Starting phenix.real_space_refine on Mon Aug 25 04:15:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz3_41732/08_2025/8tz3_41732_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz3_41732/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tz3_41732/08_2025/8tz3_41732_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz3_41732/08_2025/8tz3_41732_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tz3_41732/08_2025/8tz3_41732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz3_41732/08_2025/8tz3_41732.map" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} 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: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} 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: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} 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: 5.18, per 1000 atoms: 0.21 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: 2.42 Conformation dependent library (CDL) restraints added in 816.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.67 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: 5.84 Time building geometry restraints manager: 3.25 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: 0.04 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: 1.090 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: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.090 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.870 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.001 ARG B 355 TYR 0.012 0.002 TYR A 285 PHE 0.022 0.002 PHE C 279 TRP 0.009 0.001 TRP C 476 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.01135 (12948) covalent geometry : angle 0.99096 (17547) hydrogen bonds : bond 0.25785 ( 967) hydrogen bonds : angle 8.08470 ( 2856) *********************** 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 : 0.669 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: 0.8036 (p) REVERT: A 248 LEU cc_start: 0.8141 (tp) cc_final: 0.7832 (mp) REVERT: A 421 LYS cc_start: 0.7891 (mttt) cc_final: 0.7515 (mmtt) REVERT: A 483 TYR cc_start: 0.8200 (t80) cc_final: 0.7870 (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: 0.8006 (ttmt) REVERT: C 129 MET cc_start: 0.6650 (mtp) cc_final: 0.6327 (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: 0.7719 (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: 0.7933 (tt0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 1.0977 time to fit residues: 279.0781 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 : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3809 r_free = 0.3809 target = 0.161324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.116301 restraints weight = 29869.620| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.11 r_work: 0.3174 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12948 Z= 0.133 Angle : 0.529 4.533 17547 Z= 0.290 Chirality : 0.036 0.129 1995 Planarity : 0.005 0.049 2115 Dihedral : 14.798 146.936 1998 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.16 % Allowed : 7.52 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.20), residues: 1593 helix: 1.22 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : -0.51 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 557 TYR 0.010 0.001 TYR B 519 PHE 0.017 0.001 PHE C 279 TRP 0.008 0.001 TRP C 323 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00257 (12948) covalent geometry : angle 0.52931 (17547) hydrogen bonds : bond 0.05943 ( 967) hydrogen bonds : angle 4.21570 ( 2856) *********************** 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 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.697 Fit side-chains REVERT: A 129 MET cc_start: 0.6497 (mtp) cc_final: 0.6248 (mtp) REVERT: A 193 LEU cc_start: 0.8011 (mt) cc_final: 0.7668 (mm) REVERT: A 248 LEU cc_start: 0.8123 (tp) cc_final: 0.7700 (mp) REVERT: A 325 MET cc_start: 0.8564 (mtm) cc_final: 0.8198 (mtm) REVERT: A 483 TYR cc_start: 0.8265 (t80) cc_final: 0.7823 (t80) REVERT: A 554 MET cc_start: 0.8634 (ptt) cc_final: 0.8388 (ptt) REVERT: C 129 MET cc_start: 0.6543 (mtp) cc_final: 0.6294 (mtp) REVERT: C 231 