Starting phenix.real_space_refine on Sun Jul 5 03:14:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz3_41732/07_2026/8tz3_41732_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz3_41732/07_2026/8tz3_41732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz3_41732/07_2026/8tz3_41732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz3_41732/07_2026/8tz3_41732.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz3_41732/07_2026/8tz3_41732_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz3_41732/07_2026/8tz3_41732_trim.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 134 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'LBN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 2 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, 134 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'LBN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 2 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, 134 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'LBN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 2 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: 3.86, per 1000 atoms: 0.16 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: 2.36 Conformation dependent library (CDL) restraints added in 568.9 milliseconds 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: 0.55 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: 5.64 Time building geometry restraints manager: 3.05 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: 1.020 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.630 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 are 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/Z covalent geometry : bond 0.01135 / 0.50 (12948) covalent geometry : angle 0.99096 / 0.44 (17547) hydrogen bonds : bond 0.25785 / 17.06 ( 967) hydrogen bonds : angle 8.08470 / 5.78 ( 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 : 0.634 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: 0.9421 time to fit residues: 241.7423 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 : 0.645 ------------------------------------------------------------------------------- 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... 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 = 0.3810 r_free = 0.3810 target = 0.161346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116557 restraints weight = 29995.397| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.11 r_work: 0.3177 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2133 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= 0.134 Angle : 0.530 4.511 17547 Z= 0.290 Chirality : 0.036 0.134 1995 Planarity : 0.005 0.049 2115 Dihedral : 14.822 147.262 1998 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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 are not related in a simple way. whole: 1.29 (0.20), residues: 1593 helix: 1.17 (0.14), residues: 1329 sheet: None (None), residues: 0 loop : -0.44 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.010 0.001 TYR B 519 PHE 0.016 0.001 PHE B 279 TRP 0.008 0.001 TRP C 323 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (12948) covalent geometry : angle 0.52969 / 0.29 (17547) hydrogen bonds : bond 0.05997 / 4.06 ( 967) hydrogen bonds : angle 4.23045 / 3.02 ( 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 : 0.581 Fit side-chains REVERT: A 129 MET cc_start: 0.6498 (mtp) cc_final: 0.6252 (mtp) REVERT: A 193 LEU cc_start: 0.8011 (mt) cc_final: 0.7670 (mm) REVERT: A 231 TYR cc_start: 0.7991 (t80) cc_final: 0.7645 (t80) REVERT: A 248 LEU cc_start: 0.8125 (tp) cc_final: 0.7702 (mp) REVERT: A 325 MET cc_start: 0.8580 (mtm) cc_final: 0.8195 (mtm) REVERT: A 483 TYR cc_start: 0.8268 (t80) cc_final: 0.7830 (t80) REVERT: A 554 MET cc_start: 0.8626 (ptt) cc_final: 0.8377 (ptt) REVERT: C 129 MET cc_start: 0.6555 (mtp) cc_final: 0.6305 (mtp) REVERT: C 231 TYR cc_start: 0.7890 (t80) cc_final: 0.7685 (t80) REVERT: C 317 ILE cc_start: 0.8652 (mt) cc_final: 0.8282 (tp) REVERT: C 325 MET cc_start: 0.8651 (mtm) cc_final: 0.8109 (mtm) REVERT: C 355 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7093 (ttp80) REVERT: C 421 LYS cc_start: 0.7872 (mttt) cc_final: 0.7577 (mmtp) REVERT: B 142 VAL cc_start: 0.7729 (t) cc_final: 0.7348 (p) REVERT: B 151 ASP