit residues: 380.3848 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 : 1.891 ------------------------------------------------------------------------------- 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 = 0.152443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106657 restraints weight = 29064.826| |-----------------------------------------------------------------------------| 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: 0.8109 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12948 Z= 0.194 Angle : 0.595 6.431 17547 Z= 0.323 Chirality : 0.040 0.126 1995 Planarity : 0.005 0.048 2115 Dihedral : 14.429 146.820 1998 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.03 % Allowed : 7.13 % Favored : 91.84 % 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: 2.11 (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 0.011 0.002 TYR C 310 ARG 0.005 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.07433 ( 967) hydrogen bonds : angle 4.19561 ( 2856) covalent geometry : bond 0.00432 (12948) covalent geometry : angle 0.59456 (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 : 1.896 Fit side-chains REVERT: A 129 MET cc_start: 0.6487 (mtp) cc_final: 0.6230 (mtp) REVERT: A 193 LEU cc_start: 0.8021 (mt) cc_final: 0.7692 (mm) REVERT: A 248 LEU cc_start: 0.8332 (tp) cc_final: 0.7821 (mp) REVERT: A 483 TYR cc_start: 0.8264 (t80) cc_final: 0.7744 (t80) REVERT: A 497 MET cc_start: 0.8813 (tmm) cc_final: 0.8557 (tmm) REVERT: C 129 MET cc_start: 0.6542 (mtp) cc_final: 0.6311 (mtp) REVERT: C 231 TYR cc_start: 0.8162 (t80) cc_final: 0.7749 (t80) REVERT: C 253 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6891 (tp30) REVERT: C 355 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7120 (ttp80) REVERT: C 421 LYS cc_start: 0.7812 (mttt) cc_final: 0.7585 (mmtp) REVERT: B 142 VAL cc_start: 0.7753 (t) cc_final: 0.7368 (p) REVERT: B 231 TYR cc_start: 0.7999 (t80) cc_final: 0.7602 (t80) REVERT: B 248 LEU cc_start: 0.8319 (tp) cc_final: 0.7899 (mp) REVERT: B 305 MET cc_start: 0.8870 (mmm) cc_final: 0.8612 (mmm) REVERT: B 325 MET cc_start: 0.8676 (mtm) cc_final: 0.8012 (mtm) REVERT: B 421 LYS cc_start: 0.7874 (mttt) cc_final: 0.7215 (mmtp) REVERT: B 440 GLU cc_start: 0.8611 (tt0) cc_final: 0.8391 (tt0) REVERT: B 448 SER cc_start: 0.8962 (m) cc_final: 0.8760 (p) outliers start: 13 outliers final: 7 residues processed: 186 average time/residue: 1.8102 time to fit residues: 382.3268 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 171 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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 444 GLN 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: 0.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.153146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107567 restraints weight = 29499.696| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.06 r_work: 0.3031 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2851 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= 0.169 Angle : 0.553 5.758 17547 Z= 0.299 Chirality : 0.038 0.123 1995 Planarity : 0.004 0.046 2115 Dihedral : 14.031 147.701 1998 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.19 % Allowed : 7.21 % Favored : 91.61 % 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: 1314 sheet: None (None), residues: 0 loop : -0.40 (0.35), residues: 279 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 0.026 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 0.06601 ( 967) hydrogen bonds : angle 4.06081 ( 2856) covalent geometry : bond 0.00369 (12948) covalent geometry : angle 0.55327 (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 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 5.022 Fit side-chains REVERT: A 193 LEU cc_start: 0.8055 (mt) cc_final: 0.7740 (mm) REVERT: A 248 LEU cc_start: 0.8321 (tp) cc_final: 0.7809 (mp) REVERT: A 483 TYR cc_start: 0.8240 (t80) cc_final: 0.7765 (t80) REVERT: C 129 MET cc_start: 0.6669 (mtp) cc_final: 0.6416 (mtp) REVERT: C 253 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6867 (tp30) REVERT: C 355 ARG cc_start: 0.7935 (ttt180) cc_final: 