TYR cc_start: 0.7891 (t80) cc_final: 0.7682 (t80) REVERT: C 317 ILE cc_start: 0.8653 (mt) cc_final: 0.8285 (tp) REVERT: C 355 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7089 (ttp80) REVERT: C 421 LYS cc_start: 0.7865 (mttt) cc_final: 0.7568 (mmtp) REVERT: B 142 VAL cc_start: 0.7733 (t) cc_final: 0.7352 (p) REVERT: B 151 ASP cc_start: 0.7799 (m-30) cc_final: 0.7511 (m-30) REVERT: B 154 MET cc_start: 0.6851 (mmt) cc_final: 0.6582 (mmm) REVERT: B 231 TYR cc_start: 0.7916 (t80) cc_final: 0.7582 (t80) REVERT: B 248 LEU cc_start: 0.8015 (tp) cc_final: 0.7706 (mp) REVERT: B 325 MET cc_start: 0.8591 (mtm) cc_final: 0.7982 (mtm) REVERT: B 421 LYS cc_start: 0.7842 (mttt) cc_final: 0.7156 (mmtp) REVERT: B 440 GLU cc_start: 0.8365 (tt0) cc_final: 0.8145 (tt0) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.9768 time to fit residues: 200.0577 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.152228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.106522 restraints weight = 29164.428| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.05 r_work: 0.3016 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12948 Z= 0.199 Angle : 0.605 6.476 17547 Z= 0.329 Chirality : 0.040 0.127 1995 Planarity : 0.005 0.048 2115 Dihedral : 14.595 147.025 1998 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.11 % Allowed : 7.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.21), residues: 1593 helix: 1.76 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -0.50 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 589 TYR 0.011 0.002 TYR C 310 PHE 0.031 0.002 PHE A 279 TRP 0.011 0.001 TRP B 323 HIS 0.006 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00444 (12948) covalent geometry : angle 0.60466 (17547) hydrogen bonds : bond 0.07542 ( 967) hydrogen bonds : angle 4.22868 ( 2856) *********************** 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 192 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.785 Fit side-chains REVERT: A 129 MET cc_start: 0.6468 (mtp) cc_final: 0.6212 (mtp) REVERT: A 193 LEU cc_start: 0.7991 (mt) cc_final: 0.7660 (mm) REVERT: A 231 TYR cc_start: 0.8095 (t80) cc_final: 0.7702 (t80) REVERT: A 248 LEU cc_start: 0.8340 (tp) cc_final: 0.7824 (mp) REVERT: A 483 TYR cc_start: 0.8245 (t80) cc_final: 0.7853 (t80) REVERT: A 497 MET cc_start: 0.8821 (tmm) cc_final: 0.8610 (tmm) REVERT: A 554 MET cc_start: 0.8783 (ptt) cc_final: 0.8474 (ptt) REVERT: C 129 MET cc_start: 0.6507 (mtp) cc_final: 0.6284 (mtp) REVERT: C 231 TYR cc_start: 0.8160 (t80) cc_final: 0.7772 (t80) REVERT: C 253 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6894 (tp30) REVERT: C 355 ARG cc_start: 0.7958 (ttt180) cc_final: 0.7120 (ttp80) REVERT: C 421 LYS cc_start: 0.7791 (mttt) cc_final: 0.7548 (mmtp) REVERT: B 142 VAL cc_start: 0.7733 (t) cc_final: 0.7346 (p) REVERT: B 231 TYR cc_start: 0.8019 (t80) cc_final: 0.7615 (t80) REVERT: B 248 LEU cc_start: 0.8317 (tp) cc_final: 0.7904 (mp) REVERT: B 305 MET cc_start: 0.8872 (mmm) cc_final: 0.8616 (mmm) REVERT: B 325 MET cc_start: 0.8679 (mtm) cc_final: 0.8007 (mtm) REVERT: B 421 LYS cc_start: 0.7854 (mttt) cc_final: 0.7214 (mmtp) REVERT: B 440 GLU cc_start: 0.8608 (tt0) cc_final: 0.8387 (tt0) REVERT: B 448 SER cc_start: 0.8966 (m) cc_final: 0.8761 (p) outliers start: 14 outliers final: 8 residues processed: 187 average time/residue: 0.9281 time to fit residues: 195.8401 Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 537 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 77 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.154636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.109453 restraints weight = 29290.760| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.04 r_work: 0.3057 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12948 Z= 0.135 Angle : 0.500 4.798 17547 Z= 0.271 Chirality : 0.036 0.117 1995 Planarity : 0.004 0.044 2115 Dihedral : 13.371 146.317 1998 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.79 % Allowed : 7.