cc_start: 0.7748 (m-30) cc_final: 0.7449 (m-30) REVERT: B 231 TYR cc_start: 0.7920 (t80) cc_final: 0.7590 (t80) REVERT: B 248 LEU cc_start: 0.8028 (tp) cc_final: 0.7710 (mp) REVERT: B 325 MET cc_start: 0.8623 (mtm) cc_final: 0.8088 (mtm) REVERT: B 421 LYS cc_start: 0.7848 (mttt) cc_final: 0.7170 (mmtp) REVERT: B 440 GLU cc_start: 0.8366 (tt0) cc_final: 0.8143 (tt0) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.8311 time to fit residues: 171.5529 Evaluate side-chains 172 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3679 r_free = 0.3679 target = 0.152081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106303 restraints weight = 29194.534| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.06 r_work: 0.3013 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12948 Z= 0.212 Angle : 0.624 6.737 17547 Z= 0.339 Chirality : 0.041 0.130 1995 Planarity : 0.005 0.048 2115 Dihedral : 14.852 146.885 1998 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.03 % Allowed : 7.28 % Favored : 91.69 % 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 are not related in a simple way. whole: 2.00 (0.21), residues: 1593 helix: 1.72 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 589 TYR 0.011 0.002 TYR C 310 PHE 0.032 0.002 PHE A 279 TRP 0.011 0.002 TRP B 323 HIS 0.006 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (12948) covalent geometry : angle 0.62375 / 0.34 (17547) hydrogen bonds : bond 0.07728 / 5.20 ( 967) hydrogen bonds : angle 4.26769 / 3.05 ( 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 193 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.550 Fit side-chains REVERT: A 129 MET cc_start: 0.6458 (mtp) cc_final: 0.6206 (mtp) REVERT: A 193 LEU cc_start: 0.7980 (mt) cc_final: 0.7639 (mm) REVERT: A 231 TYR cc_start: 0.8116 (t80) cc_final: 0.7719 (t80) REVERT: A 248 LEU cc_start: 0.8359 (tp) cc_final: 0.7838 (mp) REVERT: A 483 TYR cc_start: 0.8224 (t80) cc_final: 0.7842 (t80) REVERT: A 497 MET cc_start: 0.8821 (tmm) cc_final: 0.8604 (tmm) REVERT: A 554 MET cc_start: 0.8776 (ptt) cc_final: 0.8468 (ptt) REVERT: C 129 MET cc_start: 0.6507 (mtp) cc_final: 0.6295 (mtp) REVERT: C 231 TYR cc_start: 0.8178 (t80) cc_final: 0.7805 (t80) REVERT: C 253 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6901 (tp30) REVERT: C 355 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7105 (ttp80) REVERT: C 421 LYS cc_start: 0.7734 (mttt) cc_final: 0.7492 (mmtp) REVERT: B 142 VAL cc_start: 0.7784 (t) cc_final: 0.7392 (p) REVERT: B 231 TYR cc_start: 0.8037 (t80) cc_final: 0.7646 (t80) REVERT: B 248 LEU cc_start: 0.8358 (tp) cc_final: 0.7925 (mp) REVERT: B 305 MET cc_start: 0.8870 (mmm) cc_final: 0.8627 (mmm) REVERT: B 325 MET cc_start: 0.8700 (mtm) cc_final: 0.8026 (mtm) REVERT: B 421 LYS cc_start: 0.7854 (mttt) cc_final: 0.7210 (mmtp) REVERT: B 440 GLU cc_start: 0.8622 (tt0) cc_final: 0.8420 (tt0) REVERT: B 448 SER cc_start: 0.8972 (m) cc_final: 0.8767 (p) REVERT: B 601 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8471 (tp) outliers start: 13 outliers final: 6 residues processed: 189 average time/residue: 0.8324 time to fit residues: 179.0287 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 601 LEU 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: 2.9990 chunk 4 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3714 r_free = 0.3714 target = 0.155277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110194 restraints weight = 29412.509| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.05 r_work: 0.3070 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12948 Z= 0.126 Angle : 0.488 4.886 17547 Z= 0.265 Chirality : 0.036 0.119 1995 Planarity : 0.004 0.044 2115 Dihedral : 13.270 145.285 1998 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.71 % Allowed : 7.84 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.21), residues: 1593 helix: 2.30 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.40 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.007 0.001 TYR C 310 PHE 0.021 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/Z covalent geometry : bond 0.00254 / 0.13 (12948) covalent geometry : angle 0.48834 / 0.26 (17547) hydrogen bonds : bond 0.05595 / 3.79 ( 967) hydrogen bonds : angle 3.89515 / 2.78 ( 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 