0.7163 (ttp80) REVERT: C 421 LYS cc_start: 0.7835 (mttt) cc_final: 0.7614 (mmtp) REVERT: B 142 VAL cc_start: 0.7725 (t) cc_final: 0.7376 (p) REVERT: B 231 TYR cc_start: 0.7990 (t80) cc_final: 0.7627 (t80) REVERT: B 248 LEU cc_start: 0.8291 (tp) cc_final: 0.7837 (mp) REVERT: B 325 MET cc_start: 0.8748 (mtm) cc_final: 0.8003 (mtm) REVERT: B 421 LYS cc_start: 0.7884 (mttt) cc_final: 0.7164 (mmtp) REVERT: B 440 GLU cc_start: 0.8574 (tt0) cc_final: 0.8365 (tt0) REVERT: B 448 SER cc_start: 0.8978 (m) cc_final: 0.8750 (p) outliers start: 15 outliers final: 9 residues processed: 178 average time/residue: 2.3166 time to fit residues: 469.2505 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 2.498 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 124 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.153712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109988 restraints weight = 29523.094| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.08 r_work: 0.3050 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12948 Z= 0.140 Angle : 0.507 4.919 17547 Z= 0.273 Chirality : 0.037 0.120 1995 Planarity : 0.004 0.044 2115 Dihedral : 13.107 146.779 1998 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.87 % Allowed : 7.60 % 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: 2.85 (0.21), residues: 1593 helix: 2.34 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 276 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 0.022 0.001 PHE C 279 TYR 0.008 0.001 TYR C 310 ARG 0.002 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.05951 ( 967) hydrogen bonds : angle 3.89001 ( 2856) covalent geometry : bond 0.00291 (12948) covalent geometry : angle 0.50650 (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 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.956 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7985 (mt) cc_final: 0.7666 (mm) REVERT: A 231 TYR cc_start: 0.8030 (t80) cc_final: 0.7627 (t80) REVERT: A 248 LEU cc_start: 0.8268 (tp) cc_final: 0.7827 (mm) REVERT: A 483 TYR cc_start: 0.8241 (t80) cc_final: 0.7793 (t80) REVERT: A 506 ASP cc_start: 0.7920 (p0) cc_final: 0.7582 (p0) REVERT: C 231 TYR cc_start: 0.8070 (t80) cc_final: 0.7660 (t80) REVERT: C 253 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6789 (tp30) REVERT: C 355 ARG cc_start: 0.7872 (ttt180) cc_final: 0.7086 (ttp80) REVERT: C 421 LYS cc_start: 0.7862 (mttt) cc_final: 0.7614 (mmtp) REVERT: B 142 VAL cc_start: 0.7703 (t) cc_final: 0.7356 (p) REVERT: B 231 TYR cc_start: 0.7898 (t80) cc_final: 0.7554 (t80) REVERT: B 248 LEU cc_start: 0.8178 (tp) cc_final: 0.7787 (mm) REVERT: B 325 MET cc_start: 0.8743 (mtm) cc_final: 0.8013 (mtm) REVERT: B 421 LYS cc_start: 0.7818 (mttt) cc_final: 0.7199 (mmtt) REVERT: B 448 SER cc_start: 0.8971 (m) cc_final: 0.8754 (p) outliers start: 11 outliers final: 10 residues processed: 176 average time/residue: 1.9550 time to fit residues: 390.5509 Evaluate side-chains 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU 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 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 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: 0.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.152091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107505 restraints weight = 29365.328| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.03 r_work: 0.3030 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12948 Z= 0.171 Angle : 0.560 7.135 17547 Z= 0.302 Chirality : 0.039 0.133 1995 Planarity : 0.004 0.046 2115 Dihedral : 13.710 148.184 1998 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.43 % Allowed : 7.68 % Favored : 90.89 % 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: 2.19 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 276 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 0.026 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 0.06660 ( 967) hydrogen bonds : angle 4.01740 ( 2856) covalent geometry : bond 0.00371 (12948) covalent geometry : angle 0.56001 (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 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.866 