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.73 (0.21), residues: 1593 helix: 2.26 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.43 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 599 TYR 0.008 0.001 TYR C 310 PHE 0.022 0.001 PHE C 279 TRP 0.010 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00276 (12948) covalent geometry : angle 0.50048 (17547) hydrogen bonds : bond 0.05832 ( 967) hydrogen bonds : angle 3.92966 ( 2856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.681 Fit side-chains REVERT: A 129 MET cc_start: 0.6375 (mtp) cc_final: 0.6142 (mtp) REVERT: A 189 LEU cc_start: 0.6967 (tp) cc_final: 0.6433 (tm) REVERT: A 248 LEU cc_start: 0.8224 (tp) cc_final: 0.7698 (mp) REVERT: A 483 TYR cc_start: 0.8251 (t80) cc_final: 0.7773 (t80) REVERT: A 506 ASP cc_start: 0.7925 (p0) cc_final: 0.7585 (p0) REVERT: C 129 MET cc_start: 0.6602 (mtp) cc_final: 0.6343 (mtp) REVERT: C 231 TYR cc_start: 0.8081 (t80) cc_final: 0.7764 (t80) REVERT: C 253 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6816 (tp30) REVERT: C 317 ILE cc_start: 0.8618 (mt) cc_final: 0.8204 (tp) REVERT: C 355 ARG cc_start: 0.7863 (ttt180) cc_final: 0.7071 (ttp80) REVERT: C 421 LYS cc_start: 0.7818 (mttt) cc_final: 0.7579 (mmtp) REVERT: C 506 ASP cc_start: 0.8195 (p0) cc_final: 0.7990 (p0) REVERT: B 142 VAL cc_start: 0.7735 (t) cc_final: 0.7350 (p) REVERT: B 231 TYR cc_start: 0.7902 (t80) cc_final: 0.7511 (t80) REVERT: B 248 LEU cc_start: 0.8143 (tp) cc_final: 0.7729 (mp) REVERT: B 325 MET cc_start: 0.8726 (mtm) cc_final: 0.7994 (mtm) REVERT: B 421 LYS cc_start: 0.7875 (mttt) cc_final: 0.7186 (mmtt) REVERT: B 440 GLU cc_start: 0.8538 (tt0) cc_final: 0.8313 (tt0) REVERT: B 448 SER cc_start: 0.8965 (m) cc_final: 0.8742 (p) outliers start: 10 outliers final: 7 residues processed: 180 average time/residue: 0.9746 time to fit residues: 197.4613 Evaluate side-chains 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 537 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 0 optimal weight: 50.0000 chunk 119 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.152505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107147 restraints weight = 29333.860| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.05 r_work: 0.3025 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2949 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= 0.172 Angle : 0.562 5.993 17547 Z= 0.304 Chirality : 0.039 0.133 1995 Planarity : 0.004 0.046 2115 Dihedral : 13.658 146.087 1998 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.50 % Allowed : 6.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.21), residues: 1593 helix: 2.12 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 589 TYR 0.010 0.002 TYR C 310 PHE 0.026 0.002 PHE A 279 TRP 0.009 0.001 TRP B 323 HIS 0.005 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00374 (12948) covalent geometry : angle 0.56157 (17547) hydrogen bonds : bond 0.06774 ( 967) hydrogen bonds : angle 4.05384 ( 2856) *********************** 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 190 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.735 Fit side-chains REVERT: A 193 LEU cc_start: 0.8031 (mt) cc_final: 0.7713 (mm) REVERT: A 231 TYR cc_start: 0.8092 (t80) cc_final: 0.7681 (t80) REVERT: A 248 LEU cc_start: 0.8336 (tp) cc_final: 0.7824 (mp) REVERT: A 483 TYR cc_start: 0.8234 (t80) cc_final: 0.7769 (t80) REVERT: C 129 MET cc_start: 0.6662 (mtp) cc_final: 0.6401 (mtp) REVERT: C 231 TYR cc_start: 0.8154 (t80) cc_final: 0.7809 (t80) REVERT: C 253 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6902 (tp30) REVERT: C 355 ARG cc_start: 0.7942 (ttt180) cc_final: 0.7181 (ttp80) REVERT: C 421 LYS cc_start: 0.7822 (mttt) cc_final: 0.7598 (mmtp) REVERT: B 142 VAL cc_start: 0.7697 (t) cc_final: 0.7346 (p) REVERT: B 231 TYR cc_start: 0.7988 (t80) cc_final: 0.7548 (t80) REVERT: B 248 LEU cc_start: 0.8289 (tp) cc_final: 0.7852 (mp) REVERT: B 325 MET cc_start: 0.8755 (mtm) cc_final: 0.7945 (mtm) REVERT: B 421 LYS cc_start: 0.7835 (mttt) cc_final: 0.7204 (mmtt) REVERT: B 440 GLU cc_start: 0.8557 (tt0) cc_final: 0.8319 (tt0) REVERT: B 448 SER cc_start: 0.8979 (m) cc_final: 0.8758 (p) outliers start: 19 outliers final: 12 residues processed: 183 average time/residue: 0.9425 time