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.681 Fit side-chains REVERT: A 129 MET cc_start: 0.6379 (mtp) cc_final: 0.6148 (mtp) REVERT: A 189 LEU cc_start: 0.7007 (tp) cc_final: 0.6474 (tm) REVERT: A 248 LEU cc_start: 0.8197 (tp) cc_final: 0.7672 (mp) REVERT: A 483 TYR cc_start: 0.8254 (t80) cc_final: 0.7779 (t80) REVERT: C 129 MET cc_start: 0.6611 (mtp) cc_final: 0.6353 (mtp) REVERT: C 231 TYR cc_start: 0.8059 (t80) cc_final: 0.7728 (t80) REVERT: C 253 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6802 (tp30) REVERT: C 317 ILE cc_start: 0.8612 (mt) cc_final: 0.8208 (tp) REVERT: C 355 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7074 (ttp80) REVERT: C 421 LYS cc_start: 0.7823 (mttt) cc_final: 0.7583 (mmtp) REVERT: C 472 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8431 (t) REVERT: B 142 VAL cc_start: 0.7742 (t) cc_final: 0.7355 (p) REVERT: B 231 TYR cc_start: 0.7930 (t80) cc_final: 0.7632 (t80) REVERT: B 248 LEU cc_start: 0.8129 (tp) cc_final: 0.7718 (mp) REVERT: B 325 MET cc_start: 0.8741 (mtm) cc_final: 0.8005 (mtm) REVERT: B 421 LYS cc_start: 0.7879 (mttt) cc_final: 0.7200 (mmtt) REVERT: B 440 GLU cc_start: 0.8533 (tt0) cc_final: 0.8311 (tt0) REVERT: B 448 SER cc_start: 0.8961 (m) cc_final: 0.8734 (p) outliers start: 9 outliers final: 2 residues processed: 178 average time/residue: 0.8878 time to fit residues: 179.4201 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER 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: 3.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3678 r_free = 0.3678 target = 0.151912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106571 restraints weight = 29398.542| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.05 r_work: 0.3017 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2930 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 : 0.600 6.493 17547 Z= 0.325 Chirality : 0.040 0.137 1995 Planarity : 0.004 0.046 2115 Dihedral : 14.089 146.960 1998 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.50 % Allowed : 7.28 % Favored : 91.21 % 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 are not related in a simple way. whole: 2.46 (0.21), residues: 1593 helix: 2.04 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 273 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 0.029 0.002 PHE A 279 TRP 0.010 0.001 TRP B 323 HIS 0.005 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (12948) covalent geometry : angle 0.60008 / 0.32 (17547) hydrogen bonds : bond 0.07261 / 4.90 ( 967) hydrogen bonds : angle 4.14462 / 2.96 ( 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 : 0.695 Fit side-chains REVERT: A 193 LEU cc_start: 0.8050 (mt) cc_final: 0.7732 (mm) REVERT: A 231 TYR cc_start: 0.8121 (t80) cc_final: 0.7699 (t80) REVERT: A 248 LEU cc_start: 0.8376 (tp) cc_final: 0.7912 (mm) REVERT: A 483 TYR cc_start: 0.8230 (t80) cc_final: 0.7771 (t80) REVERT: C 129 MET cc_start: 0.6683 (mtp) cc_final: 0.6425 (mtp) REVERT: C 231 TYR cc_start: 0.8182 (t80) cc_final: 0.7754 (t80) REVERT: C 253 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6925 (tp30) REVERT: C 355 ARG cc_start: 0.7944 (ttt180) cc_final: 0.7184 (ttp80) REVERT: C 421 LYS cc_start: 0.7689 (mttt) cc_final: 0.7464 (mmtp) REVERT: B 142 VAL cc_start: 0.7714 (t) cc_final: 0.7360 (p) REVERT: B 231 TYR cc_start: 0.8025 (t80) cc_final: 0.7589 (t80) REVERT: B 248 LEU cc_start: 0.8325 (tp) cc_final: 0.7891 (mp) REVERT: B 325 MET cc_start: 0.8772 (mtm) cc_final: 0.8025 (mtm) REVERT: B 421 LYS cc_start: 0.7897 (mttt) cc_final: 0.7169 (mmtp) REVERT: B 440 GLU cc_start: 0.8561 (tt0) cc_final: 0.8326 (tt0) REVERT: B 448 SER cc_start: 0.8984 (m) cc_final: 0.8768 (p) outliers start: 19 outliers final: 14 residues processed: 183 average time/residue: 0.8671 time to fit residues: 180.0322 Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 376 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.152352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106947 restraints weight = 29367.410| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.06 r_work: 0.3023 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3005 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= 0.186 Angle : 0.577 6.712 17547 Z= 0.311 Chirality : 0.039 0.128 