Fit side-chains REVERT: A 193 LEU cc_start: 0.7953 (mt) cc_final: 0.7641 (mm) REVERT: A 231 TYR cc_start: 0.8086 (t80) cc_final: 0.7727 (t80) REVERT: A 248 LEU cc_start: 0.8357 (tp) cc_final: 0.7913 (mm) REVERT: A 483 TYR cc_start: 0.8238 (t80) cc_final: 0.7793 (t80) REVERT: C 222 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8105 (tt) REVERT: C 253 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6908 (tp30) REVERT: C 355 ARG cc_start: 0.7942 (ttt180) cc_final: 0.7181 (ttp80) REVERT: C 421 LYS cc_start: 0.7832 (mttt) cc_final: 0.7614 (mmtp) REVERT: B 142 VAL cc_start: 0.7749 (t) cc_final: 0.7373 (p) REVERT: B 231 TYR cc_start: 0.7977 (t80) cc_final: 0.7559 (t80) REVERT: B 248 LEU cc_start: 0.8268 (tp) cc_final: 0.7876 (mm) REVERT: B 325 MET cc_start: 0.8755 (mtm) cc_final: 0.8019 (mtm) REVERT: B 421 LYS cc_start: 0.7828 (mttt) cc_final: 0.7212 (mmtt) REVERT: B 448 SER cc_start: 0.8981 (m) cc_final: 0.8760 (p) outliers start: 18 outliers final: 14 residues processed: 179 average time/residue: 1.7711 time to fit residues: 359.5041 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 : 1.752 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain C residue 413 PHE 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: 0.7980 chunk 19 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.152681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108180 restraints weight = 29338.323| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.03 r_work: 0.3039 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12948 Z= 0.158 Angle : 0.535 6.419 17547 Z= 0.289 Chirality : 0.038 0.122 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.575 149.801 1998 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.19 % Allowed : 8.31 % Favored : 90.50 % 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: 2.80 (0.21), residues: 1593 helix: 2.29 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.25 (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 C 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 0.06320 ( 967) hydrogen bonds : angle 3.95987 ( 2856) covalent geometry : bond 0.00339 (12948) covalent geometry : angle 0.53518 (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 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.801 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7915 (mt) cc_final: 0.7599 (mm) REVERT: A 231 TYR cc_start: 0.8066 (t80) cc_final: 0.7712 (t80) REVERT: A 248 LEU cc_start: 0.8341 (tp) cc_final: 0.7900 (mm) REVERT: A 483 TYR cc_start: 0.8248 (t80) cc_final: 0.7707 (t80) REVERT: C 151 ASP cc_start: 0.8104 (m-30) cc_final: 0.7891 (m-30) REVERT: C 253 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6883 (tp30) REVERT: C 355 ARG cc_start: 0.7941 (ttt180) cc_final: 0.7174 (ttp80) REVERT: C 421 LYS cc_start: 0.7832 (mttt) cc_final: 0.7613 (mmtp) REVERT: C 472 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8450 (t) REVERT: B 142 VAL cc_start: 0.7766 (t) cc_final: 0.7391 (p) REVERT: B 231 TYR cc_start: 0.7944 (t80) cc_final: 0.7526 (t80) REVERT: B 248 LEU cc_start: 0.8239 (tp) cc_final: 0.7845 (mm) REVERT: B 325 MET cc_start: 0.8744 (mtm) cc_final: 0.7997 (mtm) REVERT: B 421 LYS cc_start: 0.7827 (mttt) cc_final: 0.7207 (mmtt) REVERT: B 448 SER cc_start: 0.8971 (m) cc_final: 0.8742 (p) outliers start: 15 outliers final: 14 residues processed: 177 average time/residue: 1.7842 time to fit residues: 359.1916 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 : 1.953 ------------------------------------------------------------------------------- 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 A residue 620 ASN 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: 0.6980 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.157470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112969 restraints weight = 29343.985| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.05 r_work: 0.3107 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3297 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= 0.105 Angle : 0.451 6.137 17547 Z= 0.243 Chirality : 0.035 0.115 1995 Planarity : 0.003 0.042 2115 Dihedral : 12.180 147.188 1998 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.79 % Allowed : 8.87 % Favored : 90.34 % 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: 3.39 (0.21), residues: 1593 helix: 2.66 (0.14), residues: 1332 sheet: None (None), residues: 0 loop : -0.07 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.002 0.000 HIS C 288 PHE 0.015 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 0.04691 ( 967) hydrogen bonds : angle 3.62937 ( 2856) covalent geometry : bond 0.00202 (12948) covalent geometry : angle 0.45058 (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: 10 poor density : 172 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7858 (mt) cc_final: 0.7521 (mm) REVERT: A 248 LEU cc_start: 0.8079 (tp) cc_final: 0.7559 (mp) REVERT: A 483 TYR cc_start: 0.8231 (t80) cc_final: 0.7736 (t80) REVERT: C 253 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6717 (tp30) REVERT: C 317 ILE cc_start: 0.8582 (mt) cc_final: 0.8138 (tp) REVERT: C 355 ARG cc_start: 0.7803 (ttt180) cc_final: 0.6982 (ttp80) REVERT: C 357 TYR cc_start: 0.8417 (m-80) cc_final: 0.8023 (m-80) REVERT: C 421 LYS cc_start: 0.7868 (mttt) cc_final: 0.7585 (mmtp) REVERT: C 472 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8390 (t) REVERT: B 142 VAL cc_start: 0.7673 (t) cc_final: 0.7351 (p) REVERT: B 231 TYR cc_start: 0.7791 (t80) cc_final: 0.7558 (t80) REVERT: B 248 LEU cc_start: 0.8013 (tp) cc_final: 0.7605 (mm) REVERT: B 325 MET cc_start: 0.8697 (mtm) cc_final: 0.7920 (mtm) REVERT: B 421 LYS cc_start: 0.7853 (mttt) cc_final: 0.7152 (mmtp) REVERT: B 448 SER cc_start: 0.8949 (m) cc_final: 0.8706 (p) outliers start: 10 outliers final: 4 residues processed: 176 average time/residue: 2.2183 time to fit residues: 446.5176 Evaluate side-chains 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 171 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 THR 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 306 SER 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: 0.7980 chunk 71 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.154506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110078 restraints weight = 29432.106| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.03 r_work: 0.3063 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12948 Z= 0.130 Angle : 0.491 6.430 17547 Z= 0.264 Chirality : 0.036 0.117 1995 Planarity : 0.004 0.044 2115 Dihedral : 12.730 145.627 1998 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.71 % Allowed : 9.11 % Favored : 90.18 % 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: 3.28 (0.21), residues: 1593 helix: 2.59 (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 0.009 0.001 TRP A 323 HIS 0.004 0.001 HIS C 288 PHE 0.020 0.001 PHE A 279 TYR 0.007 0.001 TYR C 310 ARG 0.002 0.000 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.05621 ( 967) hydrogen bonds : angle 3.75401 ( 2856) covalent geometry : bond 0.00266 (12948) covalent geometry : angle 0.49093 (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 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 1.932 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7859 (mt) cc_final: 0.7550 (mm) REVERT: A 248 LEU cc_start: 0.8214 (tp) cc_final: 0.7750 (mm) REVERT: A 483 TYR cc_start: 0.8298 (t80) cc_final: 0.7807 (t80) REVERT: C 222 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8057 (tt) REVERT: C 231 TYR cc_start: 0.8051 (t80) cc_final: 0.7720 (t80) REVERT: C 253 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6781 (tp30) REVERT: C 317 ILE cc_start: 0.8616 (mt) cc_final: 0.8184 (tp) REVERT: C 355 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7076 (ttp80) REVERT: C 421 LYS cc_start: 0.7870 (mttt) cc_final: 0.7596 (mmtp) REVERT: C 472 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8438 (t) REVERT: C 556 MET cc_start: 0.8309 (mtp) cc_final: 0.8100 (mtp) REVERT: B 142 VAL cc_start: 0.7719 (t) cc_final: 0.7355 (p) REVERT: B 231 TYR cc_start: 0.7869 (t80) cc_final: 0.7567 (t80) REVERT: B 248 LEU cc_start: 0.8071 (tp) cc_final: 0.7671 (mm) REVERT: B 325 MET cc_start: 0.8758 (mtm) cc_final: 0.7887 (mtm) REVERT: B 421 LYS cc_start: 0.7892 (mttt) cc_final: 0.7188 (mmtp) REVERT: B 448 SER cc_start: 0.8977 (m) cc_final: 0.8756 (p) outliers start: 9 outliers final: 6 residues processed: 174 average time/residue: 1.8194 time to fit residues: 358.6925 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 222 LEU 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 306 SER 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: 1.9990 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.152985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108431 restraints weight = 29258.869| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.03 r_work: 0.3040 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12948 Z= 0.161 Angle : 0.545 7.033 17547 Z= 0.293 Chirality : 0.038 0.139 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.357 148.197 1998 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.87 % Allowed : 9.26 % Favored : 89.87 % 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: 2.98 (0.21), residues: 1593 helix: 2.39 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -0.25 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 323 HIS 0.004 0.001 HIS C 288 PHE 0.024 0.002 PHE A 279 TYR 0.009 0.002 TYR C 310 ARG 0.003 0.001 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.06392 ( 967) hydrogen bonds : angle 3.93133 ( 2856) covalent geometry : bond 0.00348 (12948) covalent geometry : angle 0.54453 (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 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.854 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7933 (mt) cc_final: 0.7625 (mm) REVERT: A 231 TYR cc_start: 0.8065 (t80) cc_final: 0.7730 (t80) REVERT: A 248 LEU cc_start: 0.8348 (tp) cc_final: 0.7892 (mm) REVERT: A 483 TYR cc_start: 0.8331 (t80) cc_final: 0.7829 (t80) REVERT: C 222 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8070 (tt) REVERT: C 253 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6879 (tp30) REVERT: C 355 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7163 (ttp80) REVERT: C 421 LYS cc_start: 0.7837 (mttt) cc_final: 0.7592 (mmtp) REVERT: C 556 MET cc_start: 0.8338 (mtp) cc_final: 0.8119 (mtp) REVERT: B 142 VAL cc_start: 0.7763 (t) cc_final: 0.7393 (p) REVERT: B 231 TYR cc_start: 0.7939 (t80) cc_final: 0.7523 (t80) REVERT: B 248 LEU cc_start: 0.8251 (tp) cc_final: 0.7841 (mm) REVERT: B 325 MET cc_start: 0.8760 (mtm) cc_final: 0.7891 (mtm) REVERT: B 421 LYS cc_start: 0.7828 (mttt) cc_final: 0.7206 (mmtt) REVERT: B 448 SER cc_start: 0.8974 (m) cc_final: 0.8736 (p) outliers start: 11 outliers final: 10 residues processed: 176 average time/residue: 1.9684 time to fit residues: 395.9920 Evaluate side-chains 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 222 LEU 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 458 VAL 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: 0.7980 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: 2.9990 chunk 6 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.152263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107635 restraints weight = 29228.306| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.03 r_work: 0.3029 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12948 Z= 0.185 Angle : 0.575 6.756 17547 Z= 0.310 Chirality : 0.039 0.132 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.591 150.111 1998 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.87 % Allowed : 9.50 % Favored : 89.63 % 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: 2.77 (0.21), residues: 1593 helix: 2.22 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.19 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 323 HIS 0.006 0.001 HIS C 288 PHE 0.029 0.002 PHE A 279 TYR 0.011 0.002 TYR C 310 ARG 0.005 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.06780 ( 967) hydrogen bonds : angle 4.02222 ( 2856) covalent geometry : bond 0.00409 (12948) covalent geometry : angle 0.57489 (17547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20344.50 seconds wall clock time: 360 minutes 0.15 seconds (21600.15 seconds total)