to fit residues: 194.6823 Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 108 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.153224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.108732 restraints weight = 29374.272| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.02 r_work: 0.3046 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12948 Z= 0.147 Angle : 0.517 5.814 17547 Z= 0.280 Chirality : 0.037 0.121 1995 Planarity : 0.004 0.044 2115 Dihedral : 13.304 147.580 1998 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.35 % Allowed : 7.60 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.21), residues: 1593 helix: 2.32 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.28 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 599 TYR 0.009 0.001 TYR C 310 PHE 0.022 0.002 PHE C 279 TRP 0.010 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00311 (12948) covalent geometry : angle 0.51746 (17547) hydrogen bonds : bond 0.06106 ( 967) hydrogen bonds : angle 3.93319 ( 2856) *********************** 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 187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.662 Fit side-chains REVERT: A 193 LEU cc_start: 0.8057 (mt) cc_final: 0.7744 (mm) REVERT: A 231 TYR cc_start: 0.8046 (t80) cc_final: 0.7654 (t80) REVERT: A 248 LEU cc_start: 0.8281 (tp) cc_final: 0.7839 (mm) REVERT: A 483 TYR cc_start: 0.8226 (t80) cc_final: 0.7670 (t80) REVERT: C 231 TYR cc_start: 0.8102 (t80) cc_final: 0.7760 (t80) REVERT: C 253 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6809 (tp30) REVERT: C 355 ARG cc_start: 0.7874 (ttt180) cc_final: 0.7087 (ttp80) REVERT: C 421 LYS cc_start: 0.7834 (mttt) cc_final: 0.7604 (mmtp) REVERT: C 472 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8449 (t) REVERT: C 506 ASP cc_start: 0.8299 (p0) cc_final: 0.8092 (p0) REVERT: B 142 VAL cc_start: 0.7742 (t) cc_final: 0.7365 (p) REVERT: B 231 TYR cc_start: 0.7938 (t80) cc_final: 0.7609 (t80) REVERT: B 248 LEU cc_start: 0.8172 (tp) cc_final: 0.7779 (mm) REVERT: B 325 MET cc_start: 0.8747 (mtm) cc_final: 0.8014 (mtm) REVERT: B 421 LYS cc_start: 0.7838 (mttt) cc_final: 0.7212 (mmtt) REVERT: B 448 SER cc_start: 0.8973 (m) cc_final: 0.8746 (p) outliers start: 17 outliers final: 10 residues processed: 179 average time/residue: 0.9787 time to fit residues: 197.5089 Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 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 53 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 132 optimal weight: 0.0670 chunk 147 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.154748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109866 restraints weight = 29239.778| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.04 r_work: 0.3062 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3152 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= 0.129 Angle : 0.488 5.218 17547 Z= 0.263 Chirality : 0.036 0.117 1995 Planarity : 0.004 0.044 2115 Dihedral : 12.873 147.288 1998 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.19 % Allowed : 7.84 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.07 (0.21), residues: 1593 helix: 2.48 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.23 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.008 0.001 TYR C 310 PHE 0.020 0.001 PHE C 279 TRP 0.010 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00264 (12948) covalent geometry : angle 0.48770 (17547) hydrogen bonds : bond 0.05623 ( 967) hydrogen bonds : angle 3.79889 ( 2856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.6565 (mtp) cc_final: 0.6325 (mtp) REVERT: A 193 LEU cc_start: 0.8055 (mt) cc_final: 0.7741 (mm) REVERT: A 248 LEU cc_start: 0.8203 (tp) cc_final: 0.7693 (mp) REVERT: A 483 TYR cc_start: 0.8242 (t80) cc_final: 0.7706 (t80) REVERT: A 506 ASP cc_start: 0.7911 (p0) cc_final: 0.7559 (p0) REVERT: C 253 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6776 (tp30) REVERT: C 355 ARG cc_start: 0.7857 (ttt180) cc_final: 0.7068 (ttp80) REVERT: C 421 LYS cc_start: 0.7831 (mttt) cc_final: 0.7579 (mmtp) REVERT: C 472 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8432 (t) REVERT: B 142 VAL cc_start: 0.7745 (t) cc_final: 0.7412 (p) REVERT: B 231 TYR cc_start: 0.7858 (t80) cc_final: 0.7540 (t80) REVERT: B 248 LEU cc_start: 0.8105 (tp) cc_final: 0.7714 (mm) REVERT: B 325 MET cc_start: 0.8750 (mtm) cc_final: 0.7881 (mtm) REVERT: B 421 LYS cc_start: 0.7885 (mttt) cc_final: 0.7185 (mmtp) REVERT: B 448 SER cc_start: 0.8976 (m) cc_final: 0.8757 (p) outliers start: 15 outliers final: 8 residues processed: 177 average time/residue: 0.9623 time to fit residues: 192.0270 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 SER 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 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 7 optimal weight: 5.9990 chunk 128 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109153 restraints weight = 29280.479| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.02 r_work: 0.3053 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3165 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= 0.139 Angle : 0.509 7.203 17547 Z= 0.274 Chirality : 0.037 0.121 1995 Planarity : 0.004 0.044 2115 Dihedral : 13.038 147.128 1998 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.19 % Allowed : 8.08 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.21), residues: 1593 helix: 2.44 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.23 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 589 TYR 0.008 0.001 TYR C 310 PHE 0.021 0.001 PHE A 279 TRP 0.009 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00290 (12948) covalent geometry : angle 0.50919 (17547) hydrogen bonds : bond 0.05905 ( 967) hydrogen bonds : angle 3.84289 ( 2856) *********************** 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 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8025 (mt) cc_final: 0.7715 (mm) REVERT: A 231 TYR cc_start: 0.8026 (t80) cc_final: 0.7691 (t80) REVERT: A 248 LEU cc_start: 0.8254 (tp) cc_final: 0.7801 (mm) REVERT: A 483 TYR cc_start: 0.8240 (t80) cc_final: 0.7721 (t80) REVERT: C 253 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6797 (tp30) REVERT: C 355 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7075 (ttp80) REVERT: C 421 LYS cc_start: 0.7834 (mttt) cc_final: 0.7586 (mmtp) REVERT: C 472 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8436 (t) REVERT: B 142 VAL cc_start: 0.7717 (t) cc_final: 0.7346 (p) REVERT: B 231 TYR cc_start: 0.7882 (t80) cc_final: 0.7585 (t80) REVERT: B 248 LEU cc_start: 0.8140 (tp) cc_final: 0.7744 (mm) REVERT: B 325 MET cc_start: 0.8745 (mtm) cc_final: 0.7868 (mtm) REVERT: B 421 LYS cc_start: 0.7893 (mttt) cc_final: 0.7195 (mmtp) REVERT: B 448 SER cc_start: 0.8976 (m) cc_final: 0.8756 (p) outliers start: 15 outliers final: 12 residues processed: 179 average time/residue: 0.9524 time to fit residues: 192.4614 Evaluate side-chains 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.152356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107258 restraints weight = 29298.174| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.04 r_work: 0.3026 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12948 Z= 0.179 Angle : 0.573 7.456 17547 Z= 0.309 Chirality : 0.039 0.142 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.646 149.982 1998 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.43 % Allowed : 8.00 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.21), residues: 1593 helix: 2.20 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -0.25 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 589 TYR 0.010 0.002 TYR C 310 PHE 0.028 0.002 PHE A 279 TRP 0.008 0.001 TRP A 323 HIS 0.005 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00394 (12948) covalent geometry : angle 0.57276 (17547) hydrogen bonds : bond 0.06782 ( 967) hydrogen bonds : angle 4.01905 ( 2856) *********************** 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 186 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7951 (mt) cc_final: 0.7628 (mm) REVERT: A 231 TYR cc_start: 0.8085 (t80) cc_final: 0.7630 (t80) REVERT: A 248 LEU cc_start: 0.8360 (tp) cc_final: 0.7911 (mm) REVERT: A 483 TYR cc_start: 0.8290 (t80) cc_final: 