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.991 148.539 1998 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.50 % Allowed : 7.36 % Favored : 91.13 % 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 are not related in a simple way. whole: 2.53 (0.21), residues: 1593 helix: 2.10 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 589 TYR 0.011 0.002 TYR C 310 PHE 0.026 0.002 PHE C 279 TRP 0.011 0.001 TRP B 323 HIS 0.005 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (12948) covalent geometry : angle 0.57675 / 0.31 (17547) hydrogen bonds : bond 0.06851 / 4.63 ( 967) hydrogen bonds : angle 4.10374 / 2.93 ( 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: 19 poor density : 168 time to evaluate : 0.662 Fit side-chains REVERT: A 193 LEU cc_start: 0.8038 (mt) cc_final: 0.7724 (mm) REVERT: A 231 TYR cc_start: 0.8097 (t80) cc_final: 0.7689 (t80) REVERT: A 248 LEU cc_start: 0.8380 (tp) cc_final: 0.7918 (mm) REVERT: A 483 TYR cc_start: 0.8239 (t80) cc_final: 0.7703 (t80) REVERT: C 222 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8068 (tt) REVERT: C 253 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6922 (tp30) REVERT: C 355 ARG cc_start: 0.7933 (ttt180) cc_final: 0.7155 (ttp80) REVERT: C 421 LYS cc_start: 0.7684 (mttt) cc_final: 0.7459 (mmtp) REVERT: B 142 VAL cc_start: 0.7789 (t) cc_final: 0.7409 (p) REVERT: B 231 TYR cc_start: 0.7991 (t80) cc_final: 0.7570 (t80) REVERT: B 248 LEU cc_start: 0.8289 (tp) cc_final: 0.7888 (mm) REVERT: B 325 MET cc_start: 0.8769 (mtm) cc_final: 0.7938 (mtm) REVERT: B 421 LYS cc_start: 0.7882 (mttt) cc_final: 0.7160 (mmtp) REVERT: B 448 SER cc_start: 0.8985 (m) cc_final: 0.8751 (p) outliers start: 19 outliers final: 17 residues processed: 182 average time/residue: 0.8599 time to fit residues: 177.9013 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 : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 53 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 132 optimal weight: 0.0770 chunk 147 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3706 r_free = 0.3706 target = 0.154418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110266 restraints weight = 29413.256| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.03 r_work: 0.3065 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12948 Z= 0.130 Angle : 0.493 5.430 17547 Z= 0.267 Chirality : 0.036 0.117 1995 Planarity : 0.004 0.043 2115 Dihedral : 13.045 148.297 1998 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.03 % Allowed : 8.47 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.21), residues: 1593 helix: 2.43 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.008 0.001 TYR C 231 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/Z covalent geometry : bond 0.00264 / 0.13 (12948) covalent geometry : angle 0.49305 / 0.27 (17547) hydrogen bonds : bond 0.05634 / 3.82 ( 967) hydrogen bonds : angle 3.86085 / 2.76 ( 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 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8006 (mt) cc_final: 0.7682 (mm) REVERT: A 248 LEU cc_start: 0.8230 (tp) cc_final: 0.7785 (mm) REVERT: A 483 TYR cc_start: 0.8352 (t80) cc_final: 0.7885 (t80) REVERT: A 554 MET cc_start: 0.8726 (ptt) cc_final: 0.8321 (ptt) REVERT: C 222 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8037 (tt) REVERT: C 253 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6790 (tp30) REVERT: C 355 ARG cc_start: 0.7866 (ttt180) cc_final: 0.7082 (ttp80) REVERT: C 421 LYS cc_start: 0.7850 (mttt) cc_final: 0.7618 (mmtp) REVERT: C 472 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8431 (t) REVERT: B 142 VAL cc_start: 0.7709 (t) cc_final: 0.7380 (p) REVERT: B 231 TYR cc_start: 0.7894 (t80) cc_final: 0.7573 (t80) REVERT: B 248 LEU cc_start: 0.8121 (tp) cc_final: 0.7736 (mm) REVERT: B 325 MET cc_start: 0.8772 (mtm) cc_final: 0.8026 (mtm) REVERT: B 421 LYS cc_start: 0.7824 (mttt) cc_final: 0.7206 (mmtt) REVERT: B 448 SER cc_start: 0.8975 (m) cc_final: 0.8750 (p) outliers start: 13 outliers final: 6 residues processed: 174 average time/residue: 0.8990 time to fit residues: 177.5430 Evaluate side-chains 173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 222 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 413 PHE 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: 