0.7769 (t80) REVERT: C 253 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6916 (tp30) REVERT: C 355 ARG cc_start: 0.7948 (ttt180) cc_final: 0.7177 (ttp80) REVERT: C 421 LYS cc_start: 0.7823 (mttt) cc_final: 0.7599 (mmtp) REVERT: B 142 VAL cc_start: 0.7710 (t) cc_final: 0.7332 (p) REVERT: B 231 TYR cc_start: 0.7974 (t80) cc_final: 0.7575 (t80) REVERT: B 248 LEU cc_start: 0.8280 (tp) cc_final: 0.7881 (mm) REVERT: B 325 MET cc_start: 0.8770 (mtm) cc_final: 0.8037 (mtm) REVERT: B 421 LYS cc_start: 0.7816 (mttt) cc_final: 0.7210 (mmtt) REVERT: B 448 SER cc_start: 0.8984 (m) cc_final: 0.8758 (p) outliers start: 18 outliers final: 16 residues processed: 181 average time/residue: 0.9576 time to fit residues: 196.0289 Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.154146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110630 restraints weight = 29404.576| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.08 r_work: 0.3054 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12948 Z= 0.129 Angle : 0.493 7.145 17547 Z= 0.266 Chirality : 0.036 0.122 1995 Planarity : 0.004 0.043 2115 Dihedral : 12.998 149.542 1998 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.03 % Allowed : 8.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.06 (0.21), residues: 1593 helix: 2.44 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 599 TYR 0.007 0.001 TYR C 310 PHE 0.021 0.001 PHE C 279 TRP 0.009 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00266 (12948) covalent geometry : angle 0.49314 (17547) hydrogen bonds : bond 0.05619 ( 967) hydrogen bonds : angle 3.81659 ( 2856) ********************** 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: 13 poor density : 166 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.6602 (mtp) cc_final: 0.6343 (mtp) REVERT: A 193 LEU cc_start: 0.7933 (mt) cc_final: 0.7636 (mm) REVERT: A 248 LEU cc_start: 0.8231 (tp) cc_final: 0.7777 (mm) REVERT: A 483 TYR cc_start: 0.8249 (t80) cc_final: 0.7718 (t80) REVERT: C 253 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6767 (tp30) REVERT: C 317 ILE cc_start: 0.8608 (mt) cc_final: 0.8171 (tp) REVERT: C 355 ARG cc_start: 0.7843 (ttt180) cc_final: 0.7025 (ttp80) REVERT: C 421 LYS cc_start: 0.7817 (mttt) cc_final: 0.7567 (mmtp) REVERT: C 472 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8429 (t) REVERT: B 142 VAL cc_start: 0.7793 (t) cc_final: 0.7432 (p) REVERT: B 231 TYR cc_start: 0.7860 (t80) cc_final: 0.7444 (t80) REVERT: B 248 LEU cc_start: 0.8105 (tp) cc_final: 0.7715 (mm) REVERT: B 325 MET cc_start: 0.8754 (mtm) cc_final: 0.7882 (mtm) REVERT: B 421 LYS cc_start: 0.7853 (mttt) cc_final: 0.7175 (mmtp) REVERT: B 448 SER cc_start: 0.8960 (m) cc_final: 0.8729 (p) outliers start: 13 outliers final: 10 residues processed: 176 average time/residue: 0.9648 time to fit residues: 191.4020 Evaluate side-chains 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 C residue 199 THR Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 153 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.152453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.107969 restraints weight = 29279.065| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.03 r_work: 0.3032 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3191 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= 0.170 Angle : 0.557 7.889 17547 Z= 0.300 Chirality : 0.039 0.131 1995 Planarity : 0.004 0.046 2115 Dihedral : 13.499 150.353 1998 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.27 % Allowed : 8.47 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.21), residues: 1593 helix: 2.23 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -0.20 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 589 TYR 0.010 0.002 TYR C 310 PHE 0.026 0.002 PHE A 279 TRP 0.009 0.001 TRP A 323 HIS 0.005 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00370 (12948) covalent geometry : angle 0.55746 (17547) hydrogen bonds : bond 0.06573 ( 967) hydrogen bonds : angle 3.97111 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9684.27 seconds wall clock time: 164 minutes 40.49 seconds (9880.49 seconds total)