0.7980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3713 r_free = 0.3713 target = 0.154995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111044 restraints weight = 29423.266| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.02 r_work: 0.3076 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12948 Z= 0.123 Angle : 0.481 6.460 17547 Z= 0.259 Chirality : 0.036 0.117 1995 Planarity : 0.004 0.043 2115 Dihedral : 12.748 146.745 1998 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.11 % Allowed : 8.63 % 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 are not related in a simple way. whole: 3.16 (0.21), residues: 1593 helix: 2.50 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -0.16 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.007 0.001 TYR B 231 PHE 0.020 0.001 PHE C 279 TRP 0.010 0.001 TRP B 323 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (12948) covalent geometry : angle 0.48141 / 0.26 (17547) hydrogen bonds : bond 0.05424 / 3.67 ( 967) hydrogen bonds : angle 3.76771 / 2.69 ( 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: 14 poor density : 169 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.6558 (mtp) cc_final: 0.6305 (mtp) REVERT: A 193 LEU cc_start: 0.7979 (mt) cc_final: 0.7674 (mm) REVERT: A 248 LEU cc_start: 0.8188 (tp) cc_final: 0.7741 (mm) REVERT: A 483 TYR cc_start: 0.8378 (t80) cc_final: 0.7923 (t80) REVERT: A 554 MET cc_start: 0.8750 (ptt) cc_final: 0.8350 (ptt) REVERT: C 222 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8041 (tt) REVERT: C 253 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6765 (tp30) REVERT: C 317 ILE cc_start: 0.8608 (mt) cc_final: 0.8182 (tp) REVERT: C 355 ARG cc_start: 0.7848 (ttt180) cc_final: 0.7076 (ttp80) REVERT: C 421 LYS cc_start: 0.7884 (mttt) cc_final: 0.7615 (mmtp) REVERT: C 472 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8426 (t) REVERT: B 142 VAL cc_start: 0.7741 (t) cc_final: 0.7406 (p) REVERT: B 231 TYR cc_start: 0.7873 (t80) cc_final: 0.7578 (t80) REVERT: B 248 LEU cc_start: 0.8076 (tp) cc_final: 0.7677 (mm) REVERT: B 325 MET cc_start: 0.8778 (mtm) cc_final: 0.7908 (mtm) REVERT: B 421 LYS cc_start: 0.7894 (mttt) cc_final: 0.7204 (mmtp) REVERT: B 448 SER cc_start: 0.8975 (m) cc_final: 0.8758 (p) outliers start: 14 outliers final: 9 residues processed: 177 average time/residue: 0.8936 time to fit residues: 179.3357 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 : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 155 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108404 restraints weight = 29320.862| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.06 r_work: 0.3044 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12948 Z= 0.151 Angle : 0.528 6.815 17547 Z= 0.285 Chirality : 0.037 0.124 1995 Planarity : 0.004 0.045 2115 Dihedral : 13.273 147.247 1998 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.19 % Allowed : 8.87 % Favored : 89.94 % 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 are not related in a simple way. whole: 2.97 (0.21), residues: 1593 helix: 2.41 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.23 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 589 TYR 0.009 0.001 TYR C 310 PHE 0.024 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/Z covalent geometry : bond 0.00320 / 0.15 (12948) covalent geometry : angle 0.52824 / 0.28 (17547) hydrogen bonds : bond 0.06166 / 4.17 ( 967) hydrogen bonds : angle 3.89873 / 2.79 ( 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 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.7957 (mt) cc_final: 0.7649 (mm) REVERT: A 248 LEU cc_start: 0.8323 (tp) cc_final: 0.7871 (mm) REVERT: A 483 TYR cc_start: 0.8407 (t80) cc_final: 0.7951 (t80) REVERT: A 554 MET cc_start: 0.8717 (ptt) cc_final: 0.8291 (ptt) REVERT: C 222 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8064 (tt) REVERT: C 253 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6876 (tp30) REVERT: C 355 ARG cc_start: 0.7921 (ttt180) cc_final: 0.7155 (ttp80) REVERT: C 421 LYS cc_start: 0.7840 (mttt) cc_final: 0.7590 (mmtp) REVERT: C 472 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8439 (t) REVERT: B 142 VAL cc_start: 0.7754 (t) cc_final: 0.7380 (p) REVERT: B 231 TYR cc_start: 0.7933 (t80) cc_final: 0.7526 (t80) REVERT: B 248 LEU cc_start: 0.8176 (tp) cc_final: 0.7777 (mm) REVERT: B 325 MET cc_start: 0.8806 (mtm) cc_final: 0.7947 (mtm) REVERT: B 421 LYS cc_start: 0.7891 (mttt) cc_final: 0.7188 (mmtp) REVERT: B 448 SER cc_start: 0.8979 (m) cc_final: 0.8757 (p) outliers start: 15 outliers final: 13 residues processed: 179 average time/residue: 0.8372 time to fit residues: 170.6923 Evaluate side-chains 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain C residue 376 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 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: 0.5980 chunk 12 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3701 r_free = 0.3701 target = 0.153953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109594 restraints weight = 29399.682| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.04 r_work: 0.3058 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3232 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= 0.138 Angle : 0.507 6.570 17547 Z= 0.273 Chirality : 0.037 0.117 1995 Planarity : 0.004 0.044 2115 Dihedral : 13.142 148.017 1998 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.11 % Allowed : 9.03 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.21), residues: 1593 helix: 2.44 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -0.19 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 599 TYR 0.008 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/Z covalent geometry : bond 0.00287 / 0.14 (12948) covalent geometry : angle 0.50668 / 0.27 (17547) hydrogen bonds : bond 0.05833 / 3.94 ( 967) hydrogen bonds : angle 3.85130 / 2.75 ( 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 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.6597 (mtp) cc_final: 0.6350 (mtp) REVERT: A 193 LEU cc_start: 0.7928 (mt) cc_final: 0.7628 (mm) REVERT: A 248 LEU cc_start: 0.8251 (tp) cc_final: 0.7799 (mm) REVERT: A 483 TYR cc_start: 0.8400 (t80) cc_final: 0.7947 (t80) REVERT: A 554 MET cc_start: 0.8748 (ptt) cc_final: 0.8333 (ptt) REVERT: C 222 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8055 (tt) REVERT: C 253 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6792 (tp30) REVERT: C 317 ILE cc_start: 0.8614 (mt) cc_final: 0.8182 (tp) REVERT: C 355 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7070 (ttp80) REVERT: C 421 LYS cc_start: 0.7838 (mttt) cc_final: 0.7586 (mmtp) REVERT: C 472 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8437 (t) REVERT: B 142 VAL cc_start: 0.7778 (t) cc_final: 0.7411 (p) REVERT: B 231 TYR cc_start: 0.7902 (t80) cc_final: 0.7507 (t80) REVERT: B 248 LEU cc_start: 0.8133 (tp) cc_final: 0.7739 (mm) REVERT: B 325 MET cc_start: 0.8785 (mtm) cc_final: 0.7911 (mtm) REVERT: B 421 LYS cc_start: 0.7870 (mttt) cc_final: 0.7184 (mmtp) REVERT: B 448 SER cc_start: 0.8960 (m) cc_final: 0.8727 (p) outliers start: 14 outliers final: 12 residues processed: 177 average time/residue: 0.8337 time to fit residues: 167.8055 Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 376 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 306 SER Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 153 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3677 r_free = 0.3677 target = 0.151830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106668 restraints weight = 29236.559| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.05 r_work: 0.3019 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12948 Z= 0.207 Angle : 0.614 7.420 17547 Z= 0.330 Chirality : 0.041 0.138 1995 Planarity : 0.004 0.046 2115 Dihedral : 13.888 151.002 1998 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.50 % Allowed : 8.47 % Favored : 90.02 % 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 are not related in a simple way. whole: 2.59 (0.21), residues: 1593 helix: 2.12 (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 0.005 0.001 ARG B 589 TYR 0.012 0.002 TYR C 310 PHE 0.030 0.002 PHE A 279 TRP 0.009 0.002 TRP A 323 HIS 0.006 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (12948) covalent geometry : angle 0.61352 / 0.33 (17547) hydrogen bonds : bond 0.07240 / 4.89 ( 967) hydrogen bonds : angle 4.11696 / 2.95 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8977.74 seconds wall clock time: 152 minutes 28.70 seconds (9148.70 seconds total)